RIKEN IMSAnnual Report 2018
RIKEN Center for Integrative Medical Sciences

RIKEN Center for Integrative Medical Sciences
Organization Chart
Director

Tadashi Yamamoto

Deputy Directors
Piero Carninci
Haruhiko Koseki
Kazuhiko Yamamoto

Senior Advisor

Shizuo Akira

Advisory Council
Max Cooper (chair)Mark Lathrop (vice chair)
Hiroyuki Aburatani
Rudi Balling
Ewan Birney
Riccardo Dalla-Favera
Michel Georges
Ronald N. Germain
Yukiko Gotoh
David A. Hafler
Hajime Karasuyama
Yutaka Kawakami
Juha KerePaul W. Kincade
Bernard MalissenJohn O'Shea
Fiona Powrie
Shimon Sakaguchi
Sarah Teichmann
Arthur Weiss

Office of the Center Director

Division of Genomic Medicine
Laboratory for Transcriptome Technology: Piero Carninci

Nucleic Acid Diagnostic System Development Unit: Kengo Usui

Laboratory for Cellular Function Conversion Technology: Harukazu Suzuki

Preventive Medicine and Applied Genomics Unit: Hideya Kawaji

Laboratory for Genome Information Analysis: Chung Chau Hon

RIKEN-IFOM Joint Laboratory for Cancer Genomics: Yasuhiro Murakawa

Laboratory for Applied Computational Genomics: Michel De Hoon

Laboratory for Genotyping Development: Yukihide Momozawa

Laboratory for Single Cell Technologies: Piero Carninci

Laboratory for Statistical Analysis: Yoichiro Kamatani

Large Scale Data Managing Unit: Takeya Kasukawa

Laboratory for Pharmacogenomics: Taisei Mushiroda

Laboratory for Advanced Genomics Circuit: Jay W. Shin

Laboratory for International Alliance on Genomic Research: Taisei Mushiroda

Genetic Diagnosis Technology Unit: Kengo Usui

Laboratory for Bone and Joint Diseases: Shiro Ikegawa

Epigenome Technology Exploration Unit: Aki Minoda

Laboratory for Endocrinology,
Metabolism and Kidney Diseases: Momoko Horikoshi

Laboratory for Comprehensive Genomic Analysis: Yasushi Okazaki
Laboratory for Applied Regulatory Genomics Network Analysis: Erik Arner

Laboratory for Cardiovascular Diseases: Kaoru Ito

Division of Human Immunology
Laboratory for Autoimmune Diseases: Kazuhiko Yamamoto

Laboratory for Innate Immune Systems: Kazuyo Moro

Laboratory for Respiratory and Allergic Diseases: Kazuhiko Yamamoto

Laboratory for Immune Homeostasis: Taishin Akiyama

Laboratory for Cell Signaling: Takashi Saito

Laboratory for Immune Crosstalk: Hilde Cheroutre

Laboratory for Lymphocyte Differentiation: Tomohiro Kurosaki

Laboratory for Inflammatory Regulation: Takashi Tanaka

Laboratory for Transcriptional Regulation: Ichiro Taniuchi

Laboratory for Cytokine Regulation: Masato Kubo

Laboratory for Immune Cell Systems: Shigeo Koyasu

Division of Disease Systems Biology
Laboratory for Developmental Genetics: Haruhiko Koseki

Laboratory for Tissue Dynamics: Takaharu Okada

Laboratory for Intestinal Ecosystem: Hiroshi Ohno

Laboratory for Integrated Cellular Systems: Mariko Okada

Laboratory for Integrative Genomics: Osamu Ohara

Laboratory for Metabolomics: Makoto Arita

Laboratory for Mucosal Immunity: Sidonia Fagarasan

Laboratory for Microbiome Sciences: Masahira Hattori

Laboratory for Gut Homeostasis: Kenya Honda

Drug Discovery Antibody Platform Unit: Toshitada Takemori

Laboratory for Skin Homeostasis: Masayuki Amagai

Division of Cancer Immunology
Laboratory for Immunogenetics: Tadashi Yamamoto

Laboratory for Immunotherapy: Shin-ichiro Fujii

Laboratory for Medical Science Mathematics: Tatsuhiko Tsunoda

Laboratory for Human Disease Models: Fumihiko Ishikawa

Laboratory for Cancer Genomics: Hidewaki Nakagawa

Liver Cancer Prevention Research Unit: Soichi Kojima

RIKEN Hakubi Research Team
Genome Immunobiology RIKEN Hakubi Research Team: Nicholas Parrish

Young Chief Investigator Program
YCI Laboratory for Cellular Bioenergetic Network: Toshimori Kitami

YCI Laboratory for Next-Generation Proteomics: Yibo Wu

YCI Laboratory for Trans-omics: Katsuyuki Yugi

YCI Laboratory for Metabolic Epigenetics: Azusa Inoue

YCI Laboratory for Immunological Transcriptomics: Hideyuki Yoshida

I

Contents

Organization................................................................................ I
Contents.......................................................................................II

Director’s report........................................................................ IVPart 1
Research Highlights
Massive genetic analyses link genes, cell types, molecules,and diseases........................................................................... 2
Transcriptional landscape of Mycobacterium tuberculosis
infection in macrophages.................................................... 3
Researchers uncover origin of virus-fighting plasma
B cells..................................................................................... 4

Three transcriptional circuits found between hematopoietic
stem cells and B cells............................................................ 5
Genome sequencing analysis reveals genes associated withsurvival in biliary tract cancers.......................................... 6

Part 2Lab Activities
Division of Genomic Medicine......................................... 8
Laboratory for Transcriptome Technology....................... 9Laboratory for Cellular Function Conversion
Technology.................................................................... 10
Laboratory for Genome Information Analysis.............. 11
Laboratory for Applied Computational Genomics....... 12
Laboratory for Single Cell Technologies......................... 13
Large Scale Data Managing Unit...................................... 14
Laboratory for Advanced Genomics Circuit.................. 15
Genetic Diagnosis Technology Unit
Nucleic Acid Diagnostic System Development Unit..... 16
Epigenome Technology Exploration Unit....................... 17
Laboratory for Comprehensive Genomic Analysis....... 18
Laboratory for Applied Regulatory Genomics Network
Analysis......................................................................... 19
Preventive Medicine and Applied Genomics Unit........ 20
RIKEN-IFOM Joint Laboratory for Cancer
Genomics...................................................................... 21
Laboratory for Genotyping Development...................... 22
Laboratory for Statistical Analysis................................... 23
Laboratory for Pharmacogenomics................................. 24
Laboratory for Bone and Joint Diseases.......................... 25
Laboratory for Endocrinology, Metabolism andKidney Diseases........................................................... 26
Laboratory for Cardiovascular Diseases......................... 27
Division of Human Immunology.................................. 28
Laboratory for Autoimmune Diseases............................ 29
Laboratory for Cell Signaling........................................... 30
Laboratory for Lymphocyte Differentiation................... 31

II

Laboratory for Transcriptional Regulation..................... 32
Laboratory for Immune Cell Systems.............................. 33
Laboratory for Innate Immune Systems......................... 34
Laboratory for Immune Homeostasis............................. 35
Laboratory for Immune Crosstalk................................... 36
Laboratory for Inflammatory Regulation....................... 37
Laboratory for Cytokine Regulation................................ 38
Division of Disease Systems Biology........................... 39
Laboratory for Developmental Genetics......................... 40
Laboratory for Intestinal Ecosystem................................ 41
Laboratory for Integrative Genomics.............................. 42
Laboratory for Mucosal Immunity.................................. 43
Laboratory for Gut Homeostasis...................................... 44
Laboratory for Skin Homeostasis..................................... 45
Laboratory for Tissue Dynamics...................................... 46
Laboratory for Metabolomics........................................... 47
Laboratory for Microbiome Sciences.............................. 48
Drug Discovery Antibody Platform Unit....................... 49
Division of Cancer Immunology.................................... 50
Laboratory for Immunogenetics...................................... 51
Laboratory for Medical Science Mathematics................ 52
Laboratory for Cancer Genomics.................................... 53
Laboratory for Immunotherapy....................................... 54
Laboratory for Human Disease Models.......................... 55
Liver Cancer Prevention Research Unit.......................... 56
Special Programs for Young Leaders.......................... 57
Genome Immunobiology RIKEN Hakubi ResearchTeam.............................................................................. 58

YCI Laboratory for Cellular Bioenergetic Network ..... 59
YCI Laboratory for Trans-Omics..................................... 60
YCI Laboratory for Immunological Transcriptomics... 61
Laboratory for Next-Generation Proteomics................. 62
YCI Laboratory for Metabolic Epigenetics..................... 63
Central facilities
FACS Laboratory................................................................ 64
Confocal Laboratory.......................................................... 64

Genomics and related activities....................................... 65
Animal Facility................................................................... 65
Other programs
RIKEN International Program Associate (IPA)............. 66
RIKEN Junior Research Associate (JRA) Program....... 66
RIKEN Special Postdoctoral Researcher (SPDR)
Program......................................................................... 66

Part 3
Research Projects
Projects
The Human Cell Atlas project.......................................... 68
FANTOM............................................................................ 68
Human genome analysis................................................... 69
SEAPharm for establishment of stratified medicine
in Asia............................................................................ 69
International Cancer Genome Consortium (ICGC)
and PCAWG................................................................. 70
eQTL project....................................................................... 70
Search for gut microbiota-associated biomarkers
involved in the pathogenesis of T2D......................... 71

Medical Sciences Innovation Hub Program (MIH)...... 71
iPS project........................................................................... 72
Humanized mouse............................................................. 72
Cancer immunology.......................................................... 73
Linkage to RIKEN Program for Drug Discovery andMedical Technology Platforms (DMP)..................... 73
Obituary
In memory of Dr. Kimishige Ishizaka............................. 74

Part 4
EventsHuman Genome Meeting 2018.............................................. 76
Japan Prize awarded to Dr. Max D. Cooper.......................... 76
RIKEN IMS-Stanford ISCBRM Joint Symposium............... 77
The IMS-JSI International Symposium on
Immunology 2018.............................................................. 77
ZPM-RIKEN Symposium....................................................... 78
RIKEN-KI-SciLifeLab Symposium 2018.............................. 78
RIKEN-Luxembourg Joint Symposium and Workshop...... 79

Single Cell Symposium............................................................ 79
RIKEN - McGill Symposiums................................................ 80
RIKEN -Tsinghua Joint Symposium...................................... 80
Harvard Summer School 2018................................................ 81
International Conference on Innate Lymphoid Cells.......... 81
IMS Retreat 2018...................................................................... 82
Adjunct professorship programs............................................ 82

Part 5
Data and Statistics
Award winners 2018................................................................. 84
Guest lectures 2018.................................................................. 85
Publications 2018..................................................................... 87

Budget, personnel and patent................................................. 95
Original photos of the cover and front pages....................... 96
Access to RIKEN Yokohama Campus................................... 97

IIIDirector’s reportAs the Director of the RIKEN Center for Integrative Medical Sciences (IMS), I am happy and proud to report that2018 was another exceptional year for our center.
This year saw the official merger of the previous IMS centerand the Division of Genomic Technologies from the former
RIKEN Center for Life Science Technologies. Under the newcenter schema, four divisions have been established. The Division of Genomic Medicine, led by Piero Carninci, aims to elucidate disease onset mechanisms originating from the genome.
The Division of Human Immunology, led by Kazuhiko Yamamoto, aims to develop research platforms for human immunology and elucidate basic principles of the immune system. The
Division of Disease Systems Biology, led by Haruhiko Koseki,aims to understand disease as a dynamic system in the context
of environment versus the body. The Division of Cancer Immunology, led by myself, aims to explore novel principles of
the immune system, focusing on tumor cells. In addition, we
have the RIKEN Hakubi Research Team and five Young Chief
Investigator Teams. Together, we are working to create a newresearch and infrastructure platform that will contribute to
the next generation of medical science by providing advanced
research facilities and core technologies to researchers bothwithin and outside of IMS. We have several ongoing efforts
to incentivize research initiatives within our newly structured
center in order to get to know each other and to establish collaborations. Some examples are described later in this report.
In 2018, our investigators in the new IMS continued toperform outstanding research and published a total of 223 papers, many using interdisciplinary approaches, in significant
journals. Ichiro Taniuchi and colleagues reported on Runxdependent and silencer-independent repression of a maturation enhancer in the Cd4 gene, which encodes a glycoprotein
involved in recognition of antigenic peptides presented bymajor histocompatibility complex class II molecules (Nature
Communications, 2018). Tomohiro Kurosaki and colleagues

IVreported on how T follicular helper cell-germinal center B cellinteraction strength regulates entry into the plasma cell or recycling GC cell fate (Immunity, 2018). The paper ‘IgA regulates
the composition and metabolic function of gut microbiota bypromoting symbiosis between bacteria’ by Keiichiro Suzuki,
Sidonia Fagarasan, and colleagues was one of the top 10 mostrequested articles in 2018 in the Journal of Experimental Medicine.
We are driving innovative multidisciplinary science in otherways, including through the work led by Piero Carninci in thefield of non-coding RNAs (ncRNAs). Under his leadership,
scientists worldwide are constructing ncRNA datasets. His
group, working with scientists from the FIRC Institute of Molecular Oncology in Italy, developed a method called TargetEnrichment of small RNAs (TEsR), which enables targeted
sequencing of rare small ncRNAs and diverse precursor andmature forms of small ncRNAs (Nature Protocols, 2018). In addition, research led by Soichi Kojima demonstrated that acyclic
retinoid prevents the recurrence of hepatocellular carcinoma(HCC) through selective targeting of one class of cancer stem
cells. A phase 3 clinical trial of acyclic retinoid (or Peretinoin)
is currently underway in at least three countries to test the
drug’s ability to prevent HCC recurrence.
We continue to nurture young researchers, and 2018 was no
exception. As part of the recently established RIKEN Hakubi
Fellows Program, we welcomed Nicholas Parrish as leader of
the Genome Immunobiology RIKEN Hakubi Research Team.
As part of the IMS Young Chief Investigator (YCI) program,
this year we welcomed Azusa Inoue as leader of the YCI Laboratory for Metabolic Epigenetics.
As part of our international collaborative efforts, several
symposiums and workshops were held throughout the year.
Collaborative partners include McGill University, Stanford
University, the University of Luxembourg, Tubingen University,
Tsinghua University, and others (see Part 4 for further details).
In 2019 and the years ahead, as we continue to develop our
research and infrastructure platform aimed toward providing
individuals the means for a healthy, long life, I expect we will
see an increase in our center’s activities both internally andthrough outside collaborations.

Tadashi Yamamoto
Director
RIKEN Center for Integrative Medical Sciences

Part 1
Research
Highlights

Research highlights

Massive genetic analyses link genes, cell types,
molecules, and diseases

Figure: By analyzing the DNA of more than
162,000 Japanese, researchers have discovered
new connections between genes and diseases in
the Japanese population.

Technological advances have enabled biomedical researchers to obtain enormous amounts of genetic andclinical data. However, it is still difficult to perform integrative analysis that link the genome, epigenome, cells, andtissues, and systematically elucidate disease mechanisms.
Yoichiro Kamatani of the RIKEN Center for Integrative
Medical Sciences and his colleagues are making efforts
using genetic studies of human samples, along with various
epigenetic data, to illustrate and understand the relationships of genetic traits, regulation of gene expression in cells
and tissues, and diseases.
One of their recent achievements was a large genomewide association study (GWAS) of 160,000 people basedon 58 clinical traits, combined with genetic studies of 32
complex diseases (Kanai et al., Nature Genetics, 2018). In
this large study, they successfully identified 1,407 regionsof the genome that affect clinical traits, and 679 of thesewere completely new to science. The identified genes andloci may be risk factors for specific diseases, and the genetic variants could be used in the future to predict risks ofdeveloping a particular disease. To better understand therole of these genes, they cross-referenced their combined
dataset with cell-type-specific maps of epigenetic marks that
denote which parts of the genome are active and which aresilenced. Among their findings, there were links between
Treg cells and Graves’ disease, an autoimmune disease that
results in hyperthyroidism, and between helper T cells andOriginal paper:
Kanai M, Akiyama M, Takahashi A, Matoba N, Momozawa Y, Ikeda M, Iwata N, Ikegawa S,
Hirata M, Matsuda K, et al. Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. Nature Genetics 50, 390-400 (2018)

Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki
K, Akiyama M, et al. Integration of genetics and miRNA-target gene network identified
disease biology implicated in tissue specificity. Nucleic Acids Research 46, 1189811909 (2018)2

allergic diseases. “Genetic studies of human samples, alongwith epigenetics data, can depict the relationship between
traits and cell types,” Kamatani commented.
In November 2018, in collaboration with Yukinori Okada
of Osaka University, Kamatani’s team also established anovel integrative analytic approach they named “MIGWAS(miRNA-target gene networks enrichment on GWAS)”,which links GWAS and microRNA (miRNA) expression(Sakaue et al., Nucleic Acids Research, 2018). In this study,
they collected 49 GWAS statistics from 500,000 people
and combined them with in silico analyses of the extensive
miRNA expression dataset released by the FANTOM5 consortium. miRNAs are small (~22nt long) noncoding RNAs
that bind to mRNAs to negatively regulate gene expression
at the posttranscriptional level. Their new approach successfully revealed miRNA/target gene combinations thatwere associated with genetic traits, such as height and type2 diabetes. To validate this approach, they used a GWAS of
20,000 rheumatoid arthritis (RA) patients and 60,000 controls, and identified four miRNAs linked to RA. “The analytical power of our approach shows its potential for finding
new networks of miRNAs and their target genes linked
to traits and diseases in a tissue-specific way,” observed
Yukinori Okada. “This should make it easier to find new
targets that we can focus on for developing new therapeuticstrategies for a wide range of diseases.”Research highlights

Transcriptional landscape of Mycobacterium
tuberculosis infection in macrophages

Nos2
Gbp5
Cxcl10
Serpinb9
Procr
Irf8
AW112010
Irf1

IL4IL13_Mtb_48h

IL4IL13_Mtb_24h

IL4IL13_Mtb_12h

IL4IL13_Mtb_4h

IFNg_Mtb_48h

IFNg_Mtb_24h

IFNg_Mtb_12h

IFNg_Mtb_4h

Mtb_48h

Mtb_24h

Mtb_12h

Mtb_4hespite the availability of four anti-tubercular drugs
and the BCG vaccine for Mycobacterium tuberculosis(Mtb), tuberculosis still remains one of the most deadly
infectious diseases. Annually 9.6 million people become illwith Mtb and 1.5 million die from the disease worldwide.
Macrophages are the primary Mtb target cells, where hostprotective inflammatory and immune response genes are
induced in Mtb infection. On the other hand, the pathogen
exquisitely subverts cellular immune responses by molding
the transcriptional landscape of the host macrophages toallow it to hide in these cells. Thus, there are complex anddynamic host-pathogen interactions that can lead to hostprotection or pathogenesis.
Using a RIKEN-original unique transcriptome technology, Cap Analysis of Gene Expression (CAGE), Harukazu Suzuki and his colleagues at the RIKEN Center for Integrative
Medical Sciences, in collaboration with Prof. Frank Brombacher of the International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town component,
investigated the promoter-based transcriptional landscapeof IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages
during Mtb infection in a time-kinetic manner. Mtb infection widely and dramatically altered macrophage-specificgene expression, an effect that is far larger than that of M1
or M2 activation alone. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed
various terms related to host-protection and inflammationthat were enriched among up-regulated genes. On the other
hand, terms related to dysregulation of cellular functions
were enriched in down-regulated genes. Differential expres-

Unstimulated_48h

Unstimulated_24h

Unstimulated_12h

DUnstimulated_4h

Gene expression levels are represented from blue (lowexpression) to red (high expression). Mtb infection induces inflammatory and immune-responsive M1 activation genes, such as Nos2, Cxcl10, Cxcl9, and Cxcl11, thatare further augmented in Mtb-infected M1 pre-activatedmacrophages.

Acpp
Cxcl11
Cxcl9

Unstimulated_0h

Figure: Augmentation of M1 activation gene expression in Mtb-infected M1 pre-activated macrophages

sion analysis revealed known as well as novel transcription
factor genes in Mtb infection, many of them significantly
down-regulated. Together, the observed transcriptional
regulatory dynamics of Mtb-infected macrophages might be
the result of the cellular war between host immune defense
and pathogen evasion responses.
Next, the collaborative research team explored how Mtb
infection with IFNγ (M1) or IL-4/IL-13 (M2) pre-stimulation affects gene expression changes in macrophages. IFNγ
or IL-4/IL-13 pre-stimulation induced distinct and additional differentially expressed genes in Mtb-infected macrophages. Further, cluster analysis uncovered a significant
number of genes displaying prolonged expression changes,
demonstrating that Mtb infection of M1 and M2 polarized
macrophages results in drastic transcriptional changes,
compared to Mtb-infected but otherwise unstimulated
macrophages. Importantly, they found that Mtb infection
augmented cytokine-mediated M1 and M2 pre-activation,
which is considered to be more host-protective in M1 preactivated macrophages, but more pathogen-evasive in M2
pre-activated macrophages.
“This work was conducted as a satellite project of the
Functional Annotation of Mammalian Genome (FANTOM5) project. We have provided a comprehensive indepth gene expression/regulation profile in Mtb-infected
macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection. Based on this work, we are now planning to explore
host-directed drug targeting for tuberculosis,” says Suzuki.

Original paper:
Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk
M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T,
Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB,
Brombacher F, Suzuki H. Transcriptional landscape of
Mycobacterium tuberculosis infection in macrophages. Sci
Rep 8, 6758 (2018)3

Research highlights

Researchers uncover origin of virus-fighting plasma
B cells
LZ

TFH
Weak

Figure: Key factors in the selection of germinal
center B cells to become plasma B cells

Ag

GC-B

T-B interaction Strong

Bcl6hiCD69hi

Bcl6loCD69hi
IRF4+

Recycling

DZ

Plasma cellIn a work published in Immunity, a group of researchers
from RIKEN and Osaka University have discovered an
important mechanism that governs how B cells are chosen
to become plasma cells. They found that the key to the commitment to a new state involves the strength of the interaction between the B cells and another type of immune cell,
called T follicular helper cells.
It is known that plasma cells express a transcription
factor called IRF4, and conversely do not express a transcription factor called Bcl6. The group wondered whether
the fate of the cells was already being determined while
they were in the germinal centers—groups of cells locatedin lymph nodes and the spleen where B cells mature. They
examined the expression of these two factors in B cells still
located in the germinal centers and found that in a subset
of cells, Bcl6 was expressed at a low level and IRF4 at a highlevel. They also found that these cells express a cellularmarker called CD69.
To determine whether these cells they had identified
were indeed precursors to plasma B cells, they comparedthem to germinal center-derived plasma B cells, and foundthat the gene sequences of their B cell receptors, which govern the antibodies they produce, were very similar, indicating that they were from the same cell group. It was also clearthat these cells shared the same developmental features withThis article was reproduced from RIKEN Press Release
http://www.riken.jp/en/pr/press/2018/20180418_1/

4

germinal center-derived plasma B cells, suggesting that they
were indeed precursors.
Lastly, they decided to examine the relationship between
these cells and T follicular helper cells, which are important
for the maturation of B cells. Since the T follicular helper
cells stimulate B cells via a surface protein called CD40, theteam created B cells that express CD40 at low levels, andfound that the number of plasma B cells dropped dramatically. Further experiments showed that the strength of theinteraction between the plasma B cell precursors and the
T follicular helper cells determines whether the B cell precursors are chosen to be plasma B cells or to remain in thegerminal center to undergo further mutation before either
being selected to perish or to become high-affinity plasma B
cells.
Tomohiro Kurosaki of the RIKEN Center for Integrative
Medical Science, who led the study, says, “Understanding
how the body generates high-affinity plasma B cells, which
are important in fighting viral infections such as influenza,
which kills around 1,000 people per year in Japan, is important for creating more powerful vaccinations. Our work
has given us important insights into how these cells are produced, and we hope it will be useful in this effort.”

Original paper:
Ise W, Fujii K, Shiroguchi K, Ito A, Kometani K, Takeda K,
Kawakami E, Yamashita K, Suzuki K, Okada T, Kurosaki T.
T Follicular Helper Cell-Germinal Center B Cell Interaction
Strength Regulates Entry into Plasma Cell or Recycling
Germinal Center Cell Fate. Immunity 48, 702-715 (2018)

Research highlights

Three transcriptional circuits found between
hematopoietic stem cells and B cells
B cells pass through three distinct gene expression networks on their way from stem cells to B cells
Early (0.5-4hr)
Cebpa

Nfil3

Nfatc1
Jund
Kdm6b Junb
Egr1

Arid3aFigure: Three-step transcriptional programmingthat determines B cell fate

Klf4

Mid (6-48hr)

Late (72-168hr)
Irf8

Vdr

Gfi1b

Tead1

Srf

Fosb Fos

Tead4
Yap1

Atf3
Egr2

Klf2

Rarb
Snai1

Rel

Pitx1

Smad1

Spib

Zfp57
Gli3

Irf4

Lhx2

Klf5

Tead2

Lmnb1 Phf19

Msx1

Gata4
Fosl2
Gata2
Fosl1
Pparg
Nr2f2

Gfi1 Ikzf3
Tal1
Ncapg2

Smarca4
Ezh2

Ebf1

Lmo2

Lyl1

Per2

Per1

A model of transcriptional networks during B cell commitment is shown. The gene expression profiles and bioinformatic analysis defined the three major transcriptional
phases during B cell fate determination.

Cebpb

Tle2
Relb

Men1

Nfib

Maff

Mtf2
Ets1
Stat4

Tbx19

Nfic

Myb
Wt1

Parp1

Eomes

E2f2
Foxo1
Pax5
Prdm9

Erg

Thrb

Nfe2

Three-step programming

Differentiation
Hematopoietic stem cellBy analyzing the expression of thousands of genes,
RIKEN researchers have shed light on how a stem cellgrows up to become a certain type of immune cell. Thisknowledge will form the basis for future research into B cellleukemia.
B cells are a type of white blood cells, and they help the
body fight infections by producing antibodies. They start offlife as hematopoietic stem cells (HSCs)―stem cells that goon to become blood cells.
Tomokatsu Ikawa of the RIKEN Center for Integrative
Medical Sciences has long been interested in understanding
the differentiation process that commits a stem cell to thefate of becoming a B cell. “Key transcription factors havebeen identified, but the underlying mechanisms remain to
be revealed,” he notes.
To discover how the expression of genes changes as an
HSC becomes a B cell, Ikawa’s team used a cell system they
had previously developed: the induced leukocyte system. It
consists of multipotent progenitor cells―stepping stones
between stem cells and mature cells―that can be efficiently
differentiated into B cells by triggering the expression of
the protein E2A, which is a transcription factor essential
for priming HSCs toward the B cell lineage. This cell system allowed Ikawa’s team to synchronize the differentiation
process and examine the cells’ transcriptome at various time

This article was reproduced from RIKEN Research
http://www.riken.jp/en/research/rikenresearch/highlights/20180427_FY20180001/

B cellpoints.
When the team analyzed the expression of thousands ofgenes, they observed distinct waves of expression as cells
committed to the B cell lineage. They combined data on thetranscription factors that were active in each wave and thegenes they regulated with epigenetic data of histone marks.
This allowed the researchers to construct three distinct networks: the early network of multipotent progenitor cells, atransitional state, and the network of committed B cells.
While all these data were originally obtained from cells
differentiated in a culture dish, the team observed the same
expression patterns in B cell progenitors isolated directlyfrom the bone marrow.
“We were surprised to find that the B cell lineage commitment process could be separated into three main stages
based on messenger RNA expression profiles,” recalls Ikawa.
Ikawa now wants to explore the metabolic pathways andnon-coding RNA that underlie the development and function of immune cells; he is particularly interested in the roleof long non-coding RNAs in the regulatory process.
Ikawa and his team are focusing on normal B cell development, but he predicts that this approach can also be used
to study the mechanism by which B cell leukemia develops.
“The more we understand this process, the more likely efficient points of intervention will be found,” Ikawa comments.

Original paper:
Miyai T, Takano J, Endo TA, Kawakami E, Agata Y, Motomura Y, Kubo M, Kashima Y, Suzuki Y, Kawamoto H. Ikawa
T. Three-step transcriptional priming that drives thecommitment of multipotent progenitors toward B cells.
Genes Dev 32, 112-126 (2018)5

Research highlights

Genome sequencing analysis reveals genes
associated with survival in biliary tract cancers
TMA

MUC17 expression

Prognostic factors

Figure:Genomic profiles of 412 BTCs
(WGS, WES, target seq, CN analysis)

Germline variants ofcancer predisposing genes
Cell‐of‐origin prediction by
WGS and epigenome

Liver origin

Although biliary tract cancers (BTCs) are rare worldwide, they frequently occur in Japan. They are highly
malignant, invasive, and difficult to resect due to theiranatomical location and proximity to the bile ducts. Additionally, the current standard of treatment is chemotherapy
regimens involving drugs such as cisplatin and gemcitabine.
The results with these drugs are poor at best, resulting in
a 5%–10% 5-year survival rate. Thus, targeted treatments
against BTCs may help to improve survival. Genetic profiling of BTCs can identify treatments that are likely to be efficacious; however, the genetic characteristics of BTCs remain
unknown.
To begin to shed light on the genetic characteristics of
BTCs, an international research team led by Hidewaki Nakagawa, Team Leader of the RIKEN Center for Integrative
Medical Sciences in Japan, conducted a large-scale genome
sequencing analysis of BTC samples in Japanese and Italian
populations.
The researchers analyzed a total of 412 BTC samples andfound 32 significantly mutated genes, broadly classified as
DNA maintenance genes, epigenetic genes, and signaling
pathway genes. Sixty-five percent of these samples contained at least one mutation in the list of these 32 genes. The
proportion of genes in each of the classifications differedby subtype of BTC; for example, intrahepatic cholangiocarcinoma samples contained more mutations in epigenetic
genes, whereas extrahepatic subtypes of BTC contained
more mutations in cell cycle genes.
Original paper:
Wardell CP*, Fujita M*, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K,
Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H,
Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H. (*equallycontributed) Genomic Characterization of Biliary Tract Cancers Identifies Driver Genes
and Predisposing Mutations. J Hepatol 68, 959-969 (2018)6

The researchers subsequently performed an SNP array
analysis of 95 samples and discovered that 64% of theanalyzed samples had a large deletion (100-kb region) in
chromosome 7, which was linked to a reduction in diseasefree survival (median, 644 days) and overall survival (median, 428 days). Further expression analysis revealed thatcomplete ablation of a gene located in this 100-kb region,
MUC17, was responsible for the observed shortening ofsurvival time.
Finally, a cell-of-origin analysis was conducted to help
further classify BTC subtypes for treatment. This analysis
revealed that BTCs had two major cells of origin: hepatocytes and epithelium. Identifying the cell-of-origin of BTCs
could help clinicians find treatments that better target thecancer, as well as aid scientists as they continue the search
for novel agents to target BTCs.
The researchers conclude that, based on the genetic
profile of BTCs and the identified genes, almost 60% of thelesions have actionable treatment options. Through thisstudy, the authors have opened the doorway to treatments
for a previously intractable cancer via genetic profiling. “We
found 11% of Japanese BTC cases had deleterious germline
mutations in cancer-predisposing genes. Universal tumor
screening for these cancer-predisposing genes in general
BTC cases might be beneficial to patients with BTC andtheir family members, enabling assessment of their cancer
development risk and of the effectiveness of new anti-cancer
drugs,” concludes Nakagawa.

Part 2Lab Activities

Division of Genomic Medicine

Division of Genomic Medicine will develop new methods for genomebased drug discovery and produce supporting evidence for the realization of genomic medicine.

8Lab activities

Laboratory forTranscriptome
Technology
Team Leader: Piero Carninci
A
B

Figure: SINEUPs, antisense lncRNAs that enhance protein translation

C(A) Schematic image of a SINEUP and its target mRNA.
SINEUPs contain an Effector Domain and a Binding
domain. (B) Secondary structure of SINEB2 RNA. Stems
marked in red were determined by NMR spectroscopy.
The A48C mutant increased protein translation bychanging the stem structure. (C) SINEUPs are strong
candidates for therapeutic applications, particularly
when diseases are caused by decreased levels/lack ofproteins, e.g., in haploinsufficiencies.
Recent Major Publications
Takahashi H, Sharma H, Carninci P. Cell Based Assays of
SINEUP Non-coding RNAs That Can Specifically EnhancemRNA Translation. J Vis Exp doi: 10.3791/58627 (2019)

Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa
T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)
Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki K, Akiyama M, Suita
N, Masuda T, Ogawa K, Yamamoto K, Saeki Y, Matsushita
M, Yoshimura M, Matsuoka H, Ikari K, Taniguchi A,
Yamanaka H, Kawaji H, Lassmann T, Itoh M, Yoshitomi
H, Ito H, Ohmura K, R Forrest AR, Hayashizaki Y, Carninci
P, Kumanogoh A, Kamatani Y, de Hoon M, Yamamoto K,
Okada Y. Integration of genetics and miRNA-target gene
network identified disease biology implicated in tissue
specificity. Nucleic Acids Res 46, 11898-11909 (2018)
Invited presentations
Carninci P. “An emerging landscape of transcriptome
complexity” The 20th Takeda Science Foundation Symposium on Biosceicne (Osaka, Japan) February, 2019

Carninci P. “Revealing transcription complexity in healthand diseases” Takeda Reverse Translation Symposiumand Hackathon (Boston, US) October, 2018
Carninci P. “An emerging landscape of transcriptional
complexity” Developmental and medical genomics withanimal models ZENCODE-ITN Sounio workshop (Attica,
Greece) October, 2018
Hashimoto K. “The single cell PBMC transcriptome ofsupercentenarians” Informatics in Biology, Medicine andPharmacology (IIBMP2018) (Yamagata Japan) September, 2018
Carninci P. “An atlas of human long non-coding RNAs”
European Human Genetics Conference in conjunction
with the European Meeting on Psychosocial Aspects ofGenetics (Milan, Italy) June, 2018O

ur team has traditionally developed technologies, including Cap Analysisof Gene Expression (CAGE), to identify genomic elements and infer theirfunction and regulation. Among the main outputs, we have had a fundamentalrole in the discovery of long non-coding RNAs (lncRNAs) and the creation ofmaps of promoters and enhancers in the FANTOM project. The team is currently
involved in technology development and exploration of RNA biology, as summarized below.
(1) We are optimizing CAGE for various sequencing platforms to accommodate
novel platforms like MGI sequencing, which allows for dramatic cost cutting
compared to Illumina sequencing.
(2) The team is developing RADICL-seq, a novel technology to identify functionsof non-coding RNAs, with particular emphasis on those that regulate chromatin
activity. The goal is to create global RNA-chromatin interactome maps, with thesimultaneous identification of chromatin-regulatory RNAs and their targets. Suchglobal RNA-chromatin bound regions identify a large number of regulatory RNAs
and a novel function of RNA as a structural component of the chromatin.
(3) We explore new functions of the genome, in particular related to insertion/
recombination of retrotransposon elements in somatic tissues in health and brain
diseases. We will identify the degree of somatic mosaicism, a genomics aspect so
far underestimated, which may change the way we understand genomic regulation.
(4) We contribute to the RIKEN ageing study by analyzing the transcriptome ofsupercentenarians, individuals at least 110-years-old, with the objective of identifying the signature of healthy aging as well as the aging signature, both in terms oftranscriptome deregulation and changes in cell populations.
(5) We analyze the mechanism of action of SINEUPs, antisense lncRNAs thatenhance protein translation. We aim at broadening our knowledge of the role of
SINE elements and the definition and characterization of the structural motifs
that they form as regulators of translation in mammals.
The team is also involved in the coordination of FANTOM6 to decipher theinteractome, the structurome, and the function of a large fraction of the lncRNAs
in human cells. Additionally, we are deeply involved in setting up the Human Cell
Atlas, being the Asian hub for this project.

9

Lab activities

Laboratory for

Cellular Function
Conversion Technology
Team Leader: Harukazu Suzuki

Figure: Methylome analysis during hepatocyte
differentiation from iPS cells

The upper panel shows the number of methylated (red)and demethylated (blue) probes in the four stages ofthe differentiation from day 0-7 (Hep_00_07) to day
21-28 (Hep_21_28). The bottom panel shows representative TF binding motifs, GATA6_1, FOS_1, and
TFAP2C_2, that are enriched at demethylated regions inearly (Hep_00_07; day 0-7), middle, and late stages ofhepatocyte differentiation.

12000

Methylated

8000

Demethylated

40000GATA6_1
FOS_1
TFAP2C_2

150
100
50
0
−10g10P

Recent Major Publications
Guler R, Mpotje T, Ozturk M, Nono JK, Parihar SP, Chia JE,
Abdel Aziz N, Hlaka L, Kumar S, Roy S, Penn-Nicholson A,
Hanekom WA, Zak DE, Scriba TJ, Suzuki H, Brombacher F.
Batf2 differentially regulates tissue immunopathology
in Type 1 and Type 2 diseases. Mucosal Immunol 12,
390-402 (2019)

Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk
M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T,
Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB,
Brombacher F, Suzuki H. Transcriptional landscape of
Mycobacterium tuberculosis infection in macrophages.
Sci Rep 8, 6758 (2018)
Invited presentations
Suzuki H. Epigenome regulation mediated by transcription factors. The RIKEN-Luxembourg joint symposium(Luxembourg, Luxembourg) September, 201810

W

e aim to understand how gene expression is globally regulated in mammals and to apply this knowledge to cellular function conversion. DNA
methylation at gene regulatory regions plays an important role in downstream
gene expression, and we have discovered that RUNX1 promotes its binding-sitespecific DNA demethylation by recruitment of a DNA demethylation enzyme
complex. We also demonstrated DNA demethylation by RUNX1 at regulatory
regions of the SPI1/PU.1 gene, another DNA demethylation regulating transcription factor (TF). This finding suggests that a cascade of TF-mediated site-specific
DNA demethylations at gene regulatory regions is one mechanism for accurate
cellular differentiation. We have begun to explore the precise mechanisms of
TF-mediated DNA demethylation during the differentiation of iPS cells into hepatocytes. We have also started to explore the landscape of TF-mediated DNA
demethylation using a combination of publicly available International Human
Epigenome Consortium (IHEC) whole genome methylome data and our own
developed method to identify TFs that induce binding site-directed DNA methylation changes. In the epithelial-to-mesenchymal transition (EMT), we exploredmechanisms governing coupling of the dynamics of epithelial genes with those of
the mesenchymal genes. Further, we identified the Ovo-like zinc finger (OVOL2)
TF as a potent inducer of key epithelial genes during EMT, and demonstrated successful application of OVOL2 to cell reprograming accompanying EMT. We also
have begun to address the challenge of drug-induced cell reprogramming, where
we have identified a novel compound that promotes neural cell reprogrammingfrom human dedifferentiated fat cells. Finally, exploration of global transcriptional changes in Mycobacterium tuberculosis-infected macrophages has been
published as a FANTOM5 satellite paper.

Lab activities

Laboratory for

Genome Information
Analysis
FANTOM CAGE Associated Transcriptome (CAT) genes
were 1) associated with traits based on GWAS data and2) associated with cell-types based on expression data.
We identified pairs of cell types and traits with significant association, and nearly 2000 human long noncoding RNAs were implicated in such associations. Hon
et al. Nature 543, 199–204 (March 09, 2017)

Lizio M, Deviatiiarov R, Nagai H, Galan L, Arner E, Itoh
M, Lassmann T, Kasukawa T, Hasegawa A, Ros MA,
Hayashizaki Y, Carninci P, Forrest ARR, Kawaji H, Gusev O,
Sheng G. Systematic analysis of transcription start sites
in avian development. PLoS Biol 15, e2002887 (2017)
Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, DenisenkoE, Schmeier S, Poulsen
TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M,
Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva
YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez
M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina
M,Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO,de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest
AR. An atlas of human long non-coding RNAs with accurate 5’ ends. Nature 543, 199-204 (2017)
Invited presentations
Hon CC. “Building a better map to navigate through thegenetic landscape of diseases” Life of Genomes 2018
(Kazan, Russia) June, 2018

Hon CC. “Building a better map to navigate through thegenetic landscape of diseases” Advanced Study Workshop, Genetic Variation, Genome Architecture and theTranscriptome in Development and Disease (Hong Kong,
China) June, 2017
Hon CC. “Why do we need a better map for our genomes
and how we make one?” The 12th International Workshop on Advanced Genomics (Tokyo, Japan) June, 2017
Hon CC. “An Atlas of Human Long Non-Coding RNA withAccurate 5’Ends” RNA-Seq Summit 2017 (San Francisco,USA) April, 2017

Nausea and vomiting
Serum zinc measurement
Dementia
AutismAutistic disorder
Autism spectrum disorder
Bipolar disorder
Bipolar affective disorder
Behavioral abnormality
Auditory system disease
Cocaine dependence
Amyotrophic lateral sclerosis
Parkinsonian disorders
Obesity
Nicotine dependence
Abnormality of the CNS
Attention deficit disorder
Azoospermia
Mental depression
Growth abnormality
Body mass index
Schizophrenia
Major depressive disorder
Depression
Cognitive disorder
Psychomotor performance
Dyslexia
Vascular calcification
telencephalic nucleus
cerebral subcortex
nucleus of brain
spinal cord
substantia nigra
parietal lobe
cerebral cortex
occipital lobe
brain gray mattertelencephalon
forebrain
nervous systembrainmetencephalon
middle temporal gyrus
temporal lobe
gyrus
middle frontal gyrus
frontal cortex
dorsal striatum
striatum
putamencaudate nucleus
hippocampal formation
cerebellum
thalamic complex
ponsbrainstem
medulla oblongata

Recent Major Publications
Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, MotakisE, Mendez M, Severin J, Luginbühl
J, Abugessaisa I, Hasegawa A, Takizawa S,Arakawa T,
Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)

hepato-intestinal system
non-immune blood cells
cardiovascular systempigmented cells
nervous system
immune system

traits (n=277)

Figure: Association Between Diseases and Cell
Types

cell-types (n=135)

level of association

hepatic function
blood homeostasis
cardiovascular function
pigmentationneuropathy and behavior
infection and immunity

Team Leader: Chung-Chau Hon

≥9
8
7
6
5
4
3
2
1

O

ur mission is to understand the functions of non-coding transcription in
the human genome, with a focus on its roles for mis-regulation of gene
expression in diseases. Specifically, we have organized our projects towards thesethree goals: 1) To annotate and classify the origins non-coding transcription
events, focusing on long non-coding RNAs, enhancer RNAs and transposable
element-derived RNAs; 2) To integrate cell-type specific transcriptomic andepigenomic information for interpretation of non-coding germline and somatic
variants associated with diseases; 3) To identify functionally relevant non-coding
RNAs by profiling of disease models and genetic perturbations.
Notably, our laboratory participated in the FANTOM5 project, using 5’ endbased gene expression data to build an atlas of long non-coding RNAs in thehuman genome. By integrating this atlas with genetic data, we discovered thatover 3000 cell-type specific long non-coding RNAs are potentially relevant tovarious diseases. To validate these potentially functional non-coding candidate
RNAs, we initiated a collaborative project with Takeda Pharmaceutical Company
Ltd. to screen for non-coding RNAs relevant to neurodegenerative diseases usinglarge-scale genetic perturbation. We have successfully established an iPS-based invitro model of Parkinson’s disease and the perturbation experiments are ongoing.
Along the same line, our team also participates in the FANTOM6 project data
analyses, to identify long non-coding RNAs using large-scale knockdown.
In addition, our team contributes to the development of single-cell technologies by providing bioinformatics support. These single-cell technologies will be an
integral part of Japan’s contribution to the international Human Cell Atlas project.
This project will eventually lead to a comprehensive atlas of cell-type specific activity of non-coding elements in our genome, which will provide insights into theroles of non-coding variants associated with various diseases.

11

Lab activities

Laboratory for

Applied Computational
Genomics
Team Leader: Michiel de Hoon

Genome conforma�on analysis:
Hi-C interactions

Genomic
regionDe Rie D, Abugessaisa I, Alam T, Arner E, Arner P, AshoorH, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle
AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard
C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa
A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ,
Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken
P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V,
Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ,
Noma S, Ohshima M, Okada-Hatakeyama M, Persson H,
Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin
JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K,
Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M,
Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers
KM, Kawaji H, Sandelin A, Rehli M, The FANTOM Consortium Hayashizaki Y, Carninci P, Forrest ARR, De Hoon
MJL. An integrated expression atlas of miRNAs and theirpromoters in human and mouse. Nature Biotechnol
35, 872-878 (2017)
Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM,
Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA,
Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M,
Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M,
Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, De
Hoon MJL, Arner E, Hayashizaki Y, Carninci P, Forrest ARR.
An atlas of human long non-coding RNAs with accurate
5’ ends. Nature 543, 199-204 (2017)
Invited presentations
De Hoon M. “Functional Annotation of Mammalian
Genomes in the FANTOM projects” Annual Meeting of
the Brazilian Bioinformatics and Computational Biology
Association (X-Meeting) (São Pedro, Brazil) October,
2018

De Hoon M. “The FANTOM5 Integrated Expression Atlasof miRNAs and Their Promoters”. The 26th International
KOGO Annual Conference: Genomics for the Future Biology and Medicine (Seoul, Korea) September, 201712

Genomic
regioncluster-2

Genecluster-1

Fibroblast……
……

…… Cell type-N…… H1 stem cell

lncRNA-1

FAM99B……

……

FAM99B

lncRNA-2….
….
….
lncRNA-n

UBXN8
….
….
….
SEMA3B

……
……
……
……
……

……
……
……
……
……

UBXN8
….
….
….
SEMA3B

Genecluster-2

mRNA
codingFunc�onal
analysis:

GO analysiseQTLs
GWAS traits
RNA binding
Transcription factors
RNA-chromatininteraction

Gene ontology (GO) analysis:

Database providing cell type-speciﬁcfunc�onal annota�ons of lncRNAs:
Cell type-1

EnhancerAnnotation
mapping

Clustering

Recent Major Publications
Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki K, Akiyama M, Suita
N, Masuda T, Ogawa K, Yamamoto K, Saeki Y, Matsushita
M, Yoshimura M, Matsuoka H, Ikari K, Taniguchi A,
Yamanaka H, Kawaji H, Lassmann T, Itoh M, Yoshitomi
H, Ito H, Ohmura K, Forrest ARR, Hayashizaki Y, Carninci
P, Kumanogoh A, Kamatani Y, De Hoon M, Yamamoto K,
Okada Y. Integration of genetics and miRNA-target gene
network identified disease biology implicated in tissue
specificity. Nucleic Acids Res 46, 11898-11909 (2018)

lncRNA

Genomic
regioncluster-1

Chromatin organization(Common function)

Skeletal development(Cell specific function)

Figure: Functional annotation of long non-coding RNAs using genome conformation data

The majority of transcripts encoded in mammalian
genomes are long non-coding RNAs (lncRNAs). The
vast majority (97%) of these lncRNAs currently do nothave any functional annotation. We use Hi-C chromatininteraction data in different cell types to identify genomic regions that are physically close to each other inO

3D space. We then build clusters of interacting genomic
regions, and annotate lncRNAs by associating them withgenes and other genomic elements in each cluster. We
thus provide a comprehensive database of cell typespecific functional annotations of lncRNAs.

ur laboratory applies computational methods to analyze transcriptome
and other sequencing datasets to understand cellular regulation in generaland long non-coding RNAs (lncRNAs) in particular. We take a leading role inthe bioinformatics analysis of data generated by the Functional Annotation of theMammalian Genome 6 (FANTOM6) project, a pioneering effort to elucidate thefunction of long non-coding RNA. In particular, we focus on◦ The secondary and tertiary structures of lncRNAs, and the structure–function
relationship of lncRNAs;◦ The 3D structure of the genome as a framework for non-coding RNA-mediated regulatory interactions.
In both aspects, we work together closely with other laboratories in our Center, in particular, by sharing the analysis of the 3D structure of the genome to help
understand GWAS SNPs identified in genetic studies performed by colleagues in
our Center.
Additionally, we are finalizing projects remaining from FANTOM5 and fromthe pilot phase of FANTOM6. The FANTOM5 expression atlas of microRNAs wascompleted and published in 2017. A manuscript summarizing our FANTOM5
analysis of the conservation among vertebrate species of the coding and noncoding transcriptomes in primary cells is planned for submission within FY2018.
The FANTOM6 pilot phase paper is currently being written together with Dr.
Piero Carninci (Laboratory for Transcriptome Technology, RIKEN IMS) and Dr.
Jay Shin (Laboratory for Advanced Genomics Circuit, RIKEN IMS).

Lab activities

Laboratory forSingle Cell Technologies
Team Leader: Piero Carninci

A

B

Collection of single cellbarcoded cDNAs

Figure: picoCAGE protocolA) Sequencing of pooled single-cell cDNAs without PCR amplification. B) Sequencing of pooled single-cell cDNAs after
PCR amplification
Recent Major Publications
Danoy M, Bernier ML, Kimura K, Poulain S, Kato S, Mori D,
Kido T, Plessy C, Kusuhara H, Miyajima A, Sakai Y, Leclerc
E. Optimized protocol for the hepatic differentiation of
induced pluripotent stem cells in a fluidic microenvironment. Biotechnol Bioeng doi: 10.1002/bit.26970.
(2019)

Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa
T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)
Bernier ML, Poulain S, Tauran Y, Danoy M, Shinohara M,
Kimura K, Segard BD, Kato S, Kido T, Miyajima A, Sakai
Y, Plessy C, Leclerc E. Profiling of derived-hepatocyte
progenitors from induced pluripotent stem cells using
nanoCAGE promoter analysis. Biochem Eng J 142, 7–17
(2019)
Invited presentations
Poulain S. “Single-molecule transcriptome analysis
with the CAGEscan method” AIST-RIKEN Joint Exchange
Meeting for Computational Biology (Tokyo, Japan)
March, 2018O

ur laboratory started with the purpose of developing novel methodologies
for single-cell genomics and transcriptomics, providing a high resolution inorder to elucidate the regulatory mechanisms of gene expression. Data produced
from a single cell show the real condition of the cell in the midst of cellular heterogeneity and give us a richer understanding of health and diseases.
Previously, we developed nanoCAGE/CAGEscan technology, which is a powerful tool to perform whole transcriptome CAGE analysis at single-molecule resolution of biological specimens containing limited amounts of bulk RNA input.
The protocol uses template-switching oligonucleotides (TSOs) for capturing the
5’-end of RNA molecules in combination with random priming in the reversetranscription (RT) reaction. Our goal was to adapt the method to simultaneously
analyze the transcriptome of thousands of single cells isolated with a microfluidic
device (aka “picoCAGE” method). This technology contributed to the early diagnosis of cervical cancer by transcriptome analysis of single cells isolated frompatient biopsies in order to detect Human Papilloma Virus (HPV) transcripts,
especially fusion transcripts known to be created by the insertion of HPV16 subtypes within the genome of host cells during carcinogenesis.
The laboratory also has been involved in collaborative efforts to develop the
C1-CAGE, which can detect 5’-ends of transcripts at the single-cell level using theC1 microfluidic system (Fluidigm).

13

Large Scale DataManaging Unit

Lab activities

Unit Leader: Takeya Kasukawa

Figure: Web interfaces for single-cell database(SCPortalen) and reference transcription startsites (refTSS)

A

B

We have developed and published web interfaces for(A) reprocessed single-cell RNA-seq datasets and (B)a reference dataset of transcriptional start sites. These
interfaces are publicly available to all users.

Recent Major Publications
Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa
T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)

Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A,
Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carninci P, Kasukawa T, Kawaji H. Update of the FANTOM web
resource: expansion to provide additional transcriptome
atlases. Nucleic Acids Res 47, D752-D758 (2019)
Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A,
Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C,
Carninci P, Kasukawa T. SCPortalen: human and mouse
single-cell centric database. Nucleic Acids Res 46,
D781-D787 (2018)
Invited presentations
Noguchi S. “Overview and utilization of the FANTOM web
resource” The 41th annual meeting of The Molecular
Biology Society of Japan (Yokohama, Japan) November,
2018

Kasukawa T. “Data resource management in the FANTOM
projects and SCPortalen single-cell database” ConBio2017 (Kobe, Japan) December, 2017
Kasukawa T. “What is “producing data”? Technologies
for data production” The 39th annual meeting of The
Molecular Biology Society of Japan (Yokohama, Japan)
November, 2016
Abugessaisa I. “Transcriptional Regulation of Coding andNon-coding Genes Enabled by refTSS” The 39th annual
meeting of The Molecular Biology Society of Japan (Yokohama, Japan) November, 2016

14

R

ecent rapid improvements in technologies for the measurement of biologicalphenomena, including omics profiling, enable researchers to rapidly obtainlarge-scale biological data. To permit optimal utilization of such data, we arefocusing on technology development in bioinformatics analysis and also on engineering for the management of large-scale biomedical data. Towards this goal, we
now have several ongoing research projects. First, we are developing a databasesystem to support reuse of published single-cell omics data, especially single-cell
RNA-seq data, by the curation and reprocessing of metadata, quality assessment,
and development of a web interface (http://single-cell.clst.riken.jp/).
Next, we are constructing a reference dataset of human and mouse transcription start sites that will enable investigators to integrate various information anddatasets related to transcriptional regulation (http://reftss.clst.riken.jp/). Third,
we are working on data coordination for several collaborative large-scale data
production projects being done in RIKEN IMS (and formerly in RIKEN CLST),
which include curation of sequence data, metadata collection of samples and sequencing, and development of database systems. We are also comparing software
for genome mapping of CAGE (Cap Analysis of Gene Expression) data and developing computational pipelines for sequence data analysis.
Along with the above research projects, we are working to provide and support
the information infrastructure for several IMS laboratories. In practice, we havebeen managing high-performance computation servers and storage platforms
for researchers in these laboratories, taking care of computer environments forresearchers and support staff, and developing and managing web applications forsupport staff.

Lab activities

Laboratory for

Advanced Genomics
Circuit
Team Leader: Jay W. Shin

Figure: Spatial and single cell characterizationof human iPSC-derived cerebral organoids(A) Immunofluorescent staining of PAX6+ neuro-progenitor cells (red), MAP2+ neurons (green) and nuclear
staining (blue) in day 80 organoid cultures. Scale bar =0.5 mm. (B) Matching single cell 5’-RNA-seq of 80 day
cerebral organoids (red = PAX6+ cells, green = MAP2+
cells, blue = PAX6-, MAP2- cells).

Recent Major Publications
Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa
T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)

Luginbuehl J, Kouno T, Nakano R, Chater TE, Sivaraman
DM, Kishima M, Roudnicky F, Carninci P, Plessy C, Shin
JW. Decoding neuronal diversity by single-cell convertseq. BioRxiv doi: https://doi.org/10.1101/600239(2019)
Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML,
Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM,
Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y,
Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell
types. Nat Genet 48, 331-335 (2016)
Invited Presentations
Shin JW. “Functional Elucidation of Long NoncodingRNAs” Keystone Symposia: Long Noncoding RNAs - from
Molecular Mechanism to Functional Genetics (Whistler,
Canada) February, 2019

Shin JW. “Decoding neuronal diversity by single-cellconvert-seq” Cell Symposia. Single Cells: Technology to
Biology. (Singapore, Singapore) February, 2019
Shin JW. “Functional elucidation of non-coding regulatory elements” IHEC 2018 Annual Meeting & Science
Days (Hong Kong, China) October, 2018
Shin JW. “Single Cell CAGE and Single Cell Reprogramming” Single Cell Science Symposium 2018: Single Cell
Technologies Toward Human Health (Tokyo, Japan)
October, 2018
Shin JW. “More to our Junk DNA than meets the eye”
TEDx Kobe (Kobe, Japan) December, 2017T

he Laboratory for Advanced Genomics Circuit focuses on the developmentof single cell RNA-seq at the 5’-end of transcripts in order to profile thetranscriptome and epigenome landscape of human cells. In particular, we havebeen using iPSC-derived cerebral organoids in conjunction with gene-targeting
techniques to unravel the gene regulatory processes of neuronal development, reprogramming and degeneration.
The 5’-based single cell RNA-seq method, or single-cell CAGE, reveals functional DNA elements - namely promoters and enhancers - at single-cell resolution. Using this technology, we found that lung cancer cells are concurrently
proliferating or differentiating in response to TGF-β. We also report the dynamics
of enhancer RNAs, revealing transcriptional bursts arising from either strand in amutually exclusive manner.
To unravel more complex tissues such as the human brain, we established
iPSC-derived cerebral organoids and profiled promoter and enhancer activities
at the single cell resolution. We can partially recapitulate the complexity of thehuman brain through identification of TH+ dopaminergic, vGLUT1+ glutamatergic neurons and GFAP+ astrocytes after 80 days of culture. Based on single celldifferential gene analysis, we identified master regulators controlling neuronalsubtype specification along with key regulatory enhancers associated with genetic
disorders of the brain.
The lab utilizes gene-targeting tools such as CRISPR-interference, full-length
overexpression vectors, and antisense oligonucleotides to reconstruct gene regulatory networks. These tools can target transcription factors, long non-coding
RNAs and DNA regulatory elements to induce cell fate changes and ultimately
cell function. Bridging both experimental and computational techniques, we
deciphered the gene regulatory codes to direct cell reprogramming into various
neuron subtypes, including dopaminergic and GABAergic neurons.
The lab is also engaging with medical and research communities in Japan tobuild the Human Cell Atlas (HCA) at single cell- and spatial-resolution. This ‘periodic table’ of human cells will provide a navigation map to reproducibly study
diseases and to accelerate drug discovery, bringing a positive impact to our society.

15Lab activities

Genetic Diagnosis Technology Unit
Nucleic Acid Diagnostic System
Development Unit
Unit Leader: Kengo Usui

Figure: Detection sensitivity of RT-SmartAmp
for influenza

All assays were performed with A/California/07/2009(H1N1pdm2009), a cultured influenza A virus strain.
Immunochromatography was performed using the
Alere™ BinaxNow® Influenza A & B Card (Abbott). First,
we performed a plaque assay with 10-2-10-6 diluted virus
and calculated plaque forming units (pfu)/ml of theviral culture fluid. The sample volumes for immunochromatography and RT-SmartAmp were 100 µL and 180 µL,
respectively. To compare the sensitivity of each method,
the results from the three assays were normalized toviral dilutions from the original viral culture fluid.

Recent Major Publications
Tsuchiya K, Tabe Y, Ai T, Ohkawa T, Usui K, Yuri M, Misawa
S, Morishita S, Takaku T, Kakimoto A, Yang H, Matsushita
H, Hanami T, Yamanaka Y, Okuzawa A, Horii T, Hayashizaki Y, Ohsaka A. Eprobe-mediated RT-qPCR for thedetection of leukemia-associated fusion genes. PLoS
One 13, e0202429 (2018)

Gusev O, Hayashizaki Y, Usui K. Nucleic acid amplification-based diagnostics for pulmonary diseases: What isthe current state and perspectives of nucleic acid amplification technologies used in diagnostics associatedwith pulmonary diseases? In: Kaneko T. (ed), ClinicalRelevance of Genetic Factors in Pulmonary Diseases,
Singapore: Springer Singapore, Chapter 18, 333-344(2018)
Takase Y, Usui K, Shimizu K, Kimura Y, Ichihara T, Ohkawa
T, Atsumi J, Enokida Y, Nakazawa S, Obayashi K, Ohtaki
Y, Nagashima T, Mitani Y, Takeyoshi I. Highly sensitive
detection of a HER2 12-base pair duplicated insertion
mutation in lung cancer using the Eprobe-PCR method.
PLoS One 12, e0171225 (2017)
Invited Presentations
Usui K. “The 15th Annual Meeting of Japanese Society of
Hospital General Medicine” (Urayasu, Japan) September
2017

16

W

e have developed infectious diseases detection primer sets based on our
original isothermal amplification method, SmartAmp. These primers target influenza virus, Hepatitis B virus, sexually transmitted disease-related bacteria(Chlamydia trachomatis and Neisseria gonorrhoeae), and mosquito-borne viruses(Dengue, Zika, Chikungunya, and yellow fever). Additionally, we applied SmartAmp to SNP genotyping of the variant CPT-2 (carnitine palmitoyltransferase II)
gene, which is associated with a high risk of influenza encephalopathy or heat disorder. For detection of cancer-related somatic mutations in several relevant genes,
such as KRAS, PIK3CA, BRAF, and HER2, we developed a highly-sensitive detection kit using the Eprobe-PCR method and performed a clinical study involving
over 400 cancer specimens. Through the study of KRAS mutations, we found asignificant probability that KRAS G12D and G13D amino acid substitutions promote pulmonary metastasis of colorectal cancer cells. Furthermore, the EprobePCR method allowed for quantitative detection of leukemia-associated fusion
RNAs, such as BCR/ABL1, with high sensitivity and specificity.
In order to consider actual clinical application of diagnostic tools based on theabove studies, development of sample pretreatment technology is very importantfor easy operation by end-users in medical practice. We successfully developed
an influenza virus RNA isolation procedure from nasopharyngeal swab specimens requiring only five minutes of manual handling, and without the need forany special instruments. This pretreatment method has the possibility of being
universally applicable for several specimen types, and we are currently evaluating
it for urine, blood, and various tissues. Furthermore, we also considered producing the enzymes used for our nucleic acid amplification technologies ourselvesin order to reduce the cost and simplify the optimization of the diagnostic tests.
We succeeded in purifying one such enzyme, recombinant reverse transcriptase,
AMV-RT, from E. coli. The amount of purified AMV-RT from a 1 L-culture wassufficient for 10,000 RT-combined SmartAmp reactions, and resulted in a 100fold price reduction compared to a commercial product.
Currently, we are attempting to realize practical medical applications basedon our achievements outlined above. These activities are being performed by ourcounterpart unit in IMS, “Nucleic Acid Diagnostic System Development Unit”,
which is supported by the RIKEN Preventive Medicine and Diagnosis Innovation
Program (PMI).

Lab activities

Epigenome Technology
Exploration Unit
Unit Leader: Aki Minoda

Figure: Ongoing projects in the Unit, towards
understanding ageing at the epigenomic andtranscriptomic levels in whole tissues.

Recent Major Publications
Liu Y, Chang JC, Hon CC, Fukui N, Tanaka N, Zhang Z, Lee
MTM, Minoda A. Chromatin accessibility landscape ofarticular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. Sci Rep 8, 15499 (2018)

Handoko L, Kaczkowski B, Hon CC, Lizio M, Wakamori M,
Matsuda T, Ito T, Jeyamohan P, Sato Y, Sakamoto K, Yokoyama S, Kimura H, Minoda A, Umehara T. JQ1 affects
BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatinstates. Epigenetics 13, 410-431 (2018)
Koga S, Hozumi K, Hirano KI, Yazawa M, Terooatea T,
Minoda A, Nagasawa T, Koyasu S, Moro K. Peripheral
PDGFRα+gp38+ mesenchymal cells support the differentiation of fetal liver-derived ILC2. J Exp Med 215, 16091626 (2018)
Invited presentations
Minoda A. “Ageing Mouse Atlas” JSI-RIKEN IMS International Symposium on Immunology 2019 (Tokyo, Japan)
June, 2019

Minoda A. “Ageing Mouse Atlas” EMBO Workshop on
Single Cell Biology (Tokyo, Japan) May, 2019
Minoda A. “Ageing Mouse Atlas” Center for Genomic
Regulation (Barcelona, Spain) September, 2018
Minoda A. “Ageing Mouse Atlas” Human Cell Atlas Asia
Meeting (Okinawa, Japan) December, 2017
Minoda A. “RIKEN Ageing Resource Project: Of Miceand Super-centenarian Men” 4th RIKEN-Karolinska
Institutet-SciLifeLab Joint Symposium (Kobe, Japan)
November, 2017T

he mission of our lab is to carry out research that contributes to “healthy
longevity,” towards a society where people can live healthier longer, which
is becoming increasingly important as people are living longer. We would liketo understand the molecular mechanisms behind functional declines associatedwith ageing, both at the epigenomic and transcriptomic levels. To accomplish thisgoal, we apply single-cell genomic technologies to whole tissues, as well as utilize
our novel epigenomic technology that enables simultaneous mapping of multiple
epigenetic marks at single nucleosome resolution.

Research Projectsa) Mouse Ageing Atlas ProjectDue to technical reasons, much of the conventional molecular research in thefield of ageing has been carried out with one particular cell type or cell line. However, cells that make up tissues do not function in isolation, often communicating
actively with other cells, and thus it is important to understand the process of ageing at the whole tissue level to fully understand how functional decline occurs. To
achieve such insight, we are carrying out single-cell/-nucleus RNA-seq of multiple
mouse tissues from different ages, along with single-cell ATAC-seq (epigenome)
for selected tissues.
b) Novel Epigenome Technology Development
We are developing a novel epigenomic technology to enable simultaneous
mapping of multiple histone modifications at the single nucleosome level. This
technology combines single-molecule imaging of antibodies on nucleosomes andsingle-molecule sequencing. Development of such technology will likely reveal
how epigenomic regulation is dysregulated during ageing and diseases.
c) Understand plant stem cells [Kakenhi Innovative Research]
We believe it is also important to understand how other organisms, such as
plants, manage to live so long, thereby gaining clues regarding the basis of healthy
longevity. We are carrying out whole tissue single-cell RNA-seq with various
plants as part of the “Plant Stem Cells” group in an attempt to gain insight into
the secrets of longevity.

17

Lab activities

Laboratory forComprehensive Genomic
Analysis
Team Leader: Yasushi Okazaki

Figure: Future plans

Omics analysis and functional analysis focusing mainly
on mitochondrial and neurological diseases, direct
reprogramming, and cancer. In the case of technological development for genome analysis, we will focus
on target enrichment sequencing and modified RNA
analysis using a Nanopore sequencer, and single
tube Long Fragment Read (stLFR) long-read sequencing
using the MGISEQ-2000 sequencer. The diagnostic rateof mitochondrial respiratory chain disorders using wholeexome sequencing analysis is approximately 35%, while
approximately 37% of cases have variants of uncertain
significance. These variants should be evaluated to identify disease causality. Approximately 30% of cases haveno candidate genes. Whole genome sequencing, RNAsequencing, and other omics technologies are necessary
to solve these difficult cases.

Recent Major Publications
Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y,
Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi
T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y. Mitochondrial ribosomal protein PTCD3 mutations cause
oxidative phosphorylation defects with Leigh syndrome.
Neurogenetics (2019)

Noguchi S, et al. FANTOM5 CAGE profiles of human andmouse samples. Sci Data 4, 170112 (2017)
Kohda M, Tokuzawa Y, Kishita Y (Equally first author), etal, Okazaki Y. A comprehensive genomic analysis reveals
the genetic landscape of mitochondrial respiratory chain
complex deficiencies. PLOS Genet 12, e1005679 (2016)
Invited presentations
Okazaki Y. “MGISEQ-2000: the highly versatile platform
to satisfy our multiple needs” The 13th International
Conference on Genomics (Shenzhen, China) October,
2018

Okazaki Y. “Finding a way to establish Bahrain Genome
Projects through the experiences in Japan” Bahrain
Genome Symposium (Manama, Kingdom of Bahrain)
October, 2018
Okazaki Y. “Genomic solution for ADPKD” The 61st Annual Meeting of the Japanese Society of Nephrology(Niigata, Japan) June, 2018
Okazaki Y. “Mitochondrial cardiomyopathy” Cardiovascular Disease Seminar (Osaka, Japan) May, 2018
Okazaki Y. “Genome medical research aimed at nextgeneration medical care - Comprehensive genome
analysis of mitochondrial respiratory chain disorders”
The 4th Nephrology Expert Conference (NEXT) (Tokyo,
Japan) July, 201718

F

rom FY2016 to FY2017, we provided research support for researchers insideand outside of RIKEN, such as cross-disciplinary projects within RIKEN andnational projects, as a Genome Network Analysis Support facility (GeNAS). Beginning in FY2018, the Laboratory for Comprehensive Genomic Analysis (CGA)
was formed and it assumed some of the tasks of research and development fromGeNAS.
The CGA laboratory conducts omics analyses to elucidate the pathophysiology of diseases, using functional genomics, and to understand the mechanismsof diseases that disrupt the homeostatic function of various cells and tissues, andto discover new drug targets. More precisely, we will focus our research activities on identifying new disease genes and their functions and finding new drug
targets, with the goal of realization of genome medical care. As initial targets, westart with genome and transcriptome analyses of mitochondrial and neurologicaldiseases. In addition, capitalizing on the strengths of the technology developedby our research team, we contribute to ongoing IMS biomedical research. We accomplish this through state-of-the-art genome and transcriptome analysis technology, such as RIKEN’s original transcription start site analysis technology, Cap
Analysis of Gene Expression (CAGE), and epigenome analysis. As an application
using these technologies, we will first focus on single-cell analysis of taste receptor cells and also perform other collaborative studies. Furthermore, we will apply
these technologies to define the molecular mechanisms of transcription factorsthat significantly enhance the direct reprogramming of fibroblasts into pancreatic
beta cells.

Lab activities

Laboratory for

Applied Regulatory
Genomics Network Analysis
Team Leader: Erik Arner

Figure: Identification of small molecules thatfacilitate cell conversion

Drug αTarget cell type

Drug response databases such as LINCS, Library of Integrated Network-Based Cellular Signatures, are mined forcompounds that, alone or in combination, are likely tofacilitate cell conversion to a desired target cell type.

Simple query

Gene expression profile
g1
g2
.
.
.
.
.
gn

Recent Major Publications
Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang
Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa
T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa
T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin
JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun
10, 360 (2019)

Rapakoulia T, Gao X, Huang Y, de Hoon M, OkadaHatakeyama M, Suzuki H, Arner E. Genome-scale regression analysis reveals a linear relationship for promotersand enhancers after combinatorial drug treatment.
Bioinformatics 33, 3696-3700 (2017)
Ehrlund A, Mejhert N, Björk C, Andersson R, Kulyté A,Åström G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, Sandelin A, Ingelsson E,
FANTOM Consortium, Rydén M, Laurencikiene J, Arner
P, Arner E. Transcriptional Dynamics During Human
Adipogenesis and Its Link to Adipose Morphology andDistribution. Diabetes 66, 218-230 (2017)
Invited presentations
Arner E. “Modeling of the transcriptional response tomultidrug treatment for prediction of positive and negative effects of combinatorial drug therapy”. The 2nd PSTC
Japan Safety Biomarker Conference (Yokohama, Japan)
April, 2019

Arner E. “Novel genome wide technologies at RIKEN
IMS” 3rd McGill–RIKEN Symposium (Montreal, Canada)
November, 2018
Arner E. “High-resolution characterization of druginduced cellular response” Human Genome Meeting,(Yokohama, Japan) March, 2018
Arner E. “High-resolution characterization of druginduced cellular response” Human Cell Atlas Asia Meeting (Okinawa, Japan) November, 2017

Query drug
response DB

LINCS

Starting cell type

g1
g2
.
.
.
.
.
gn

g1
g2
.
.
.
Forward.
regression .
gnLab+ drug α

?
g1
g2
.
.
.
.
.
gn

+ =

Drug βDrug γ

g1
g2
.
.
.
.
.
gn

Lab

+ drug β+ drug γ?

Based on genome-wide technologies developed at the center, with emphasis
on recent technological advances such as single-cell transcriptome analysis, enhancer expression analysis, and RNA-chromatin interaction profiling, weanalyze gene regulation with a focus on clinical and medical applications. This includes exploration of the transcriptional effects of regulatory molecules at the cellular level and profiling clinical samples in order to identify regulatory networks
perturbed in disease states. One interest of the laboratory is to study the effects ofdrug treatment on the transcriptome at the single-cell level. Here we profile cancer cells (cell lines as well as primary cancer cells derived from patient samples)
after treatment with pharmaceuticals that act at the epigenomic level, e.g., histone
deacetylase inhibitors and bromodomain inhibitors, using single-cell CAGE technology. Using these approaches, we hope to identify transcriptional signaturesat promoters and enhancers that modulate a heterogeneous drug response. We
further try to uncover genetic and epigenetic mechanisms underlying diseases
by transcriptional profiling of patient cohorts and intersecting these results withdata from dynamic cell systems responding to differentiation signals. We are also
developing methods for identifying small molecules that, alone or in combination, can facilitate cell conversion. This aspect of our research is achieved throughapplying data mining and machine learning methods to publicly available drug
response transcriptional response data as well as primary cell transcriptome data
generated in the FANTOM5 project.

Arner E. “Transcriptional response at promoters andenhancers after drug treatment” The 4th RIKEN/ Karolinska Institutet/ SciLifeLab Joint Symposium: Life Science
Frontiers in Health, Disease and Aging (Kobe, Japan)
November, 2017

19

Lab activities

Preventive Medicine andApplied Genomics Unit
Unit Leader: Hideya Kawaji

ww.nature.com/scientificreports/

News & Information

Figure: Newly identified biomarkers for endometrial cancer patients
リンパ節転移
Expression levels of identified markers [Semaphorin3D(SEMA3D) and Transforming Acidic Coiled-Coil Containing Protein 2 (TACC2)] in the primary lesion ofendometrial cancers indicate lymph node metastasis,
which could lead to surgery with lower risk by skipping
lymphadenectomy in cases of non-metastatic cancers.

リンパ節転移陽性の子宮体がん

with no metastasiswith metastasis

リンパ節転移陰性の子宮体がん細胞

primary
cancer lesion

RNA

一つの遺伝子領域
News & Information
リンパ節転移陽性
metastatic cancer
リンパ節転移陰性の子宮体がん
in lymph node

primary
cancer lesionの子宮体がん細胞

No. 3
2017年 10月26日

遺伝子は活性化されると、DNA塩基配列
がRNAへとコピーされ、不要な部分（イントロン）が除去されるRNA

リンパ節転移陰性の子宮体がん細胞

リン
転移

RNA

CAGE法による網羅的遺伝子解析と発現量比較

リンパ節転移の有無によって発現差のある遺伝子群の抽出

これまでに知られていなかった部分より、遺伝子の活性化（RNAの合成）が始まっている
一つの遺伝子領域

図１：リンパ節転移診断マーカーの候補遺伝子の抽出

リンパ節転移陽性の子宮体がん細胞

遺伝子の活性化状態を全ゲノムに渡って測定することができるCAGE法を用いて、リンパ節転移陽性の子宮体がんと陰性
リンパ節転移陽性の子宮体がん
リンパ節転移陰性の子宮体がんの子宮体がんで遺伝子の発現パターンを比較しました。この結果、リンパ節転移陽性群と陰性群で発現に差がある遺伝子がバイオマーカー候補として抽出されました。とても興味深いことに、候補遺伝子のひとつであるTACC2は、リンパ節転移
of cancer陽性の子宮体がんにおいて既存のものと全く異なる部分から活性化されていたことを新しく発見しました。
CAGE法による網羅的遺伝子解析と発現量比較

遺
ると
が
れ
トロ

RNA

R

emarkable progress has recently been made in molecular profiling technolofrom
Yoshida,E.,
Terao,Y. et al. technologies developed at RIKEN, transcription
gies, including
genome-wide
and their
Promoter-level transcriptome in primary lesionsof endometrial cancerこれまでに知られていなかった部分よりリンパ節転移の有無によって発現差のある遺伝子群の抽出
散布図
ROC曲線
intronic
promoterof TACC2
活性化（RNAの合成）が始まっている
associated with
node metastasis.
effective use
is oneidentiﬁedof thebiomarkers
majorinterests
in lymph
life sciences
research, in particular tolesion1.0
Sci. Rep., 7, 14160(2017)
solve medical problems. The RIKEN Preventive Medicine and Diagnosis Inno図１：リンパ節転移診断マーカーの候補遺伝子の抽出
リンパ節転移陰性
vation Program (RIKEN PMI) is coordinating translational research projects to
Yoshida E, Terao Y, Hayashi N, Mogushi K, Arakawa
A,
遺伝子の活性化状態を全ゲノムに渡って測定することができるCAGE法を用いて、リンパ節転移陽性の子宮0.8
4 Y, Takeda S,リンパ節転移陽性
Tanaka Y, Ito Y, Ohmiya H, Hayashizaki
et al.
utilize
RIKEN technologies to solve clinical problems, and our unit is establishedの子宮体がんで遺伝子の発現パターンを比較しました。この結果、リンパ節転移陽性群と陰性群で発現に差
Promoter-level transcriptome in primary lesions of eninがバイオマーカー候補として抽出されました。とても興味深いことに、候補遺伝子のひとつであるTACC2は、
RIKEN IMS with funding from RIKEN PMI. Hence, our mission is to conduct
dometrial cancer identified biomarkers associated withlymph node metastasis. Sci Rep 7, 014160 (2017)
0.6coordinated by RIKEN PMI, in particular from
陽性の子宮体がんにおいて既存のものと全く異なる部分から活性化されていたことを新しく発見しました。
translational
research projects
AUC = 0.929のthe perspective of information sciences or computational genomics. We currently
Takamochi K, Ohmiya H, Itoh M, Mogushi K, Saito T, Hara
高精度な識別能を示した-4 J, et al. Novel
K, Mitani K, Kogo Y, Yamanaka Y, Kawai
ROC曲線
have more than 50 ongoing 散布図
projectswith RIKEN PMI and these can be roughly
0.4
primary
cancer lesion

感度

SEMA3Dの相対発現量

Recent Major Publications
Kawaji H, Kasukawa T, Forrest A, Carninci P, Hayashizaki
Y. The FANTOM5 collection, a data series underpinningmammalian transcriptome atlases in diverse cell types.
8Sci. Data 4, 170113 (2017)

biomarkers that assist in accurate discrimination ofsquamous cell carcinoma from adenocarcinoma of thelung. BMC Cancer 16, 760 (2016) -8

1.0

20

感度

SEMA3Dの相対発現量8 three categories: exploration of diagnostic markers useful in patientclassified into
treatment, identificationof cell
リンパ節転移陰性
0.2markers required for regenerative medicine, andリンパ節転移陽性
0.8 as basic science re(TACC2新規アイソフォームの相対発現量)4our own developments
to assist in such translational
as well－(SEMA3Dの相対発現量)-12!
search.
!
0.0
research led0.0
to identification
indicating-10-8-6 Our-4 collaborative
0
0.2
0.4of biomarkers
0.60.6 0.8
1.0lymph
0 -2
AUClung= 0.929の
TACC2新規アイソフォームの相対発現量
特異度
node metastasis for endometrial cancer patients,1 –biomarkers
discriminating
高精度な識別能を示した
cancer subtypes
with higher accuracy than pre-existing markers,
and biomarkers-4
0.4 mRNA
図2：SEMA3DとTACC2新規アイソフォームとリンパ節転移の関係
Figure 4. Associationof
SEMA3DmRNA
andothers,
novelwhich
TACC2
expression with lym
discriminating
cornealendothelial
cells
and
will
be
useful in regen散布図では、縦軸にSEMA3D、横軸にTACC2新規アイソフォームのそれぞれ相対発現量をとり、リンパ節転移との関連(A) The initial
setmedicineof casesinsubjected
CAGEWeanalysis.
(B) Thevalidation
set of cases no
erative
addition to to
diagnosis.
also provided
maintenancefor the性を示しています。赤丸で示したリンパ節転移陽性群では、SEMA3Dの発現が低く、TACC2新規アイソフォームの発現が
-8
0.2
**P
<
0.01;
*P
<
0.05;
n.s.,
not
significant.
(C)
Scatter
plots
of
the
low-intermediaterisk g高い傾向を示しました。そこで２つの遺伝子の発現量差を算出し、この値におけるリンパ節転移陽性群と陰性群の識別精
FANTOM5 resource, the largest database of cis-regulatory regions basedon tran(TACC2新規アイソフォームの相対発度を示したものがROC曲線になります。ROC曲線の下の部分の面積はAUCといい、識別能の尺度として用いられます。
expression of
the novel
TACC2
andtranslational
SEMA3Dresearchers
mRNAs focusingin LN +onandin LN− respectively.
－(SEMA3Dの相対発現量)
scriptome
profiles,to assist
cis-regulatory-12!
識別能がランダムであるときAUCは0.5となり、値が1に近いほど判別能が高いことを示しますが、SEMA3DとTACC2新!
the LN + samples(withRNA lessthan Our
2 µg) were calculated
correcting
for the quantit
0.0 by規アイソフォームの発現量を組み合わせると0.929と非常に高い精度が示されました。
regions as
well
University-10 as basic-8 scientists.
-6-4 collaboration-2
0 with the0.0
0.2 of Cali0.4
0.6
0.8
is indicatedfornia,
by a blackarrow.
(D)For
thescatterplotofthehigh-risk
group,
a similar
tren
Santa TACC2新規アイソフォームの相対発現量
Cruz, made possible rapid access to a widely used genome browser
1 – 特異度was not as remarkable
as ingroup.
(E,F)toROC
analysisof theandlow-intermedi
database in Asia.
Wethealsolow-risk
successfully
contributed
translational
research
図2：SEMA3DとTACC2新規アイソフォームとリンパ節転移の関係
high-risk group(F).
provided valuable resources in functional genomics.

散布図では、縦軸にSEMA3D、横軸にTACC2新規アイソフォームのそれぞれ相対発現量をとり、リンパ節性を示しています。赤丸で示したリンパ節転移陽性群では、SEMA3Dの発現が低く、TACC2新規アイソフォ
高い傾向を示しました。そこで２つの遺伝子の発現量差を算出し、この値におけるリンパ節転移陽性群と陰度を示したものがROC曲線になります。ROC曲線の下の部分の面積はAUCといい、識別能の尺度として用In cases of識別能がランダムであるときAUCは0.5となり、値が1に近いほど判別能が高いことを示しますが、SEMA3D
high risk of recurrence, ROC curves (Fig. 4F) indicate that SEMA3D ex
規アイソフォームの発現量を組み合わせると0.929と非常に高い精度が示されました。

between LN + and LN− status at a moderate level (AUC, 0.735), however the novel isof

Lab activities

RIKEN-IFOM Joint Laboratory forCancer Genomics
Team Leader: Yasuhiro Murakawa

EnhancereRNA

Figure: Enhancer-mediated gene regulation

Enhancers are small segments of distal cis-regulatory
DNA elements that significantly enhance the expressionof target genes and play key roles in the establishmentof cell type-specific function and identity.

TFs

GenomemRNA

Promoter Target gene
Recent Major Publications
Yoshihara M, Araki A, Kasama Y, Sunayama M, Abe M,
Nishida K, Kawaji H, Hayashizaki Y, *Murakawa Y. Hotspots of de novo point mutations in induced pluripotent
stem cells. Cell Reports 21, 308-315 (2017)*Murakawa Y. Yoshihara M, Kawaji H, Nishikawa M,
Zayed H, Suzuki H, Fantom Consortium, Hayashizaki
Y. Enhanced identification of transcriptional enhancers provide mechanistic insights into diseases. Trends
Genet 32, 76-88 (2016)
Hasler D, Lehmann G, Murakawa Y, Klironomos F, Jakob
L, Grässer F, Rajewsky N, Landthaler M, Meister G. The
Lupus autoantigen La prevents mis-channeling of tRNAfragments into the human microRNA pathway. Mol Cell
63, 110-124 (2016)
Invited presentations
Murakawa Y, Kume S, Maeda M, Suga M, Tamura M,
Kobayashi N. “Seeing the Kidney through Imaging Big
Data” The 61st Annual Meeting of the Japanese Societyof Nephrology (Niigata, Japan) June, 2018

Murakawa Y. “Analysis of transcriptional network using
a novel NET-CAGE method” The 91st Annual Meetingof the Japan Endocrine Society (Miyazaki, Japan) April,2018
Murakawa Y. “Hotspot of de novo point mutations in
iPSCs” The 17th Congress of the Japanese Society for
Regenerative Medicine (17JSRM) (Yokohama, Japan)
March, 2018
Murakawa Y. “Decoding the Human Genome” LINK-J
Symposium (Tokyo, Japan) March, 2017T

he body-wide transcriptome is generated by the spatiotemporal orchestration of cis-regulatory elements such as promoters and enhancers. In particular, enhancers are distal cis-regulatory DNA elements that are crucial for theestablishment of cell type-specific function and identity (Fig). We aim to decipher
the cis-regulatory code that governs the transcriptional landscapes of malignancies, thereby gaining fundamental insight into cancer development and maintenance.
To investigate the cis-regulatory code, we have developed a simple and robust
technology, NET-CAGE, to globally determine the 5’-ends of nascent RNAs,
thereby sensitively detecting unstable transcripts including enhancer-derived
RNAs. NET-CAGE enabled ultra-sensitive detection of a number of enhancers at
single-nucleotide resolution.
We are applying our original NET-CAGE technology to describe the active cisregulatory landscape across hundreds of diverse tumors, discovering differentiallyregulated enhancers, genes, and long non-coding RNAs. Furthermore, using ourunique atlas of active enhancer regions at single-nucleotide resolution, we further
aim to develop a series of original technologies to investigate connectivity andfunctionality of cis-regulatory elements at both population and single-cell levels.
We believe in the importance of developing original technologies that can solve
paradigms that cannot be otherwise solved.
Lastly, through integrated analysis of (epi)genomic data with clinical information, we explore molecular therapeutic targets and biomarkers.

Murakawa Y. “Genome-wide analysis of the post-transcriptional gene regulation” Life of Genome Symposium(Kazan, Russia) August, 2016

21

Lab activities

Laboratory for

Genotyping Development

Figure: Location and number of Japanese breast
cancer patients with pathogenic genetic variants

The figure illustrates the frequency of the indicatedgenetic variants in the BRCA1 gene (top panel) andthe BRCA2 gene (lower panel). The indicated genetic
variants can result in loss of protein function (pink, e.g.,
p.Leu63* or p.Ile605fs), nonsynonymous amino acidsubstitutions (yellow, e.g., p.Lys1095Glu), or no change
in amino acids (synonymous, green, e.g., p.Pro3039Pro).
* = translation STOP codon; fs = frame shift. Two variants newly identified as pathogenic variants are underlined.

Number of carriers in patients

Team Leader: Yukihide Momozawa

p.Leu63*
p.Gln934*

p.Ile605fs

p.Lys1095Glu

p.Ile1859fs

p.Tyr1874Cys

p.Arg2318*

p.Ser1882* p.Asn2135fs

p.Gln3026*
p.Pro3039Pro

Amino acid residues
Recent Major Publications
Momozawa Y, Dmitrieva J, Theatre E, et al: IBD risk lociare enriched in multigenic regulatory modules encompassing putative causative genes. Nat Commun 9, 2427
(2018)

Momozawa Y, Iwasaki Y, Parsons MT, et al: Germline
pathogenic variants of 11 breast cancer genes in 7,051
Japanese patients and 11,241 controls. Nat Commun 9,4083 (2018)
Tajima T, Morita H, Ito K, et al. Blood lipid-related lowfrequency variants in LDLR and PCSK9 are associatedwith onset age and risk of myocardial infarction in Japanese. Sci Rep 8, 8107 (2018)
Invited presentations
Momozawa Y. “Translational science from veterinary
medicine to human medicine” Translational and Regulatory Sciences Symposium (Tokyo, Japan) February, 2019

Momozawa Y. “Complex genetic expression pattern
involved in inflammatory bowel disease.” Annual Meeting of the Japanese Society of Clinical Immunology(Karuizawa, Japan) November, 2018
Momozawa Y. “Germline pathogenic variants of 11 hereditary breast cancer genes in Japanese” The 77th Annual Meeting of the Japanese Cancer Association (Osaka,
Japan) September, 2018
Momozawa Y. “Germline pathogenic variants of 11
hereditary breast cancer genes in 7,051 unselected
Japanese breast cancer patients and 11,241 controls”
Satellite meeting of Human Genome Meeting (Yokohama, Japan) March, 2018
Momozawa Y. “Genomic analysis of disease of companion animals in Europe.” The 160th Annual Meeting of
the Japanese Society of Veterinary Science (Kagoshima,
Japan) September, 201722

T

he aims of the Laboratory for Genotyping Development are: 1) to produce
precise, large-scale genomic data to identify genetic variants associated withdisease susceptibility, disease outcomes, and drug responses; and 2) to develop
methods and databases useful for personalized medicine.
Our laboratory published 132 papers in 2016-2018. As one main achievementof our laboratory, we estimated disease risk of each gene and revealed demographic and clinical characteristics of pathogenic variants in Japanese hereditarybreast cancer patients (Nat Commun 9: 4083). This information is already usedin hospitals for the interpretation of genetic testing. Currently, we are expanding this effort to 13 other cancer types to provide fundamental information forcancer genetic testing. We also performed fine mapping of disease-associated lociidentified by a genome-wide association study to reveal the contribution of rarevariants to age-related macular degeneration (Hum Mol Genet 25: 5027-5034),
inflammatory bowel disease (Nat Commun 9: 2427), and myocardial infarction (SciRep 8: 8107).
Our laboratory has also worked as a research hub for large-scale genomic
analysis, collaborating with domestic and international universities, research
institutes, and companies. We have contributed to the identification of diseaseassociated variants and disease biology for various diseases/phenotypes including
inflammatory bowel disease (Nature 547: 173-178), body mass index (Nat Genet
49: 1458-1467), and clinically important quantitative traits (Nat Genet 50: 390400).
We will continue to conduct our own projects and to function as a research
hub for large-scale genomic analysis so that we can contribute to the implementation of personalized medicine.

Lab activities

Laboratory for

Statistical Analysis
Team Leader: Yoichiro Kamatani

Recent Major Publications
Okazaki S, Morimoto T, Kamatani Y, Kamimura T, Kobayashi H, Harada K, TomitaT, Higashiyama A, Takahashi
JC, Nakagawara J, Koga M, Toyoda K, Washida K, Saito S,
Takahashi A, Hirata M, Matsuda K, Mochizuki H, Chong
M, Paré G, O'Donnell M,Ago T, Hata J, Ninomiya T, Dichgans M, Debette S, Kubo M, Koizumi A, Ihara M. Moyamoya Disease Susceptibility Variant RNF213 p.R4810K
Increases the Risk of Ischemic Stroke Attributable toLarge-Artery Atherosclerosis. Circulation 139, 295-8(2019)

Anttila V, Bulik-Sullivan B, Finucane HK, Walters RK,Bras
J, Duncan L, Escott-Price V, Falcone GJ, Gormley P, Malik
R, Patsopoulos NA,Ripke S, Wei Z, Yu D, Lee PH, Turley P,
Grenier-Boley B, Chouraki V, Kamatani Y, Berr C, Letenneur L, Hannequin D, Amouyel P, Boland A, Deleuze JF,
Duron E,Vardarajan BN, Reitz C, Goate AM, et al. Analysisof shared heritability in common disorders of the brain.
Science 360, eaap8757 (2018)
Kanai M, Akiyama M, Takahashi A, Matoba N, Momozawa Y, Ikeda M, Iwata N, Ikegawa S, Hirata M, Matsuda
K, Kubo M, Okada Y, Kamatani Y. Genetic analysis ofquantitative traits in the Japanese population links cell
types to complex human diseases. Nat Genet 50, 390400 (2018)
Invited Presentations
Kamatani Y. “Comprehensive genetic study for complex
diseases.” The 83rd Annual Scientific Meeting of theJapanese Circulation Society (Yokohama, Japan) March,
2019

Kamatani Y. “Finding stroke susceptibility genes throughgenomic analysis of hundreds of thousands of samples.”International Seminar of Cerebrovascular Disease (Shinjuku, Japan) February, 2019
Kamatani Y. Genetic analysis of more than 100K Japanese subjects including cardiovascular disorders” The
2nd JCS Council Forum on Basic Cardiovascular Research(Nara, Japan) September, 2018
Kamatani Y. “The Biobank Japan” 23rd workshop ofInternational Stroke Genetics Consortium (Kyoto, Japan)
April, 2018
Kamatani Y. “Whole genome analysis and its future inprecision medicine” The 22nd Annual Meeting of theSociety of Cardiovascular Endocrinology and Metabolism(Miyazaki, Japan) April, 2018

Figure: A mutation in mouse Pld4, a novel human SLE susceptibility gene identified by GWAS, resultsin autoimmune phenotypes in mice.

Homozygous Pld4 (Phospholipase D4) mutant mice had
lower body weight compared to heterozygous mice during the period of observation (Upper panel, *, p<0.05).
Splenomegaly and lymphadenopathy in Pld4 mutant

mice. Spleen, inguinal lymph node (iLN), and mesentericlymph nodes (mLN) are compared between -/+ and -/mice at 15 weeks after birth (Lower panel).

Our laboratory aims to find genetic susceptibility variants associated withcomplex traits, and to understand their biological roles by using integrative
analyses of epigenome and transcriptome data. We have performed dozens of genome-wide association studies (GWAS) and identified thousands of susceptibilityloci for multiple complex traits. Most of these accomplishments were viewed in
the field as the largest ever human genetic analyses for non-Europeans, and wefreely shared these results after their publication (http://jenger.riken.jp/en/). Our
analyses clarified the similarity and differences between populations with regard
to genetics of the traits. We performed downstream analyses to understand thebiological background underlying these genetic results, and found that traitrelevant cell types can be linked by applying integrative analysis of genetic andepigenetic data. We also support genetic analyses of our collaborators and participate in international meta-analysis consortia, including AFGen, GIANT, andMEGASTROKE, to enhance statistical power to detect genetic signals.
We then moved into two new major research fields. One is to use whole genome sequencing (WGS) analysis to expand our understanding of complex traits.
This technique is useful to detect rare variants, which are strong candidates to
explain population differences in the genetics of the traits. This study may contribute to the future Genomic Medicine for East Asians. The second is to employ
deep learning techniques to predict the biological consequences of trait-relevant
variants. Genetic evidence, in conjunction with epigenome, transcriptome, andother cellular multi-omics data set analyses, may lead to the discovery of novel
biological principals. This project can proceed more efficiently with further collaborations with other IMS laboratories, and we have begun to discuss the feasibility of such collaborations.

23

Lab activities

Laboratory for

Pharmacogenomics
Team Leader: Taisei Mushiroda

Recent Major Publications
Yoshihama T, Fukunaga K, Hirasawa A, Nomura H,
Akahane T, Kataoka F, Yamagami W, Aoki D, Mushiroda
T. GSTP1 rs1695 is associated with both hematological
toxicity and prognosis of ovarian cancer treated withpaclitaxel plus carboplatin combination chemotherapy:
a comprehensive analysis using targeted resequencingof 100 pharmacogenes. Oncotarget 9, 29789-29800(2018)

Mushiroda T, Takahashi Y, Onuma T, Yamamoto Y, Kamei
T, Hoshida T, Takeuchi K, Otsuka K, Okazaki M, Watanabe
M, Kanemoto K, Oshima T, Watanabe A, Minami S, Saito
K, Tanii H, Shimo Y, Hara M, Saitoh S, Kinoshita T, Kato M,
Yamada N, Akamatsu N, Fukuchi T, Ishida S, Yasumoto S,
Takahashi A, Ozeki T, Furuta T, Saito Y, Izumida N, Kano
Y, Shiohara T, Kubo M; GENCAT Study Group. Association of HLA-A*31:01 Screening With the Incidence ofCarbamazepine-Induced Cutaneous Adverse Reactions
in a Japanese Population. JAMA Neurol 75, 842-849(2018)
Ujiie H, Muramatsu K, Mushiroda T, Ozeki T, Miyoshi
H, Iwata H, Nakamura A, Nomoto H, Cho KY, Sato N,
Nishimura M, Ito T, Izumi K, Nishie W, Shimizu H. HLADQB1*03:01 as a Biomarker for Genetic Susceptibility
to Bullous Pemphigoid Induced by DPP-4 Inhibitors. J
Invest Dermatol 138, 1201-1204 (2018)
Invited presentations
Mushiroda T. “Adverse effects by anti-tuberculosis drug”
Social implications of scientific technology in TB control(Bangkok, Thailand) December, 2018

Mushiroda T. “Pharmacogenomics research in Southeast
Asia” The 21st GoldenHelix Pharmacogenomics Day(Singapore, Singapore) August, 2018
Hikino K. “Clinical evidence essential to PGx informed
precision medicine in pediatrics” International Symposium on Pediatric Drug Evaluation and Clinical Pharmacology (Tokyo, Japan) June, 2018
Ozeki T. “Genetic analysis for cutaneous adverse drug
reactions induced by phenobarbital and phenytoin in
Japanese population” The 3rd International StevensJohnson Syndrome Symposium (Kyoto, Japan) February,
2018

24

Figure: PKseq, targeted resequencing of a panel of 100 genes related to pharmacokinetics using a
combination of multiplex-PCR and next-generation sequencing (NGS)The newly developed NGS panel, PKseq, can analyze
common and rare variants comprehensively and accurately, which is an ideal platform for identification ofpharmacogenomics biomarkers useful for predicting
drug efficacy and risk of adverse drug reactions. Whenaccuracies of the PKseq and whole-exsome sequencing

I(WES) were compared in the same Japanese individual(Ref: reference allele, Alt: variant allele), the WES
showed some differences from the results of Sanger
sequencing, but the PKseq demonstrated the same
genotypes as Sanger sequencing, leading to higher sensitivity and specificity compared to the WES.

ndividual responses to drugs can vary widely. Lack of drug efficacy can leadto inadequate disease control and is a waste of resources; conversely, adverse
drug reactions (ADRs) are frequent and often unpredictable. Many polymorphisms have been identified in genes that affect efficacy or risk of ADRs for various drugs. In the USA, information on 161 germline genomic biomarkers is available in US FDA-approved drug labels. However, in Japan, the National Health
Insurance System currently covers only two genetic tests, UGT1A1 and BRCA1/2,
to predict drug responses prior to the drug administration.
In collaboration with domestic hospitals, we are conducting genomic analyses
for the identification of pharmacogenomic (PGx) biomarkers useful for prediction of drug responses. Since it is difficult for individual countries acting alone tocollect a sufficient number of samples for PGx research, we conduct international
PGx collaborations, such as the Southeast Asian Pharmacogenomics Research
Network (SEAPharm). In order to achieve our mission, application of PGx biomarkers to clinical practice, we advance our research according to three primarysteps: i) establishment of infrastructure for identification of PGx biomarkers, ii)
identification by genomic analyses of PGx biomarkers associated with drug efficacy/adverse drug reactions, and iii) clinical implementation of PGx biomarkers.

Lab activities

Laboratory forBone and Joint Diseases
Team Leader: Shiro Ikegawa

Figure: Manhattan plot for the AIS GWAS

The horizontal red line indicates the genome-wide
significance threshold (P = 5 × 10-8). Genetic loci withgenome-wide significance are labeled.

Recent Major Publications
Kou I, Watanabe K, Takahashi Y, Momozawa Y, Khanshour A, Grauers A, Zhou H, Liu G, Fan YH, Takeda K,
Ogura Y, Zhou T, Iwasaki Y, Kubo M, Wu Z, Matsumoto
M; Japan Scoliosis Clinical Research Group (JSCRG);
Texas Scottish Rite Hospital for Children Clinical Group(TSRHCCG), Einarsdottir E, Kere J, Huang D, Qiu G, Qiu Y,
Wise CA, Song YQ, Wu N, Su P, Gerdhem P, Ikegawa S. A
multi-ethnic meta-analysis confirms the association of
rs6570507 with adolescent idiopathic scoliosis. Sci Rep
8, 11575 (2018)

Ogura Y, Takeda K, Kou I, Khanshour A, Grauers A, Zhou
H, Liu G, Fan YH, Zhou T, Wu Z, Takahashi Y, Matsumoto
M; Japan Scoliosis Clinical Research Group (JSCRG);
Texas Scottish Rite Hospital for Children Clinical Group(TSRHCCG), Einarsdottir E, Kere J, Huang D, Qiu G, Xu L,
Qiu Y, Wise CA, Song YQ, Wu N, Su P, Gerdhem P, Watanabe K, Ikegawa S. An international meta-analysis confirms the association of BNC2 with adolescent idiopathic
scoliosis. Sci Rep 8, 4730 (2018)
Kanai M, Akiyama M, Takahashi A, Matoba N, Momozawa Y, Ikeda M, Iwata N, Ikegawa S, Hirata M, Matsuda
K, Kubo M, Okada Y, Kamatani Y. Genetic analysis ofquantitative traits in the Japanese population links cell
types to complex human diseases. Nat Genet 50, 390400 (2018)
Invited Presentations
Ikegawa S. “Genetic study of bone and joint diseases”
Invited special lecture in Chinese Academy of Medical
Sciences (Beijing, China) September, 2018

Ikegawa S. “Genomic study of skeletal dysplasia” Invitedspecial lecture in Marmara University Medical School(Istanbul, Turkey) June, 2018
Ikegawa S. “Extension of genome-wide association
study of adolescent idiopathic scoliosis”
The International Consortium for Spinal Genetics Development and Disease Conference Meeting in Guangzhou(Guangzhou, China) April, 2018
Ikegawa S. “Natural history and etiology of spine disorders” The International Consortium for Spinal Genetics
Development and Disease Conference Meeting in Shenzhen (Shenzhen, China) April, 2018
Ikegawa S. “Genomic study of common spinal diseases”
2018 Annual Meeting of Taiwan Spine Society (Taipei,
Taiwan) April, 2018

1) Genomic Study of Common Diseases
Common bone and joint diseases are serious worldwide problems for healthand the economy, as exemplified by the WHO initiative “Bone and Joint Decade”(2000-2010) and the “Locomotive syndrome campaign” in Japan. We are searching for susceptibility genes for common (polygenic) bone and joint diseases, including osteoarthritis (OA), lumbar disc disease (LDD)/herniation (LDH), osteoporosis, avascular necrosis of the femoral head (ANF), scoliosis, and ossificationof the posterior longitudinal ligament of the spine (OPLL).
Through genome-wide association studies (GWASs) and next-generation sequencing approaches, we identify and characterize susceptibility genes and clarify
their disease-causing mechanisms at the molecular level. Using the genome information obtained from these studies, we will realize our final goal of “personalized medicine”. GWASs for OA, LDD/LDH, adolescent idiopathic scoliosis (AIS),
OPLL, and ANF are in progress, and we already succeeded in the identificationof several susceptibility genes. Functional studies of the genes in vitro and using
model animals are underway.

2) Genomic Study of Skeletal Dysplasia
Skeletal dysplasia is a group of heritable (monogenic) disorders affecting theskeleton, and more than 400 diseases belong to this category. Skeletal dysplasia is
an intractable disease, so many patients are waiting for an efficacious treatment.
We are engaging in clinical and basic studies of these difficult diseases. By largescale mutation screening, including exome sequencing, we are identifying thedisease causative genes.
Through the analyses of phenotypes and diseases genes, we approach the molecular mechanisms of bone and joint formation and the pathogenesis of commonbone and joint diseases, as well as the diagnosis and treatment of rare intractablediseases. Using the disease genes for skeletal dysplasia as candidate genes, we arethen performing association studies for common bone and joint diseases corresponding to skeletal dysplasia, the so-called “rare to common” approach.

25

Lab activities

Laboratory for

Endocrinology,
Metabolism and Kidney Diseases
Team Leader: Momoko Horikoshi

Invited Presentations
Horikoshi M. “Genetics of Type 2 Diabetes in the Japanese population” Seminar at Kuroda Lab, Departmentof Biological Sciences, Graduate School of Science, The
University of Tokyo (Tokyo, Japan) January, 2019

Horikoshi M. “Maternal and fetal genetic effects on birthweight and their relevance to cardio-metabolic risk
factors” The 8th DOHaD Epidemiological Seminar (Tokyo,
Japan) October, 2018
Horikoshi M. “Discovery of genomic loci associated withbirth weight and the shared genetic contribution withadult metabolic diseases” RIKEN Summer School 2018
(Tsukuba, Japan) September, 2018
Horikoshi M. “Genetics of Type 2 Diabetes in the Japanese population” The 61st annual meeting of The Japan
Diabetes Society (Tokyo, Japan) May, 2018
Horikoshi M. “Genome-wide associations for birthweight and correlations with adult disease” The 3rd
meeting for research on metabolism and nutritional
mechanism of lifestyle disease and cancer (Tokyo, Japan) March, 201826b

Japanese T2D GWAS
r2
0.8
0.6
0.4
0.2

rs9394574
lead variant

100

European T2D GWAS
r2

15

80

10
60

40
5

80
10
60

40
5

20

0

0

rs10305492
A316T
0
GLP1R

39.03
39.04
Position on chr6 (Mb)

39.05

39.02

ECD

c

N terminal
TM1d
131 Arg
ECL1

Extracellular

20

0

GLP1R

39.02

100
0.8
0.6
0.4
0.2

rs3765467
R131Q

log10(p−value)

15

39.03
39.04
Position on chr6 (Mb)

39.05

Recombination rate (cM/Mb)

Beaumont RN, Warrington NM, Cavadino A, Tyrrell J,
Nodzenski M, Horikoshi M, Geller F, Myhre R, Richmond
RC, Paternoster L, Bradfield JP, Kreiner-Møller E, Huikari
V, Metrustry S, Lunetta KL, Painter JN, Hottenga JJ, Allard C, Barton SJ, Espinosa A, Marsh JA, Potter C, Zhang
G, Ang W, Berry DJ, Bouchard L, Das S; Early Growth
Genetics (EGG) Consortium, Hakonarson H, Heikkinen J,
Helgeland Ø, Hocher B, Hofman A, Inskip HM, Jones SE,
Kogevinas M, Lind PA, Marullo L, Medland SE, Murray A,
Murray JC, Njølstad PR, Nohr EA, Reichetzeder C, Ring
SM, Ruth KS, Santa-Marina L, Scholtens DM, Sebert S,
Sengpiel V, Tuke MA, Vaudel M, Weedon MN, Willemsen
G, Wood AR, Yaghootkar H, Muglia LJ, Bartels M, Relton
CL, Pennell CE, Chatzi L, Estivill X, Holloway JW, Boomsma DI, Montgomery GW, Murabito JM, Spector TD,
Power C, Järvelin MR, Bisgaard H, Grant SFA, Sørensen
TIA, Jaddoe VW, Jacobsson B, Melbye M, McCarthy MI,
Hattersley AT, Hayes MG, Frayling TM, Hivert MF, Felix JF,
Hyppönen E, Lowe WL Jr, Evans DM, Lawlor DA, Feenstra B, Freathy RM. Genome-wide association study ofoffspring birth weight in 86 577 women identifies fivenovel loci and highlights maternal genetic effects thatare independent of fetal genetics. Hum Mol Genet 27,
742-756 (2018)a

Recombination rate (cM/Mb)

Horikoshi M*, Day FR, Akiyama M, Hirata M, Kamatani Y,
Matsuda K, Ishigaki K, Kanai M, Wright H, Toro CA, Ojeda
SR, Lomniczi A, Kubo M, Ong KK, Perry JRB*. Elucidating
the genetic architecture of reproductive ageing in theJapanese population. Nat Commun 9, 1977 (2018).

Figure: Manhattan plot of Japanese
T2D GWAS and regional association
plots of GLP1R with its structure.

log10(p−value)

Recent Major Publications
Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J,
Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M,
Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda
M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S,
Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M,
Okada Y, Kubo M, Kamatani Y*, Horikoshi M*, Yamauchi
T*, Kadowaki T*. Identification of 28 new susceptibilityloci for type 2 diabetes in the Japanese population. Nat
Genet 51, 379-386 (2019)

Manhattan plot (top) summarizes the
genome-wide association study of Japanese
T2D in 36,614 cases and 155,150 controls.
The association P value (in –log10P) for
each of up to 12,557,761 variants (y axis)
was plotted against the genomic position (xaxis). Association signals that reached genome-wide significance (P < 5.0 × 10-8) are
shown in green if novel and in blue if previously reported. Regional association plots of
the Glucagon-like Peptide 1 Receptor (GLP1R) region in Japanese (a) and Europeans(b). T2D GWAS highlighting the Japanesespecific T2D association at the GLP1R locus.
A three-dimensional ribbon model (c) and asnake plot (d) of GLP1R shows the positionof the novel T2D missense variant R131Q(red) at a highly flexible region (yellow andorange) interacting with extracellular loop
(green).

Intracellular
ICL

E

C terminal

ver larger scale genome-wide association (GWA) meta-analyses for type 2
diabetes (T2D), in which the included samples now total nearly 1 million,
have been extensively conducted, mainly in Europeans. We have been focusing on
investigating the genetic contribution to T2D susceptibility in the Japanese population by using the rich genetic resources generated by Biobank Japan (BBJ). By
expanding our effort to the full BBJ collection, we conducted a single-population
GWA analysis of T2D in 191,764 Japanese. In addition to the >150 T2D loci established as of the end of 2018, we identified 28 novel loci (Figure). We detected
several previously unreported T2D-associated missense variants that showed adifferent spectrum of minor allele frequencies between Japanese and Europeans(Figure). A transethnic comparison of pathway analysis revealed that both groups
had shared and dissimilar impacts of a series of pathways on T2D. These findings
provided a possible explanation for the heterogeneity in response to T2D drugs
and clinical features between Japanese and Europeans. We are strengthening ourties with neighboring collaborators by contributing our T2D association data to
the Asian Genetic Epidemiology Network (AGEN) Consortium as well as to theworld-wide DIAMANTE Consortium.
We also examined the genetics of reproductive ageing, in collaboration with
the REPROgen consortium. Successful genetic studies of reproductive ageing hadlargely been limited to individuals of European ancestry, but GWA analysis in
67,029 women from the BBJ enabled us to identify 26 loci for puberty timing andage at menopause, representing the first loci for reproductive ageing in any nonEuropean population.

Lab activities

Laboratory for

Cardiovascular Diseases
Team Leader: Kaoru Ito

Figure: Imputation quality in the RIKEN-CAD
panel

The 3D plot shows the relationships among minor allele
frequency, imputation quality, and the number of variants in imputed samples. In the 1000 genomes projectbased imputation, which is the most relevant reference
panel in the world, imputation quality of rare variants islow, while numerous rare variants of high quality wereobserved in the RIKEN-CAD panel.

Recent Major Publications
Nomura S, Satoh M, Fujita T, Higo T, Sumida T, Ko T,
Yamaguchi T, Tobita T, Naito AT, Ito M, Fujita K, HaradaM, Toko H, Kobayashi Y, Ito K, Takimoto E, Akazawa H,
Morita H, Aburatani H, Komuro I. Cardiomyocyte geneprograms encoding morphological and functional signatures in cardiac hypertrophy and failure. Nat Commun 9,4435 (2018)

Roselli C, Ito K, Kamatani Y, Tanaka T, Ellinor PT, et al.
Multi-ethnic genome-wide association study for atrial
fibrillation. Nat Genet 50, 1225-1233 (2018)
Tajima T, Morita H, Ito K, Yamazaki T, Kubo M, Komuro I,
Momozawa Y. Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age
and risk of myocardial infarction in Japanese. Sci Rep 8,8107 (2018)
Invited Presentations
Ito K. “Cardiovascular Omics Research from the viewpoint of Genomics” The 22nd Annual Scientific Meetingof the Japanese Heart Failure Society (Tokyo, Japan)
October, 2018

Ito K. “Introduction to Genomic Research” Statistical
Genetics Summer School (Osaka, Japan) August, 2018
Ito K. “Elucidating Genetic Factors for Cardiovascular
Diseases” Kickoff Meeting for the Advanced Genomic
Research (Tokyo, Japan) July, 2018
Ito K. “Aberrant RNA splicing in Cardiomyopathy” The
4th Japanese Cardiomyopathy Meeting of the JapaneseHeart Failure Society (Nara, Japan) June, 2018
Ito K. “Genomic Research for Onco-cardiology” The 3rd
Otemae Seminar (Osaka, Japan) May, 2018

S

ince cardiovascular diseases cause more than 15% of the deaths in the Japanese population and represent more than 20% of the total medical expenses
in Japan, it is important for our society to understand the mechanisms underlying these disorders and to uncover new therapeutic targets for their treatment. To
achieve these goals, we aim to discover the precise genetic mechanisms underlying those diseases by utilizing leading-edge technologies, such as whole genome
sequencing and machine learning. Additionally, we conduct research to push forward the clinical applications of genetic information in the field of cardiovascular
medicine.
Our diseases of interest to date are coronary artery diseases (CAD), atrial fibrillation (AF), Kawasaki disease (KD), peripheral artery disease (PAD), chronic
thromboembolic pulmonary hypertension (CTEPH), and cardiomyopathy (CM).
We are currently seeking 1) understand the genetic causes of CAD and the genetic differences between Japanese and European populations, 2) elucidate themechanism of CTEPH development using human omics data from patients in
multiple hospitals, and 3) develop a more sophisticated genetic risk scoring system by machine learning algorithms in the MI and AF projects. Additionally, in
the CM project, we developed an in silico splicing variant prediction algorithm, ahigh-throughput cell-based splicing assay, and a downstream in silico pipeline touncover cryptic splice variants, which have been overlooked in the currently established pipelines. Using this pipeline, we are now tackling the TTN (titin) gene,which is expressed in striated muscle and encodes the largest protein in humans,consisting of 34,350 amino acids.
We are conducting our research with not only a scientific mind but also aclinical eye, because our ultimate goal is to provide improved diagnostic/management/therapeutic approaches for patients suffering from those diseases.

27

Division of Human Immunology

Division of Human Immunology will elucidate the principles of theimmune system and develop a research platform for human immunology.

28

Lab activities

Laboratory for

Autoimmune Diseases
Team Leader: Kazuhiko Yamamoto
Genotyping(>6 x10^7 cells)

Figure: Integration of genetic variations andmulti-omics data

Th1
12 subsets
Th2
Th17
Tfh
Treg
LAG3 Treg
Memory CD4Naïve CD4Naïve CD8CD8 effector
CD8+Central Memory
CD8+ effector Memory

T cells

n=200～

Whole blood (~50ml)
From healthy individuals

5 subsets

B cells

Dendritic
cellsNaïve B
Switched memory B
UnSwitched memory B
DNB
Plasmablast

Plasmacytoid DC
Myeloid DC
2 subsets
6 subsets

Recent Major Publications
Kochi Y, Kamatani Y, Kondo Y, Suzuki A, Kawakami E,
Hiwa R, Momozawa Y, Fujimoto M, Jinnin M, Tanaka
Y, Kanda T, Cooper RG, Chinoy H, Rothwell S, Lamb JA,
Vencovský J, Mann H, Ohmura K, Myouzen K, Ishigaki K,
Nakashima R, Hosono Y, Tsuboi H, Kawasumi H, Iwasaki
Y, Kajiyama H, Horita T, Ogawa-Momohara M, Takamura
A, Tsunoda S, Shimizu J, Fujio K, Amano H, Mimori A,
Kawakami A, Umehara H, Takeuchi T, Sano H, Muro Y,
Atsumi T, Mimura T, Kawaguchi Y, Mimori T, TakahashiA, Kubo M, Kohsaka H, Sumida T, Yamamoto K. Splicing variant of WDFY4 augments MDA5 signalling andthe risk of clinically amyopathic dermatomyositis. Ann
Rheum Dis 77, 602-611 (2018)

Ishigaki K, Kochi Y, Suzuki A, Tsuchida Y, Tsuchiya H,
Sumitomo S, Yamaguchi K, Nagafuchi Y, Nakachi S, Kato
R, Sakurai K, Shoda H, Ikari K, Taniguchi A, Yamanaka
H, Miya F, Tsunoda T, Okada Y, Momozawa Y, Kamatani
Y, Yamada R, Kubo M, Fujio K, Yamamoto K. Polygenic
burdens on cell-specific pathways underlie the risk ofrheumatoid arthritis. Nat Genet 49, 1120-1125 (2017)
Okada Y, Suzuki A, Ikari K, Terao C, Kochi Y, Ohmura K,
Higasa K, Akiyama M, Ashikawa K, Kanai M, Hirata J,
Suita N, Teo YY, Xu H, Bae SC, Takahashi A, Momozawa
Y, Matsuda K, Momohara S, Taniguchi A, Yamada R, Mimori T, Kubo M, Brown MA, Raychaudhuri S, Matsuda F,
Yamanaka H, Kamatani Y, Yamamoto K. Contribution ofa Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. Am J Hum Genet 99, 366-74 (2016)
Invited presentations
Yamamoto K. “Genetics and epigenetics of autoimmune
diseases” International Congress of Autoimmunity (Lisbon, Portugal) May, 2018

Yamamoto K. “Polygenic burdens on cell-specific pathways” International Forum for RA (IFRA) Karolinska
Institute (Stockholm, Sweden) Sept, 2017
Yamamoto K. “Peptidyl arginine deiminase 4 andrheumatoid arthritis” EULAR (European League Against
Rheumatism) (Madrid, Spain) June, 2017
Yamamoto K. “Genetics of rheumatoid arthritis” Advanced Target Therapies (Nice, France) March, 2017
Yamamoto K. “Regulation of B cell functions and cellular
metabolism in autoimmunity” Cold Spring Harbor Asia
Conference (Awaji, Japan) October, 2016

Genomic variations(WGS or array chip)

QTL analysis

FACS sorting

NK cell
NKT cell
NK cells/ CD14+ CD16+ Monocyte
monocyte CD14+ CD16- Monocyte

2x10^4 cells/
each subset

DNA

Bisul-seq(>5000 cells/reaction)

RNA-seq(>5000 cells/reaction)

activation

RNA
CAGE-seq(>5000 cells/reaction)
activation

Chromatin

Methylation QTL (mQTL)
Expression QTL(eQTL)
Splicing QTL (sQTL)

Whole genome
enhancer and promoter
state analysis(regulatory QTL)Long non-coding RNA
analysis (lncQTL)

ATAC-seq(>5000 cells/reaction)

ChIP-seq

activation
activation

NonClassical Monocyte
Intermidiate Monocyte

Neutrophils(4 x10^6 cells)

26 subsets

Clinical laboratory exam. (LDL, HDL, CRP, etc.)
Clinical information (Age,Gender, Weight etc.)

Stratification analysis

>1ml

PBMC

QTL data catalog andchromatin statusx

GWAS(Biobank Japan)xEpigenome datafrom Public DB
Integration ofdatasets

Identification of causative
diseases/traits associated pathwaysT

he immune system has mainly been investigated using mouse models.
However, there are several distinct and critical differences between mouseand human immune systems. Therefore, human immunology research is indispensable; however, there are several technical limitations in this area. In orderto overcome this obstacle, we believe that genetics is invaluable, because genetic
information provides us with evidence of the causal relationship to an observed
phenomenon. Recently, many of the disease susceptibility variants identified bygenome wide association study (GWAS) have been found to function as expression-quantitative trait loci (eQTL), regulating the expression levels of genes in acell type-specific manner.
We conducted a cell type-specific eQTL analysis on five immune cell populations (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes) from 105
healthy Japanese volunteers (Ishigaki K et al Nature Genetics 2017). This is one of
the largest RNA-seq-based eQTL studies focusing on multiple immune cells. We
successfully detected thousands of eQTL variants for each cell population, anddeposited the main results of our eQTL analyses into a National Bioscience Database Center (NBDC). We also developed an original method of integrating eQTL
data with pathological pathway analyses.
However, immune responses are carried out by the interactions between further differentiated and functionally distinct lymphocyte subsets. Therefore, we
are now setting up a system to obtain nearly 20 different lymphocyte subsets fromhuman peripheral blood mononuclear cells (PBMC) of healthy individuals (as theinitial project) (Figure) and several different autoimmune diseases (as the second
project). The main purpose of these projects is to elucidate the mechanisms ofeQTL and underlying epigenetic status, i.e., genetic polymorphisms and gene expression in differentiated lymphocyte subsets under physiological conditions. We
hope that insights gained from these studies will provide a way to control pathological processes.

29Lab activities

Laboratory for

Cell Signaling
Team Leader: Takashi Saito

Tumor / Infected cell
Antigen/MHC
T cell receptor(TCR-CD3)

Figure: Negative regulation of T cell activationby the CIN85 adaptor protein

T cellThe adaptor CIN85 inhibits T cell activation by recruitment of the phosphatase Sts-2 and the ubiquitin ligase
Cbl into the TCR microcluster upon TCR stimulation.

TCR
microcluster

ZAP70
CIN85

Cbl

Sts-2

T cell activation

Induction of an immune response
against tumors and pathogens

Recent Major Publications
Kong MS*, Hashimoto-Tane A*, Kawashima Y, Sakuma
M, Yokosuka T, Kometani K, Onishi R, Carpino N, Ohara
O, Kurosaki T, Phua KK and Saito T. Inhibition of T cell
activation and function by the CIN85 adaptor protein.
Sci Signal 12, eaav4373 (2019)

Imanishi T, Unno M, Kobayashi W, Yoneda N, Matsuda S,
Ikeda K, Hoshii T, Hirao A, Miyake K, Barber GN, Arita M,
Ishii KJ, Akira S, Saito T. Reciprocal regulation of STING
and TCR signaling by mTORC1 for T cell activation andfunction. Life Sci Alliance 2, e201800282 (2019)
Takeuchi A and Saito T. CD4 CTL, a Cytotoxic Subset of
CD4+ T cells, Their Differentiation and Function. Front
Immunol 8, 194 (2017)
Invited presentations
Saito T. “Dynamic regulation of inhibitory signals on T
cell activation” EMBO Workshop: Lymphocyte antigen
receptor signaling (Siena, Italy) August, 2018

Saito T. “Dynamic regulation of T cell co-stimulation
at Immune synapse” Merck special seminar (Palo Alto,
USA) June, 2018
Saito T. “Innate signal regulation in T cell activation”
German-Japan Immunology Meeting (Shizuoka, Japan)
December, 2017
Saito T, Imanishi T. “Regulation of T cell activation andfunction by innate signals – STING activation in T cells
induce growth arrest and IFN production” FASEB Summer Research conference: Signal Transduction in the
Immune System (Colorado, USA) June, 2017
Saito T. “Microsynapse composed of micro-adhesion ringsurrounding TCR micro cluster is essential for T cell activation” EMBO conference (Siena, Italy) September, 201630

T

he objective of our team is to determine the molecular mechanisms of T cell
activation, differentiation, and function. Toward this goal, we have studied
basic mechanisms such as antigen recognition, T cell activation and differentiation, and regulation of function from a signaling perspective. Processes of activation at the single cell level by molecular imaging and T cell development/homeostasis within clonal populations are both being investigated.
Our finding that TCR-microclusters (MC) initiate T cell activation led us toanalyze the dynamic recruitment/assembly of signaling molecules at the immune
synapse. Using approaches similar to those used in our studies of CTLA4 andPD-1, the dynamic regulation of other inhibitory co-stimulation receptors arebeing analyzed. These inhibitory receptors colocalized with the TCR-MC upon
TCR stimulation to mediate inhibition of T cell activation. Our analyses provide adynamic view of signal regulation and determine their inhibitory mechanism.
We have analyzed several molecules that are highly expressed upon T cell activation as possible targets to modulate T cell activation and function. CRTAM was
originally cloned as an adhesion receptor, but is now found to play a critical rolein determining the CD4+ CTL lineage. The TCR downstream signaling adaptor
CIN85 is now found to mediate negative regulation of T cell activation by recruiting the phosphatase Sts-2. CIN85-Sts-2 is recruited to the TCR-MC and may
represent a new inhibitory pathway (Figure 1). The function of the innate-sensor
STING in T cells was analyzed since it is highly expressed in T cells. STING
activation induced growth inhibition and type I-IFN production in T cells. We
showed that STING activation in T cells contributes to anti-tumor immunity.
Our ultimate aim is to elucidate the onset of and to modulate T cell function/
activation to prevent immune diseases such as autoimmunity and allergic inflammation. We have analyzed the function of autoimmune-related phosphatases
PTPN22 and PTPN2. Their deficiency per se did not induce autoimmunity; KO
mice showed enhanced activation and an increase in effector/memory T cells.
Imaging analysis and MS analysis of PTPN-associated molecules will be used to
identify the inhibitory mechanisms that maintain homeostasis.

Lab activities

Laboratory for

Lymphocyte
Differentiation
Team Leader: Tomohiro Kurosaki

Figure: Tet2 and Tet3 contribute to peripheral B
cell tolerance.

(A)(A) CD86 is normally upregulated on activated B cells,
but in the case of chronic antigen stimulation, e.g., byautoantigen, CD86 upregulation ceases. Therefore, T cell
activation and subsequent B cell proliferation are terminated (self-tolerant state). However, in the absence ofTet2 and Tet3, such chronic antigen stimulation cannot
downregulate CD86 expression, thereby changing the B
cell fate from peripheral tolerance to proliferation.
(B) Tet2 and Tet3 normally recruit HDAC to the CD86
locus in the chronic state, thereby dampening transcription of CD86.

chronic Ag (auto)

chronic Ag (auto)

Tet2/Tet3−/−(B)
Tet2/Tet3+/+

Recent Major Publications
Ise W, Fujii K, Shiroguchi K, Ito A, Kometani K, Takeda K,
Kawakami E, Yamashita K, Suzuki K, Okada T, Kurosaki T.
T Follicular Helper Cell-Germinal Center B Cell Interaction Strength Regulates Entry into Plasma Cell or Recycling Germinal Center Cell Fate. Immunity 48, 702-715(2018)

Inoue T, Moran I, Shinnakasu R, Phan TG, Kurosaki T.
Generation of memory B cells and their reactivation.
Immunol Rev 283, 138-149 (2018)
Herndler-Brandstetter D, Ishigame H, Shinnakasu R,
Plajer V, Stecher C, Zhao J, Lietzenmayer M, Kroehling
L, Takumi A, Kometani K, Inoue T, Kluger Y, Kaech SM,
Kurosaki T, Okada T, Flavell RA. KLRG1+ Effector CD8+ T
Cells Lose KLRG1, Differentiate into All Memory T Cell
Lineages, and Convey Enhanced Protective Immunity.
Immunity 48, 716-729 (2018)
Invited Presentations
Kurosaki T. “Selection mechanisms of germinal center
cells into the memory B cell compartment” Keystone
Symposia: B Cell-T Cell Interactions (Keystone, USA)
February, 2019

Kurosaki T. “Fate decision of germinal center B cells”
International Symposium on B cells (Shanghai, China)
December, 2018
Kurosaki T. “Regulation of B cell tolerance by epigenetic
factors” Cluster Science Days 2018 and the 10th international symposium of IFReC (Bonn, Germany) November,
2018
Kurosaki T. “Fate decision of germinal center B cells”
Japanese-German Immunology Workshop (Ettal, Germany) September, 2018
Kurosaki T. “Fate decision of germinal center B cells”
Keystone Symposia, B Cells: Mechanisms in Immunityand Autoimmunity (Dresden, Germany) June, 2018(self‐tolerant)

Tet2/Tet3+/+

Tet2/Tet3−/−(breaking tolerance)

OFF

HDAC
Tet2/3HDAC
Tet2/3

CD86

×

Ac

Ac

Ac

ON

CD86

A

s B cell intrinsic tolerance mechanisms, it is known that even modest alterations in B cell signaling thresholds can break tolerance, promoting
autoimmunity in the appropriate environmental context. In addition to the B cellsignaling components, the contribution of epigenetic factors has been proposed.
One of the previously observed epigenetic abnormalities associated with autoimmune diseases is altered DNA methylation, prompting us to examine the roles ofTet proteins in B cell tolerance.
We found that specific deletion of translocation proteins Tet2 and Tet3 in B
cells using CD19-Cre resulted in spontaneous hyper T cell activity, autoantibody
production, and lupus nephritis. Treatment with anti-CD20 or anti-CD4 depletion antibodies ameliorated aberrant activation of B cells or CD4+ T cells, respectively, suggesting the existence of a positive feed-forward loop between activated
B and T cells. Mechanistically, we demonstrated that self-tolerant B cells express
low levels of CD86 (B7.2), whereas ablation of Tet2/Tet3 resulted in upregulation of CD86, thereby switching the B cell fate from peripheral tolerance to proliferation through T-B interactions. We also found that Tet2 and Tet3 recruited
HDAC2, thereby repressing transcription of CD86 in self-tolerant B cells. Together, our data demonstrate that Tet2/Tet3 contribute to peripheral B cell toleranceby suppressing CD86 expression in a chromatin-modification manner (Figure).
To address the function of Tet2 and Tet3 in normal immune responses, weacutely deleted Tet2/Tet3 in B cells. We found that the initial proliferative response was normal, even in the absence of Tet2 and Tet3, whereas the deficient
B cells could not differentiate into germinal center (GC) B cells or plasma cells.
Because the transcription factors Bcl6 and IRF4 are known to be critical for GC
B cell or plasma cell differentiation, respectively, our data demonstrate the importance of Tet2/Tet3 in the induction of Bcl6 and IRF4 expression. We are now
analyzing how Tet2/Tet3 regulates Bcl6 and IRF4 transcription.

31

Lab activities

Laboratory forTranscriptional
Regulation
Team Leader: Ichiro Taniuchi

CD4

Figure: Model for Cd4 gene regulation

Activation of the E4p enhancer is critical for inductionof CD4 expression during transition from the DN to
DP stage. During maturation of MHC class II-selected
thymocytes, activation of the E4m enhancer, at least inpart by Bcl11b and SATB1 binding, is essential to establish stable and inheritable CD4 expression. Runx/Cbfβ
complexes suppress E4m activity in MHC class I-selected
thymocytes in both a Cd4 silencer (S4)-dependent and-independent fashion, leading to establishment of aheritable silenced state at the Cd4 locus.

CD4 CD8DP

CD4 Helper T cell
SP
ed
t
c
e
Bcl11b/SATB1
l
m
e
4
II-s
to E
ss
p
a
l
4
C C hift: E
Cd4
MH
rs
P4
nce
E4p
S4 E4m
a
h
En

MH

CC

Cd4
E4p

P4

las

s I-

S4 E4m

sel

CD8

ect

ed

CD8 Cytotoxic T cell
SP

Red: cis-element in active stateBlack: cis-element in inactive state

Runx Runx

Cd4
E4p

P4

S4 E4mRunx-mediated Cd4 repression

Recent Major Publications
Miyamoto C, Kojo S, Yamashita M, Moro K, Lacaud G,
Taniuchi I, Ebihara T. Runx/Cbfβ complexes protect group
2 innate lymphoid cells from exhaustion during allergic
airway inflammation. Nat Commun 10, 447 (2019)

Kojo S, Yasmin N, Muroi S, Tenno M, Taniuchi I. Runxdependent and silencer-independent repression of
maturation enhancer in the Cd4 gene. Nat Commun 9,3593 (2018)
Tenno M, Kojo S, Lawir D-F, Hess I, Shiroguchi K, Ebihara
T, Endo T, Muroi S, Satoh R, Kawamoto H, Boehm T,
Taniuchi I. Cbfb2 controls differentiation of and confers
homing capacity to pre-thymic progenitors. J Exp Med
215, 595-610 (2018)
Invited presentations
Taniuchi I. “Gene Regulation by local and long-range
chromatin loops during CD4/CD8 lineage choice” Keystone Symposia (Tahoe, USA) February, 2019

Taniuchi I. “Gene Regulation by local and long-range
chromatin loops during T cell development” Seminar at
National Cancer Institute (Bethesda, USA) November,
2018
Taniuchi I. “Unraveling pathogenesis of human primary
immune deficiency by mouse models” The 6th Kyoto
Course on Bioinformatics for Genomic Medicine International Symposium on Disease Genomics (Kyoto, Japan)
October, 2018
Taniuchi I. “Regulation of dendritic cell development by
Runx factors” The 1st International Symposium on NEOSELF (Awaji, Japan) July, 2018
Taniuchi I. “Roles of Runx factors during skin immune
cell development” The 67th Annual meeting of JapaneseSociety of Allergology (Makuhari, Japan) June, 201832

T

he vertebrate immune system consists of two components, innate andacquired. The acquired immune system appeared later during evolution,
minimally by acquisition of a system for generating pools of lymphocytes with abroad variety of antigen specificities. Thus, the primary developmental programof T lymphocytes that occurs in the thymus has been shaped to select useful andnon-self-reactive immune soldiers using a sophisticated nuclear program that
integrates environmental cues sensed by T cell antigen receptors (TCR). My laboratory has been addressing how TCR signals are sensed and coupled with cell fate
determination programs in the nucleus by using helper versus cytotoxic lineage
choice as a model in which expression of the ThPOK transcription factor serves
as a key determinant. Our previous studies identified a transcriptional silencer,
referred to as a Thpok silencer, in the Thpok locus as a switch to turn off Thpok
expression to direct MHC class-I selected thymocytes to become cytotoxiclineage T cells. We identified Bcl11b and SATB11 as novel Thpok silencer binding
proteins. Our current results using site-specific chromatin-immune precipitation(ChIP) technology revealed that a cytotoxic-lineage-specific higher-ordered chromatin structure is formed at the Thpok locus through mechanisms that dependon the last zinc finger motif in the Bcl11b protein.
Our second objective is to understand the functions of Runx transcription
factor complexes, which consist of a Runx protein and a non-DNA binding Cbfβ
protein. Our goal is to reveal regulatory mechanisms that modulate the functionof Runx complexes, and to provide insights into how Runx complexes regulate
immune system development and immune responses. Our recent studies revealed
novel roles of Runx/Cbfβ complexes in regulating differentiation of dendritic cellsubsets and innate lymphoid cell (ILC) subsets. Our studies also contributed tounderstanding the roles of two RNA splice variants, Cbfβ1 and Cbfβ2, generated
from the Cbfb gene, each of which differs only at the C-terminal end.

Lab activities

Laboratory for

Immune Cell Systems
Team Leader: Shigeo Koyasu

Inflammation

Figure: Tolerance break by immunoglobulinclass switch recombination

B cells bearing self-reactive IgM are ignored by selftolerance mechanisms (left: clonal ignorance). However,strong inflammation induces class switching of IgM
to IgG, which binds the keratinocyte cell surface andresults in the onset of pemphigus vulgaris (right: pathogenic response)class switch

IgM+ B cell
Clonal ignorance

Recent Major Publications
Kabata H, Moro K, Koyasu S. The group 2 innate lymphoid cell (ILC2) regulatory network and its underlying
mechanisms. Immunol Rev 286, 37-52 (2018)

Vivier E, Artis D, Colonna M, Diefenbach A, Di Santo JP,
Eberl G, Koyasu S, Locksley RM, McKenzie ANJ, Mebius
RE, Powrie F, Spits H. Innate lymphoid cells: ten years
on. Cell 174, 1054-1066 (2018)
Namkoong H, Ishii M, Fujii H, Yagi K, Asami T, Asakura
T, Suzuki S, Hegab AE, Kamata H, Tasaka S, Atarashi K,
Nakamoto N, Honda K, Kanai T, Hasegawa N, Koyasu S,
Betsuyaku, T. Clarithromycin expands CD11b+Gr-1+
cells to ameliorate shock and post-influenza pneumonia. PLoS Pathog 14, e1006955 (2018)
Invited Presentations
Koyasu S. “Tolerance break by class switch recombination for auto-antibody production” The 7th FIMSA Congress (Bangkok, Thailand) November, 2018

Koyasu S. “Innate lymphoid cells, a new type of lymphocytes without antigen receptors” Interdiscipilinary
Science Conference (Tainan, Taiwan) May, 2018

IgG+ B cell

Pathogenic responseT

he prevention of autoimmunity involves multiple and complex processes
to maintain self-tolerance. Mechanisms that break tolerance, leading to autoimmune diseases, are largely unknown. In collaboration with the Departmentof Dermatology of Keio University School of Medicine, we employed as a model
pemphigus vulgaris, an autoantibody-mediated skin blistering disease induced by
IgG autoantibodies against desmoglein 3, a desmosomal cell adhesion molecule
expressed in the skin and mucous membranes. We generated a knock-in mousewhose B cells express desmoglein 3-reactive immunoglobulin. The naïve knock-in
mouse did not develop any disease phenotype, although IgM-bearing B cells were
not deleted and migrated into the periphery. IgM autoantibodies were producedin these mice, suggesting that B cells bearing self-reactive IgM are ignored by selftolerance mechanisms. Immunoglobulin class switching from IgM to IgG inducedin the mouse by induction of erosive dermatitis with 1-fluoro-2,4-dinitrobenzene
application or by vaccinia virus infection resulted in the development of pemphigus vulgaris with acantholysis, as determined by histology and IgG deposition on
the keratinocyte cell surfaces. Based on these results, we propose a novel conceptthat class switching of self-reactive antibodies is one mechanism for breaking
tolerance, a critical step in the development of certain autoantibody-mediatedautoimmune diseases.

33

Lab activities

Laboratory for

Innate Immune Systems
Team Leader: Kazuyo Moro

Monoclonal IgE
Figure: ILC2-derived IL-4 induces innate IgE production from B1 cells

IL-33 and IL-2 upregulate interferon regulatory factor
4 (IRF4) and Cysteinyl leukotriene receptor 1 (Cysltr1)
expression by ILC2, respectively. Eosinophil-derived
CysLT initiates IL-4 production by ILC2 through a Ca2+
signaling pathway. ILC2-derived IL-4 induces innate IgE
production by B1 cells. Innate IgE induces the expansion
and survival, but not the degranulation, of FceRIa+ cells,
resulting in increased susceptibility to allergic responses.

Degranulation

AllergenDendritic cells

B cellsIL‐4Naïve T cells

Cross-link

Th2 cells

FcRε+cells

Polyclonal IgE（Innate IgE）
Eosinophils

IL‐5

IL‐33

IRF4↑

IL‐2

CysLT
CysLTR1
Ca2+

Survival
expansion
Eosinophils

B cells

IL‐4

ILC2
Mast cells

Recent Major Publications
Kobayashi T, Voisin B, Kim DY, Kennedy EA, Jo JH, Shih
HY, Truong A, Doebel T, Sakamoto K, Cui CY, Schlessinger
D, Moro K, Nakae S, Horiuchi K, Zhu J, Leonard WJ, Kong
HH, Nagao K. Homeostatic Control of Sebaceous Glands
by Innate Lymphoid Cells Regulates Commensal Bacteria
Equilibrium. Cell 176, 982-997 (2019)

Koga S, Hozumi K, Hirano KI, Yazawa M, Terooatea T,
Minoda A, Nagasawa T, Koyasu S, Moro K. Peripheral
PDGFRalpha+gp38+ mesenchymal cells support the differentiation of fetal liver-derived ILC2. J Exp Med 215,
1609-1626 (2018)
Morita H, Moro K, Koyasu S. Innate lymphoid cells inallergic and nonallergic inflammation. J Allergy Clin
Immunol 138, 1253-1264 (2016)
Invited presentations
Moro K. “IL-4 Production of Group 2 Innate Lymphoid
Cells” VIB Conference series; Type 2 immunity in homeostasis-and-disease (Bruges, Belgium) February, 2019

Moro K. “Role of Group 2 innate lymphoid cells in idiopathic interstitial pneumonias” The 3rd International
Conference on Innate Lymphoid Cells (ILC2018) (Tokyo,
Japan) November, 2018
Moro K. “Discovery of group 2 innate lymphoid cells” 5thEuropean Congress of Immunology (Amsterdam, Netherlands) September, 2018
Moro K. “Discovery of group 2 innate lymphoid cells” The
American Association of Immunologists Annual meeting(Washington D.C., USA) May, 2017
Moro K. “Suppression mechanism of Group 2 innate
lymphoid cells” FASEB Science Research Conferences: IgE
and Allergy, 50 Years & Onward (West Palm Beach, USA)
September, 201634

Basophils

Susceptibility to allergic disordersOur team has been focused on group 2 innate lymphoid cells (ILC2), an
innate lymphocyte lineage that we identified in 2010. ILC2 localize in avariety of tissues such as fat, lung, intestine, liver, and skin, and mediate immune
responses to helminth and fungal infections via strong production of type 2 cytokines including IL-5, IL-13, IL-9, and GM-CSF. Unlike T and B lymphocytes,
ILC2 lack antigen-specific receptors and are activated by epithelial cell-derived
cytokines such as IL-33. Because ILC2 are also known to produce type 2 cytokines
in allergic disorders, including asthma and atopic dermatitis, we wish to identify
pathways for regulation of ILC2 function with a goal to establish new therapies forallergic disorders by targeting ILC2. While it well-known that ILC2 produce IL-4,
mechanisms for its production and subsequent function in allergic responses are
unknown. We have identified a mechanism by which ILC2 increase susceptibility
to allergic disorders through production of innate IgE induced by IL-4. We previously reported a negative feedback mechanism for suppression of tissue-resident
ILC2 in ILC2-mediated lung inflammation in vivo. Interestingly, we found thatmice lacking such suppressive mechanisms in the lung spontaneously develop
lung fibrosis in an age-dependent manner. The pathogenesis of the disease in thismouse model is very similar to that of human idiopathic pulmonary fibrosis (IPF).
At this time, there is no cure for IPF and the currently established mouse models
used for IPF research do not adequately model the human disease. We are now
characterizing ILC2 regulation and disease development in these mice and we
aim to translate this research to the human disease to develop targeted treatment
and prevention strategies.
Along with our colleagues, we are also focused on understanding the cytokine
regulation and development of ILC2 and on elucidating the role of ILC2 in a variety of type 2 diseases.

Lab activities

Laboratory for

Immune Homeostasis
Team Leader: Taishin Akiyama

Figure: Introduction of WT pMECs suppressed
the onset of autoimmunity provoked by mTEC
dysfunction.

Introduction of pMECs into the thymus successfully
prevented autoimmunity in aly/aly mice, which have no
Aire-expressing mTECs. Upper panels show detection of
autoantibody against liver cells. Lower panels show the
inflammatory infiltrates into the liver, both of which are
eliminated in the mice receiving pMECs.

Recent Major Publications
Horie K, Kudo T, Yoshinaga R, Akiyama N, Sasanuma H,
Kobayashi TJ, Shimbo M, Jeon H, Miyao T, Miyauchi M,
Shirakawa M, Shiba D, Yoshida N, Muratani M, Takahashi
S, Akiyama T. Long-term hindlimb unloading causes a
preferential reduction of medullary thymic epithelial
cells expressing autoimmune regulator (Aire). Biochem
Biophys Res Commun 501, 745-75 (2018)

Kanaya T, Sakakibara S, Jinnohara T, Hachisuka M,
Tachibana N, Hidano S, Kobayashi T, Kimura S, Iwanaga T,
Nakagawa T, Katsuno T, Kato N, Akiyama T, Sato T, Williams IR, Ohno H.Development of intestinal M cells andfollicle-associated epithelium is regulated by TRAF6mediated NF-κB signaling. J Exp Med 215, 501-519(2018)
Akiyama N, Takizawa N, Miyauchi M, Yanai H, Tateishi R,
Shinzawa M, Yoshinaga R, Kurihara M, Demizu Y, Yasuda
H, Yagi S, Wu G, Matsumoto M, Sakamoto R, Yoshida
N, Penninger JM., Kobayashi Y, Inoue J, and Akiyama T
Identification of embryonic precursor cells that differentiate into thymic epithelial cells expressing autoimmune
regulator J Exp Med 213, 1441-1458 (2016)
Invited Presentations
Akiyama T. “Epithelial cells controlling immunologicalself-tolerance in the thymus” The 2nd RIKEN – McGill
Symposium (Yokohama, Japan) February, 2018

Akiyama T. “Differentiation program of thymic epithelial
cells essential for preventing onset of autoimmune disease” RIKEN IMS-Stanford Joint Symposium (Yokohama,Japan) May, 2018
Akiyama T. “Dependence of homeostatic maturation ofthymic antigen presenting cells on TNF receptor family
signaling” The RIKEN IMS-JSI International Symposium
on Immunology (Tokyo, Japan) June, 2018

A

pproximately 5%-10% of the world population is affected by autoimmune
diseases. Understanding mechanisms to suppress the onset of autoimmunity is important for developing therapeutic and preventive strategies for autoimmune diseases.
The thymus contributes to suppression of autoimmunity by eliminating selfreactive T cells and generating regulatory T cells. Self-antigen presenting cells(APCs) in the thymic medulla are necessary for this thymic function. We aim to
uncover molecular mechanisms regulating development and functions of thymic
APCs and to address the significance of these mechanisms in suppressing autoimmune disease onset.
Medullary thymic epithelial cells (mTECs) have the unique property of “promiscuously” expressing different tissue-specific self-antigens (TSAs, e.g., insulin
and C-reactive protein), thereby removing TSA-reactive T cells and generating
regulatory T cells. The autoimmune regulator (Aire) is expressed in mTECs andcontrols expression of certain TSAs. Importantly, dysfunctional Aire mutations
provoke the human autoimmune disease autoimmune polyendocrinopathycandidiasis-ectodermal dystrophy (APECED). A recent study further showed
involvement of Fez family zinc finger 2 (Fezf2) in TSA expression.
Aire and Fezf2 reportedly control expression of 30%-40% of TSAs in mTECs.
Thus, expression of many TSAs is regulated by Aire-independent and Fezf2-independent mechanisms; however, the mechanisms are largely unknown. Moreover,even the underlying mechanisms by which Aire and Fezf2 control “promiscuous”
TSA expression still remain elusive. One of our goals is to elucidate molecular andcellular mechanisms regulating the promiscuous TSA expression in mTECs.
mTECs seem to originate from stem/progenitor cells common to thymic cortical TECs. However, the identification of fetal and adult stem/progenitor cells
is a controversial area. Moreover, mechanisms for maintaining mTECs in adults
remain unclear. We are also attempting to identify molecular and cellular mechanisms regulating mTEC differentiation and mTEC recovery after damage.

35

Lab activities

Laboratory for

Immune Crosstalk
Team Leader: Hilde Cheroutre

Recent Major Publications
Wada H, Yasmin N, Kakugawa K, Ohno-Oishi M, Nieke S,
Miyamoto C, Muroi S, Taniuchi I. Requirement for intron
structures in activating the Cd8a locus. Proc Natl Acad
Sci U S A 115, 3440-3445 (2018)

Kakugawa K, Kojo S, Tanaka H, Seo W, Endo TA, Kitagawa
Y, Muroi S, Tenno M, Yasmin N, Kohwi Y, Sakaguchi S,
Kowhi-Shigematsu T, Taniuchi I. Essential Roles of SATB1in Specifying T Lymphocyte Subsets. Cell Rep 19, 11761188 (2017)
Verstichel G, Vermijlen D, Martens L, Goetgeluk G, Brouwer M, Thiault N, Van Caeneghem Y, De Munter S, Weening K, Bonte S, Leclercq G, Taghon T, Kerre T, Saeys Y, Van
Dorpe J, Cheroutre H, Vandekerckhove B. The checkpoint
for agonist selection precedes conventional selection inhuman thymus. Sci Immunol 2, eaah4232 (2017)
Invited presentations
Cheroutre H. “Dietary Antigens Induce the Antipode of
Immune Tolerance at the Mucosal Epithelial Barrier of
the Intestine.” Chiba University-UCSD symposium. (San
Diego, USA) February, 2019

Cheroutre H. “A Long (non-coding RNA) Stretch in CD4plasticity” Genentech, 2018-19 Immunology and Infectious Disease seminar series at Genentech, Inc. (SanFrancisco, USA) December, 2018
Cheroutre H. “Non-genomic function of RARalpha in T
cells” Institute for Research in Biomedicine (Bellinzona,
Switzerland) April, 2017
Cheroutre H. “Give-and-Take Relation between TGFbeta
and the Gut Environment Drives the CD4 CTL Fate.” Keystone Symposia: TGF-β in Immunity, Inflammation andCancer (Taos, USA) January, 2017
Cheroutre H. “Food for Thought – Mucosal Immune
Protection and Regulation Controlled by the Diet” The
Korean Association of Immunologists – Academy of
Immunology and Microbiology Joint Conference (Seoul,
Korea) November, 2016

36

x3FLAGs Themis(A) Themis binds a T cell specific transcriptional factor X.
We pulled down Themis protein using FLAG-tag-knockin Themis thymocytes and anti-FLAG antibody andfound that it interacts with T cell specific transcriptional
factor X. Wild type thymocytes were used as a negative
control. (B) Our model of Themis function. As an adaptor
molecule, cytosolic Themis becomes phosphorylated
upon TCR stimulation and recruits SHP1, which downregulates TCR signaling. These activation events also
result in the nuclear translocation of Themis. In the
nucleus, Themis functions as a transcription factor and,through interaction with other nuclear transcription factors, modulates the transcription profile of the signaled
thymocyte or mature T cell.

complex

Plasma membrane

Total thymocyte
IP:anti-FLAG
blot:anit-X

wild typeFigure: Dual function of Themis� � TCR/CD3

B
NucleusZAP

cRAR�nTHEMIS(transcription factor)

X
Transcriptional regulationW� � �� � �
LAT

A

tra
ns
loc
ati
on
?

70

GRB2 SHP1cTHEMIS(adaptor)e identified Themis as an essential gene for T cell development and function. Many GWAS analyses of inflammatory diseases, including celiac
disease, multiple sclerosis, and atopic dermatitis, have shown an association with
the THEMIS gene locus. Themis is reported to function as an adaptor and modulate T cell receptor (TCR) signal strength together with Grb2 and SHP1, andThemis-deficiency causes reduction of conventional mature T cells in mice. However, the mechanisms used by Themis to control TCR signaling remain unclear
and controversial. Interestingly, besides its expression in the cytoplasm, Themis
is also expressed in the nucleus, but its role in the nucleus has not been explored.
In order to understand the importance of its cellular localization and possibly
diverse functions, we established two Themis mutant mice that express Themis
either exclusively in the cytoplasm or solely in the nucleus, by either deleting thenuclear localization signal (NLS) sequence or by adding the SV40 NLS to Themis,
respectively. Surprisingly, in both mutant mice, thymic development is impaired,similar to Themis germ line knock-out mice, suggesting that both cytosolic andnuclear Themis proteins are critical for thymocyte development. Since Themis
is also expressed in mature T cells in the periphery, it is likely that it continues toplay essential roles for the activation, function, and/or regulation of peripheral T
cells. Furthermore, we identified a T cell specific transcription factor as a Themis
binding partner in the nucleus, indicating that transcriptional regulation is one
Themis function in the nucleus.
Our overall goal is to dissect the mechanisms employed by Themis to modulate TCR signals and control gene expression and ultimately to elucidate the correlation between Themis and protective immunity as well as its role in T cellspecific inflammatory diseases as mentioned above.
Besides Themis, additional research interests of the Immune Crosstalk lab are
focused on other molecules, including the Pre-TCR and the retinoic acid receptors, which influence the communication between environmental signals andgene transcription programs that ultimately determine the fate of developing andmature T cells in health and disease.

Lab activities

Laboratory for

Inflammatory Regulation
Team Leader: Takashi Tanaka

Genetic factor

・PDLIM2 deficiency

Environmental factors
・Taconic microbiota
・High fat diet

Figure: Microbiota-dependent development of
NASH in PDLIM2-deficient mice

Onset of NASH in PDLIM2 deficient mice

Representative Hematoxylin and Eosin (HE) and Sirius
Red-stained liver histopathology in wild-type and
PDLIM2-deficient mice. Only PDLIM2-deficient micewith a Taconic microbiota develop NASH, characterized
by a massive accumulation of lipid droplets in the hepatocytes, infiltration of inflammatory cells, and enhanced
fibrosis (detected as red areas by Sirius Red staining).

RIKEN microbiota

Recent Major Publications
Kimura A, Kitajima M, Nishida K, Serada S, Fujimoto M,
Naka T, Fujii-Kuriyama Y, Sakamoto S, Ito T, Hanada H,
Tanaka T, Yoshimura A, Suzuki H. “NQO1 inihibits the
TLR-dependent production of selective cytokines bypromoting IκB-ζ degradation. J Exp Med 215, 21972209 (2018)

Shin C, Ito, Y, Ichikawa, S, Tokunaga, M, Sakata-Sogawa
K, Tanaka T. MKRN2 is a novel ubiquitin E3 ligase for the
p65 subunit of NF-κB and negatively regulates inflammatory responses. Sci Rep 7, 46097 (2017)
Tanaka T. Clarification of the molecular mechanismsthat negatively regulate inflammatory responses. In:
Miyasaka M, Takatsu K. (eds.), Chronic Inflammation,
Mechanisms and Regulation, Tokyo, Japan: Springer
Japan, pp.109-118 (2016)
Invited presentations
Tanaka T. “Microbiota-dependent development of nonalcoholic steatohepatitis (NASH) in PDLIM2-deficientmice” ZPM-RIKEN Symposium: Integrative Personalised
Medicine -Connecting genomics, microbiomics andmetabolomics (Tubingen, Germany) July, 2018

Tanaka T. “Biological function of Nahlsgen® to control
inflammatory responses in the skin” The 117th Annual
Meeting of the Japanese Society for Dermatology (Hiroshima, Japan) June, 2018
Tanaka T. “Microbiota-dependent development of nonalcoholic steatohepatitis (NASH) in PDLIM2-deficientmice” Luxembourg FNR-RIKEN Joint Symposium: Understanding Inflammatory Diseases beyond Complexity(Yokohama, Japan) October, 2017
Tanaka T. “Negative regulation of inflammatory responses by LIM proteins” The 1st RIKEN-McGill Symposium: Excellence in Immunology & Genetics (Montreal,
Canada) May, 2017
Tanaka T. “The roles of LIM protein family in the regulation of inflammatory responses” The 45th Annual
Meeting of the Japanese Society for Immunology, S10.
Dynamic control of inflammatory signaling by organelle
in DC/macrophages (Okinawa, Japan) December, 2016

wild-type mice

Taconic microbiota
wild-type mice

PDLIM2 KO miceHE
staining

Sirius red
stainingT

he inflammatory response is an important host defense mechanism to sense
and eliminate invading microbial pathogens. However, these responses
must be terminated at the appropriate time, otherwise excessive and unlimited
responses can damage normal tissue and lead to chronic inflammatory diseases.
Our research goal is to identify the key negative regulators of inflammation andclarify the complete picture of the molecular mechanisms for regulating inflammatory responses.
Non-alcoholic steatohepatitis (NASH) is a chronic liver inflammation associated with immune cell infiltration and fibrosis. In recent years, NASH has become
clinically important, since 10%-20% of NASH cases can progress to liver cirrhosis
and hepatocellular carcinoma. However, molecular mechanisms underlying thedevelopment of NASH remain unclear. PDLIM2 is a nuclear ubiquitin E3 ligase
containing PDZ and LIM domains. In our previous study, we demonstrated thatPDLIM2 functions as a ubiquitin E3 ligase for NF-κΒ and STAT3/4 transcription
factors, thereby negatively regulating inflammatory responses. We recently foundthat PDLIM2-deficient mice spontaneously develop NASH-like pathology. Notably, the onset of NASH in PDLIM2-deficient mice completely depends on theirenvironment. PDLIM2-deficient mice develop NASH in the animal facility at
Harvard University, but not in the RIKEN facility. It is well known that systemic
inflammation can be modulated by gut microbiota. We therefore colonized gut
microbiota of mice from Taconic Farms into germ-free PDLIM2-deficient mice.
We found that PDLIM2-deficient mice with a Taconic microbiota could develop
NASH even in the RIKEN facility when they were fed a higher fat diet. Microarray analysis of PDLIM2-deficient liver showed the upregulation of several inflammation- and metabolism-related genes. These data suggest that the Taconic microbiota environment is essential for the development of NASH in combination
with PDLIM2-deficiency. We are now trying to identify the specific microbiotaorganism(s) or microbiota-derived metabolites that contribute to the NASH phenotype.

37

Lab activities

Laboratory for

Cytokine Regulation
Team Leader: Masato Kubo

Genetic defect=STAT3

Figure: The combination of a genetic defect andexternal environmental stimuli are essential for
AD disease onset

Environmental
external stimuli

2nd hitMicrobiome

1st hit

Skin residential bacteria

LPS

S. Aureus
2

CWild
ontroltype
KO-H
KO healthy
KO disease
KO-D
S low slow
stratum granulosum
KO disease
KO-D
E arly fast
Krt1
Krt10
Krt1
Krt14
6000

12000

4000

8000

2000

4000

0
2 4 6 8 10 12

Recent Major Publications
Kubo M. Innate and adaptive type 2 immunity in lungallergic inflammation. Immunol Rev 278, 162-172(2017)

Dominguez-Huttinger E, Christodoulides P, Miyauchi K,
Irvine AD, Okada-Hatakeyama M, Kubo M, Tanaka RJ.
Mathematical modeling of atopic dermatitis reveals“double-switch” mechanisms underlying 4 common
disease phenotypes. J Allergy Clin Immunol 139, 18611872 e7 (2017)
Miyauchi K, Sugimoto-Ishige A, Harada Y, Adachi Y,
Usami Y, Kaji T, Hasegawa H, Watanabe T, Hijikata A,
Fukuyama S, Maemura T, Ohara O, Kawaoka Y, Takahashi
Y, Takemori T, Kubo M. Protective neutralizing influenza
antibody response in the absence of T follicular helper
cells. Nat Immunol 17, 1447-1458 (2016)
Invited presentations
Kubo M. “Th2 cytokines in allergic responses; from Th2
to ILC2” Cytokine 2018 (Boston, USA) October, 2018

Miyauchi K, Kubo M. “Virus replication drive mucosal
antibody against heterologous influenza viruses” The
46th Annual Meeting of the Japanese Society for Immunology (JSI) (Sendai, Japan) December, 2017
Kubo M. “Role of T follicular helper (TFH) and TH1 in flu
specific humoral immunity” Cytokine 2017 (Kanazawa,
Japan) October-November, 2017
Kubo M. “A Role of STAT3 in Barrier Integrity and Microbiota Composition of the Skin” Annual conference ofthe Wide River Institute of Immunology International
Symposium (Soul Korea) October, 2017
Kubo M. “Role of T follicular helper (TFH) in humoral
immunity” The 13th International Workshop on Autoantibodies and Autoimmunity (IWAA2016) (Kyoto, Japan)
October, 2016

38

I

0

300

200

0

TSLP
NF-B
IL-4/STAT6
activation

Ivl

TH2

100
2 4 6 8 10 12

TSLP

Microbiome
S. Aureus

TH2 inflammatory loop

AD-like dermatitis
2 4 6 8 10 12n the last three years, we have focused on the role of T cells in humoral responses to influenza virus and that of cytokine signals in atopic dermatitis.
The adaptive immune system has evolved to mount different types of responses that are matched to the type of invading pathogen. Effector CD4+ T cells arebroadly divided into two: T follicular helper (TFH) cells and non-TFH effector cells,
including type I helper T (TH1), TH2, and TH17 cells. In the response to Influenza
A virus (IAV) in mice, we found that IgG2 antibodies predominated after vaccination with inactivated virus and were responsible for protective immunity to lethal
challenge with IAV. Surprisingly, this response emerged even in mice that lacked
TFH cells and germinal centers (GC). TH1 cell-derived interferon-γ (IFN-γ) was
essential for the high titers of IgG2 protective antibodies. These results indicatedthat vaccination with inactivated flu virus is effective for generating neutralizing
IgG2 antibodies that protect against the IAV strain used in the vaccine.
In contrast, we found that nasal administration of live virus preferentiallyinduced broadly reactive antibodies. The live-virus vaccine induced high titersof neutralizing IgG antibody that could recognize HA antigens on different viralstrains. This response largely depended on TFH cells and GC, and particularly IL-4
derived from TFH cells played an important role in GC formation. Therefore, livevirus vaccination is a useful strategy for producing effective broadly reactive IgG
antibody.
Atopic dermatitis (AD) is a common chronic skin disease. We found that
Stat3flox/flox K5-cre mice were a suitable TH2-dependent AD-like dermatitis model.
Based on multidimensional transcriptome comparisons between asymptomaticand diseased mice, we found that AD onset was dependent on thymic stromal
lymphopoietin (TSLP) and IL-4 receptor signaling. Stat3 deficiency contributed
to alterations in the skin barrier structure at an early age and allowed an increasein the threshold of NFkB activation and TSLP induction. Therefore, the STAT3
mouse model has been valuable in identifying TSLP as a prognosis marker for
AD onset caused by the TH2 inflammatory loop.

Division of Disease
Systems Biology

Division of Disease Systems Biology will elucidate the regulation of
homeostasis and disease onset as a dynamic living system.

39

Lab activities

Laboratory for

Developmental Genetics
Team Leader: Haruhiko Koseki

Recent Major Publications
Almeida M, Pintacuda G, Masui O, Koseki Y, Gdula M,
Cerase A, Brown D, Mould A, Innocent C, Nakayama M,
Schermelleh L, Nesterova TB, Koseki H, Brockdorff N.
PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation. Science 356, 1081-1084 (2017)Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW,
Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T,
Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose RJ,
Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germcell-related genes. Elife 6, e21064 (2017)
Sharif J, Endo TA, Nakayama M, Karimi MM, Shimada M,
Katsuyama K, Goyal P, Brind’Amour J, Sun M-A, Sun Z,
Ishikura T, Mizutani-Koseki Y, Ohara O, Shinkai Y, Nakanishi M, Xie H, Lorincz MC, Koseki H. Activation of Endogenous Retroviruses in Dnmt1-/- ESCs Involves Disruptionof SETDB1-Mediated Repression by NP95 Binding to
Hemimethylated DNA. Cell Stem Cell 19, 81-94 (2016)
Invited presentations
Koseki H. “Induced activation of Polycomb-repressed
genes in mice” The European Molecular Biology Laboratory (EMBL) (Heidelberg, Germany) August, 2018

Koseki H. “Polycomb in development” Cold Spring Harbor Asia (Suzhou, China) April, 2018
Koseki H. “Activating Polycomb-repressed genes inmammals” France-Japan Epigenetics Workshop (Paris,
France) November, 2017
Koseki H. “Polycomb in transcriptional phase transitionof developmental genes” Mini Symposium, Genetic
Control of Mouse embryonic Development at Hubrecht
Institute (Utrecht, the Netherlands) June, 2016
Koseki H. “Protoracted NP95 binding to hemimethlated
1 DNA disrupts SETB1-mediated proviral silencing”
International Symposium on Chromosome Orchestration
System, Osaka University (Awajishima, Japan) March,
2016

40

control; bufferbortezomibC

9.5 dpc MB

bufferBortezomib

Bp
R
M

D

RING1B BCOR

(A) Meis2 gene expression profiles in mice with or without PI treatment. Meis2 activation failed in mice treatedwith a PI. (B) Immuno-FISH of Meis2 promoter (blue),
RBS (red), and MEIS2 protein (green). The promoter and
RBS are separated in the cells with MEIS2 expression,
while they stay together in the cells without MEIS2. (C)
4C-seq analysis of mice with or without PI treatmentusing the Meis2 promoter as bait. Bortezomib-treatedmidbrain chromatin exhibited strong interaction between the promoter and RBS. (D) ChIP-seq comparison.
PI-treated midbrain showed higher accumulation of
BCOR, RING1B, and ubiquitylated protein at the promoter and RBS.

AUBI

Figure: Effect of a proteasome inhibitor (PI) on
Meis2 activation during midbrain development

bufferBortezomib
bufferBortezomib
bufferBortezomib

RBS

T

Meis2

2810405F15Rik

he Developmental Genetics Laboratory not only pursues its own research
program toward understanding epigenetic regulation of organ development
but also plays pivotal roles in maintaining core facilities for experimental animals
and human induced pluripotent stem cells (iPSCs), and in leading a charged mission toward understanding the pathogenesis of human atopic dermatitis (AD).
In the epigenetics project, we are focusing on understanding how CpG island(CGI) promoters are linked with enhancers and how epigenetic inheritance ismaintained after DNA replication. Particular emphasis has been placed on epigenetic regulation mediated by the combinatorial actions of Polycomb group (PcG)
and DNA methylation mechanisms.
A large part of our group is devoted to the maintenance of a high-standard
mouse facility in IMS. Through the Animal Core Facility, the group is also responsible for the generation of knock-out and transgenic animals for the various
research laboratories at the center, and for the generation of germ-free, gnotobiote
and humanized mice.
We have started a study to apply iPSC technology for human immunology
research and therapeutic development. The core facility for iPSC research is engaged in developing efficient protocols to reprogram various lymphocytes andinduce differentiation of iPSCs into lymphoid lineage cells. We are particularly
engaged in generation of iPSC-derived NKT cells toward their clinical use forcancer therapy and are close to initiating a Phase I clinical study to approve theirsafety. This research is partly supported by AMED.
No matter what the human disease, it is becoming important to find a way tostratify patients in order to provide the best option of therapeutic intervention. To
tackle this issue, we found that atopic dermatitis (AD) is a good model because of
its clinical diversity in both symptoms and therapeutic responses. Our approachis to establish mathematical models for AD based on mouse AD models inducedby various genetic perturbations and then to extrapolate the model into humans,
mainly by using marker genes and protein expression in patients.

Lab activities

Laboratory for

Intestinal Ecosystem
Team Leader: Hiroshi Ohno

Figure: Updated model of M cell differentiation.

RANKL activates canonical NF-κB through TRAF6. The
canonical NF-κB transcription factor (p50-RelA) is critical for the activity of the noncanonical NF-κB transcription factor (p52-RelB), which in turn largely contributes
to the expression of Marcksl1, one of the Spi-B-independent M cell markers. p52-RelB directly binds the Spibpromoter and is responsible for Spi-B expression. On theother hand, neither canonical nor noncanonical NF-κB
alone is sufficient to induce the final differentiation of
M cells with expression of GP2. As yet unidentified transcription factor(s) activated by RANKL are required forthe development of mature M cells. ISC: Intestinal stem
cell, TA cell: Transit-amplifying cell.

Kanaya et al., J. Exp. Med , 2018

Recent Major Publications
Kato T, Yamazaki K, Nakajima M, Date Y, Kikuchi J, Hase
K, Ohno H, Yamazaki K. Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum
metabolome. mSphere 3, e00460-18 (2018)

Kanaya T, Sakakibara S, Jinnohara T, Hachisuka M,
Tachibana N, Hidano S, Kobayashi T, Kimura S, Iwanaga T,
Nakagawa T, Katsuno T, Kato N, Akiyama T, Sato T, Williams IR, Ohno H. Development of intestinal M cells andfollicle-associated epithelium is regulated by TRAF6mediated NF-κB signaling. J Exp Med 215, 501-519(2018)
Invited presentations
Ohno H. “Obesity, Impaired Glucose Tolerance and gut
microbiota” 5th International Probiotics and Prebiotics
Symposium (Surabaya, Indonesia) December, 2018

Ohno H. “The role of gut microbiota and digestive
diseases” Educational Lecture, Japan Digestive Disease
Week 2018 (Kobe, Japan) November, 2018
Ohno H. “Host-commensal microbiota interaction”
Keynote Lecture, The 25th Anual Meeting of The Japan
Society for Portal Hypertension (Osaka, Japan) September, 2018
Ohno H, Miyauchi E, Ohkusa T. “Impact of smoking on
the gut microbiota in IBD patients” FALK Sympoium “IBD
and Liver: East Meets West” (Kyoto, Japan) September,
2018
Ohno H. “Ruminococcus-induced CD8+ regulatory T cells
prevent type 1 diabetes” International Conference on
Beneficial Microbes 2018 (Kuching, Malaysia) August,2018E

normous numbers of commensal bacteria, collectively called the gut microbiota, reside in our intestines. We do not unconditionally accept thosemicroorganisms. The intestinal immune system somehow senses the kinds andquantity of bacteria in the gut lumen and tries to contain them. Reciprocally, thegut microbiota shape the host immune system. Furthermore, the host-gut microbiota interaction profoundly impacts our physiology and pathology. We are
studying this sophisticated and complex host-gut microbiota interaction by applying an integrated omics approach, with different layers of cyclopedic analyses,
including (meta)genomics, epigenomics, (meta)transcriptomics, and metabolomics. This approach is applied to understand the molecular basis for the influenceon host physiology and pathology by gut microbiota in mice, as well as the impact
of gut microbiota on human diseases such as infantile allergic diseases and type 2
diabetes.
To evoke immune responses against gut microbes, they have to be delivered
across the intestinal epithelial barrier to gut-associated lymphoid tissue (GALT)
such as Peyer’s patches. This delivery is thought to be mainly achieved by a uniquesubset of epithelial cells, M cells. These cells reside in a limited region of the epithelial layer called the follicle-associated epithelium (FAE), overlaying the GALT
lymphoid follicles. FAE has a unique feature distinct from the surrounding villous epithelium, and we also study how this occurs. We are studying the function
and differentiation of M cells at the molecular level. We identified M cell-specificbacterial uptake receptors that could serve as a vaccine delivery target, and we are
studying this possibility.

41

Lab activities

Laboratory for

Integrative Genomics
Team Leader: Osamu Ohara

Figure: A decomposition and clustering system
of multivariate data

This example shows decomposition and clustering ofmulti-color flow cytometry data. Several algorithm
options (such as tSNE, UMAP, or PCA) are supported.
The system can be installed locally and is available athttps://github.com/takaho/clusterflowcell/tree/master.

Recent Major Publications
Kawashima Y, Miyata J, Watanabe T, Shioya J, Arita M,
Ohara O. Proteogenomic Analyses of Cellular Lysates
Using a Phenol-Guanidinium Thiocyanate Reagent. J
Proteome Res 18, 301-308 (2019)

Kawashima Y, Ohara O. Development of a NanoLC-MS/MS System Using a Nonporous Reverse Phase Column
for Ultrasensitive Proteome Analysis. Anal Chem 90,
12334-12338 (2018)
Shirasaki Y, Ohara O. Challenges in Developing Protein
Secretion Assays at a Single-Cell Level. Methods Mol
Biol 10808, 1-7 (2018)

Invited presentations
Ohara O. “Omics analyses of immune cell society for acomprehensive understanding of immune disorders” The
46th Annual Meeting of the Japanese Society of Clinical
Immunology (Nagano, Japan) November, 2018

Ohara O. “Quality consideration in NGS” The 6th AsianCongress for LSD Screening (Tokyo, Japan) August, 2018
Ohara O. “Technical challenges for newborn screening”
The 121st Annual Meeting of the Japan Pediatric Society(Fukuoka, Japan) April, 201842

T

he mission of our laboratory was originally to serve as a gateway to genomics for immunologists. However, the situation has dramatically changed in
the past 10 years. Because genomics has become a popular approach, particularly
when we tackle complex problems in biomedical sciences, the actual research
activities of our team now are now three-pronged into the following categories:
central technical service (non-interactive technical support for researchers in thecenter), collaborative research programs, and technology development activities.
As collaborative research, our laboratory is currently involved in many intramuraland extramural collaborations and various strategic projects organized by the center. Because of the increasing need for “omics” analyses in various medical sciencefields, this category has become the biggest research activity of my laboratory inrecent years.
However, besides collaborative research and central support, we certainly keep
in mind that technology development is another important mission of my laboratory. For this purpose, we consider “Integration” of omics data as a key word, and,thus, our technology development is focused in two directions: one is integrationof different omics technologies and the other is linking bulk data with data at single-cell resolution. Along these lines, we developed some new methods for multiomics analyses and implemented some newly emerging technologies in the center.
We have also contributed to enhancement of bioinformatics analysis power in thecenter because data analyses play a crucial role in multi-omics approaches. For
example, we devised a simple bioinformatics analysis tool for dimension reduction of multivariate data on a personal computer in our collaborating laboratories.
The Figure shows an example of dimension reduction of multi-color FACS data.
As more data become available in terms of volume and types, the more critical
will be the setting of the data analysis pipeline in the center. In collaboration with
the Medical Sciences Innovation Hub program (MIH, http://www.riken.jp/en/
research/labs/mih/), our laboratory is working for this purpose.

Lab activities

Laboratory for

Mucosal Immunity
Team Leader: Sidonia Fagarasan

intestinal content

Bacteroides spp.
(B.theta / B.vulgatus)

IgA(1) polysaccharide
association(mucus/diet)inner mucus

Fagarasan S. “Involvement of PD-1 in antibody diversification and body homeostasis” NHRI/IBMS International
conference on inflammation and disease (Taipei, Taiwan) February, 2017
Fagarasan S. “Involvement of T cells in antibody diversification and shaping of the microbial landscape” Immune Profiling in Health and Disease 2016 (The Nature
Conference) (Seattle, USA) October, 2016
Fagarasan S. “On germinal centers, IgA synthesis andthe intestinal ecosystem” International Congress of Immunology ICI 2016 (Melbourne, Australia) August, 2016

SCFA

(4) epithelial health

MAFF

-1

(maffC/D)

SSC
IgA Binding

Colon 10 days after DSS
WT
B.theta69

IgA

Fagarasan S. “Involvement of PD-1 in antibody diversification and immune homeostasis” The 19th International
Conference on Lymphatic Tissues and Germinal Centres
in Immune Reactions (Venice, Italy) September, 2017.
Organizer

metabolic activity↑

B. theta genes

B.theta

Invited presentations
Fagarasan S. “Excessive T cell activation in the absenceof PD-1 affects behavior”. Cold Spring Asia meeting on
inflammation: Basic Mechanisms & Relevant Diseases(Suzhou, China) December, 2017

bacteria-bacteriainteraction(2) MAFF↑
mucosal associatedfunctional factor

outer mucus

Recent Major Publications
1. Nakajima A, Vogelzang A, Maruya M, Miyajima M,
Murata M, Son A, Kuwahara T, Tsuruyama T, Yamada S,
Matsuura M, Nakase H, Peterson DA, Fagarasan S, Suzuki K. IgA regulates the composition and metabolic
function of gut microbiota by promoting symbiosis
between bacteria. J Exp Med 215, 2019-2034 (2018)
2. Miyajima M, Zhang B, Sugiura Y, Sonomura K, Guerrini MM, Tsutsui Y, Maruya M, Vogelzang A, Chamoto
K, Honda K, Hikida T, Qin H, Sanuki R, Suzuki K, Furukawa T, Ishihama Y, Matsuda F, Suematsu M, Honjo
T, Fagarasan S. Metabolic shift induced by systemic
activation of T cells in PD-1 deficient mice perturbs
brain monoamines and emotional behavior. Nat
Immunol 18, 1342-1352 (2017)
3. Chamoto K, Chowdhury PS, Kumar A, Sonomura
K, Matsuda F, Fagarasan S, Honjo T. Mitochondrial
activation chemicals synergize with surface receptor
PD-1 blockade for T cell-dependent antitumor activity. Proc Natl Acad Sci U S A 114, E761-E770 (2017)

Clostridiales↑(3) metabolic activity↑∆MAFF
B.thetaFigure: A schematic representation of how IgA
binding to Bacteroides species impacts its localization and metabolic reprogramming contributing to symbiosis with Firmicutes species andfitness of the epithelial barrier

diverse microbiota

1

expression

IgA (-)

(+)

level

IgA-dependent transcriptional modulation

Protection from colitis

Understanding the role of IgA in shaping gut microbiota
Our group has obtained over the years robust evidence that the adaptive immune system controls the growth and distribution of commensals within theintestinal lumen. We demonstrated that mucosal IgA is required for maintaining
diverse and balanced communities of commensal bacteria, and that such IgA production is highly controlled by the expression of T cell signaling receptors (PD1) and transcription factors (Foxp3, Bcl6) of T cells. However, how exactly IgAfunctions in symbiotic process is not well understood. Our recent work showed anovel mechanism by which heavily glycosylated IgA efficiently coats bacterial surfaces, especially Bacteroidetes sp., thereby modulating bacterial genes within the
mucus environment. We provisionally named the set of genes upregulated in thepresence of IgA as Mucus-Associated Functional Factors (MAFF). Importantly,
glycosylated IgA and MAFF upregulation by Bacteroidetes sp. promoted symbiotic interactions between different bacterial phyla, like Firmicutes, and regulated
the composition and metabolic function of the overall microbial community (Figure). This work was featured by the JEM among the ten best papers published in
2018.

Understanding how activation of the immune system shifts
metabolites, leading to neuro-endocrine disorders in mouse
We revealed novel and unexpected effects of immune system activation on
systemic metabolic homeostasis with far-reaching effects on major physiologicalsystems of the body. We demonstrated that persistent T cell activation resulted in
drastic systemic metabolic changes, including depletion of serum amino acids.
Furthermore, we linked the depletion of tyrosine and tryptophan in the periphery
to reduced synthesis of brain monoamine neurotransmitters such as dopamineand serotonin. We showed that such biochemical alterations caused abnormal behavior in mice, dominated by anxiety and enhanced fear responses.

43

Lab activities

Laboratory for

Gut Homeostasis
Team Leader: Kenya Honda

Figure: Germ-free mice inoculated with humanderived 11 commensal bacterial strains showa large accumulation of IFNγ-producing CD8 T
cells in the colonic lamina propria.

Germ-freeGerm-free+11 strains

CD8α

IFNγ+CD8T

Recent Major Publications
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W,
Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K,
Shiota A, Takeshita K, Yasuma K, Riethmacher D, Kaisho
T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V,
Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier
RJ, Atarashi K, Honda K. A defined commensal consortium elicites CD8 T cells and anti-cancer immunity.
Nature 565, 600-605 (2019)

Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T,
Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, RiceSA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK,Elinav E, Morita H, Xavier RJ, Hattori M, Honda K. Ectopic
colonization of oral bacteria in the intestine drives TH1
cell induction and inflammation. Science 358, 359-365(2017)
Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature 535, 75-84(2016)
Invited presentations
Honda K. “Microbial Regulation of Host Immune Responses” KEYSTONE SYMPOSIA Microbiome: Chemical
Mechanisms and Biological Consequences (Montreal,
Canada) March, 2019

Honda K. “Immune modulation by the gut microbiota”
NYC Inflammatory Bowel Disease Research Day (NewYork, USA) September, 2018
Honda K. “Modulation of the immune system by the gut
microbiota” Cell-Weizmann Institute of Science Symposium: Next Gen Immunology (Rehovot, Israel) February,
2018
Honda K. “Modulation of the immune system by thegut microbiota” CSHL Fundamental Immunology & Its
Therapeutic Potential (Cold Spring Harbor, USA) April,2017
Honda K. “Regulation of T Cells by the Gut Microbiota”
Gordon Research Conference (GRC) in Immunochemistry
and Immunobiology (Lucca, Italy) June, 2016

44

IFNγ
(gated on CD3ε+ TCRβ+ cells in colon LP)

There are multiple immune cell subsets residing in the intestine, many ofwhich may be correlated with the diversity of the microbiota. The Laboratory for Gut Homeostasis has been aiming to identify microbial consortia responsible for regulation of specific branches of the host immune system and to understand the underlying mechanisms. Our long-term goal is to establish strategies totreat/prevent pathological conditions such as inflammatory bowel disease (IBD),
allergy, cancer, and obesity by manipulation of the microbiota.
Previously, we succeeded in isolating 17 human gut-derived clostridial strainsthat together are able to induce intestinal CD4+Foxp3+ regulatory T (Treg) cells,in part through production of short chain fatty acids. Oral introduction of these
17 strains in mouse models reduced the disease severity of allergy, colitis, andgraft versus host disease (GVHD). In addition to Treg-inducing strains, we isolated and identified Klebsiella strains from saliva samples of IBD patients. These
Klebsiella strains were innocuous in the oral cavity but potently induced TH1 cells
when they colonized the intestine. The isolated Klebsiella strains were resistant tomultiple antibiotics, tended to colonize in dysbiotic microbiota, and elicited a severe gut inflammation in mice genetically prone to colitis, indicating that the oralcavity may serve as a reservoir for potential intestinal pathobionts and exacerbate
intestinal disease. In our latest project, we have succeeded in identifying 11 bacterial strains of healthy human donor origin that are capable of robust inductionof IFNγ-producing CD8+ T cells in the intestine. Colonization with the 11-strain
consortium protected mice from Listeria monocytogenes infection and enhanced
the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour
models. We have also succeeded in identifying trypsin-degrading gut bacteria anddermatitis-suppressing skin commensal bacteria. Our findings should ultimately
permit the design of bacterial consortia that durably activate or suppress specificadaptive immune programs, resulting in development of state-of-the-art therapeutics for numerous human diseases.

Lab activities

Laboratory for

Skin Homeostasis
Team Leader: Masayuki Amagai

Figure: Comprehensive analysis of skin barrier
homeostasis

Our team is trying to clarify the mechanisms of skin barrier homeostasis by focusing on the stratum corneum(SC), tight junction (TJ), and SG1 cells. We established alive imaging system, especially focusing on keratin andpH, to study the cornification process in mice. We also
study host-microbe interactions on skin.

Recent Major Publications
Someya T, Amagai M: Toward a new generation of smart
skins. Nat Biotechnol 37, 382-388 (2019)

Yokouchi M, Atsugi T, Logtestijn MV, Tanaka RJ, Kajimura
M, Suematsu M, Furuse M, Amagai M, Kubo A. Epidermal cell turnover across tight junctions based on Kelvin’s
tetrakaidecahedron cell shape. eLife 5 e19593 (2016)
Invited presentations
Amagai M. “Peripheral tolerance to autoimmune target
in pemphigus” The 3rd Inflammatory Skin Disease Summit (Vienna, Austria) December, 2018

Amagai M. “Peripheral tolerance to desmoglein3, pemphigus vulgaris antigen”“Frontiers in Skin Immunity”
International Symposium of the CRC156 (Heidelberg,
Germany) June, 2018
Amagai M. “3D in Vivo Imaging of Skin Barrier” International Investigative Dermatology 2018 (Orlando, USA)
May, 2018
Amagai M. “Cracking the Codes of Autoimmune andAllergic Skin Diseases” Rudi Cormane Lecture at the 47th
Annual Meeting of the European Society of Dermatological Research (Salzburg, Austria) September, 2017
Amagai M. “Skin barrier homeostasis and its failure in
atopic dermatitis” Plenary lecture at 25th European
Academy of Dermatology and Venereology Congress(Vienna, Austria) September, 2016

S

kin is where immunity meets external antigens. Cutaneous sensitization
is now considered to be the initial key step in many allergic disorders, notonly atopic dermatitis (AD), but also asthma, food allergy, and anaphylaxis. Skin
harbors several barriers to prevent easy penetration of external antigens into thebody. However, the exact molecular mechanisms by which the skin barriers form
and are maintained are largely unknown.
Epidermis, the outermost component of the skin, is composed of keratinizedstratified squamous epithelia and consists of the stratum basale, stratum spinosum, stratum granulosum (SG), and stratum corneum (SC) from bottom to top.
Our group has been focusing on the SC as an air-liquid barrier and the tight junction (TJ) as a liquid-liquid barrier formed between SG2 cells among many otherskin barriers. A fundamental biophysical paradox regarding the function of theepidermis is how it can maintain the barrier, yet still constantly replace and shedcells.
Our group is trying clarify how epidermal barrier homeostasis is maintained
under normal conditions and how impaired barrier function occurs and affects
microenvironments of the skin in various disease conditions. Our experimental
approaches are comprehensive, combining molecular biology, biochemistry, ultrastructural anatomy, live imaging, microbiology, and systems biology. For example,
we have recently succeeded in characterizing isolated SG1 cells and performing
intravital imaging of Ca2+/organelles/pH during cornification.
Another of our strengths is to be able to go back and forth between our basic
science findings in mice and those in clinical science in humans with various skindiseases. Our goal is to understand skin barrier homeostasis in health and disease
and to provide more targeted therapeutic approaches with fewer side effects topatients suffering from severe allergic diseases.

45

Lab activities

Laboratory for

Tissue Dynamics
Team Leader: Takaharu Okada

Figure: Differentiation pathways of effector
CD8+ T cells to memory CD8+ T cells

Recent Major Publications
Herndler-Brandstetter D*, Ishigame H*†, Shinnakasu R,
Plajer V, Stecher C, Zhao J, Lietzenmayer M, Kroehling
L, Takumi A, Kometani K, Inoue T, Kluger Y, Kaech SM,
Kurosaki T, Okada T†, Flavell RA†. KLRG1+ effector CD8+
T cells lose KLRG1, differentiate into all memory T celllineages, and convey enhanced protective immunity.
Immunity 48, 716-729.e8 (2018) *equal contribution,†co-corresponding authors.

Ise W, Fujii K, Shiroguchi K, Ito A, Kometani K, Takeda K,
Kawakami E, Yamashita K, Suzuki K, Okada T, Kurosaki T.
T Follicular Helper Cell-Germinal Center B Cell Interaction Strength Regulates Entry into Plasma Cell or Recycling Germinal Center Cell Fate. Immunity 48, 702-715.
e4 (2018)
Shinnakasu R, Inoue T, Kometani K, Moriyama S, Adachi
Y, Nakayama M, Takahashi Y, Fukuyama H, Okada T,
Kurosaki T. Regulated selection of germinal-center cells
into the memory B cell compartment. Nat Immunol 17,
861-869 (2016)
Invited presentations
Okada T. “Imaging of epidermal nerve dynamics andactivity in normal and pruritic dermatitis conditions” The
47th Annual Meeting of the Japanese Society for Immunology, Joint Symposium 2 “Crosstalk between immune and nervous system at surface” (Fukuoka, Japan)
December, 2018

Okada T. “Imaging of skin nerves involved in chronic
inflammation” The 39th Annual Meeting of the JapaneseSociety of Inflammation and Regeneration, Symposium
6 (Tokyo, Japan) July, 2018
Okada T. “Intravital imaging of dendritic cells” The 117th
Annual Meeting of the Japanese Dermatological Association, Educational Lecture 32 (Hiroshima, Japan) June,
2018
Okada T. “Dynamic interactions of sensory nerves,
keratinocytes, and immune cells in the skin” The Banff
International Research Station for Mathematical Innovation and Discovery (BIRS) of Casa Matemática Oaxaca(CMO). “Quantitative Analysis of Immune Cell Migrationand Spatial Processes in Health and Disease’’ (Oaxaca,
Mexico) June, 2018
Okada T. “Imaging of epidermal nerve dynamics andactivity in normal and pruritic dermatitis conditions”
IMS-JSI International Symposium on Immunology 2018
“Checkpoint in Medical Science and Its Technology”(Tokyo, Japan) June, 201846

T

he goal of the laboratory is to mechanistically understand the in vivo cellular
dynamics that underlie tissue homeostasis and their breakdown during disease development. As a most recent focus, we study how barrier tissue function is
maintained by interactions between different cell types such as peripheral nerves,
epithelial cells, and immune cells. As a strategy for tackling this problem, we use
multi-dimensional fluorescent imaging, in particular two-photon microscopy,
to analyze cellular activities in the tissues. For example, by intravital imaging, wehave found that sensory nerve endings in the skin epidermis are constitutively
remodeled through interactions with the skin barrier structure, and that impairment of the barrier in mouse models of itchy dermatitis disrupts the nerve remodeling and leads to aberrant activation of the sensory nerves. In addition, inorder to address molecular mechanisms of nerve activities observed by the imaging study, we have started internal collaborations at RIKEN to analyze the gene
expression of individual sensory neurons with different functional characteristics.
We have also been continuing our studies to understand how the fate of activated immune cells is determined during longitudinal, adaptive immune responses. For this purpose, we develop and utilize fate-mapping tools that enable us toirreversibly label lymphocytes at particular phases of their activation and/or differentiation. By utilizing this technique, in an international collaboration we haverecently found that effector cytotoxic T cells receiving intermediate amounts ofactivating and inflammatory signals become all known types of CD8+ memory T
cells while retaining high cytotoxic and proliferative capacity. In other collaborations, our fate-mapping technique contributed to elucidation of the mechanisms
by which germinal center B cells choose their differentiation pathway to memory
B cells or plasma cells.

Lab activities

Laboratory for

Metabolomics
Team Leader: Makoto Arita

Biological Phenotypes

Lipid Metabolism

Figure: Advanced lipidomics platform to discover novel links between lipid metabolism andbiological phenotypes

Inflammation

Mechanisms

Allergy
CancerMetabolicsyndrome

Advanced lipidomics platform
Software

m/z

m/z

m/z

m/z

m/z

Databasem/z

Chemicallibrary

Recent Major Publications
Miyata J, Fukunaga K, Kawashima Y, Watanabe T, Saitoh
A, Hirosaki T, Araki Y, Kikawada T, Betsuyaku T, Ohara O,
Arita M. Dysregulated fatty acid metabolism in nasal
polyp-derived eosinophils from patients with chronicrhinosinusitis. Allergy 10.1111/all.13726 (2019)

Isobe Y, Itagaki M, Ito Y, Naoe S, Kojima K, Ikeguchi M,
Arita M. Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid. Sci Rep 8, 7954 (2018)
Isobe Y, Kawashima Y, Ishihara T, Watanabe K, Ohara O,
Arita M. Identification of protein targets of 12/15-lipoxygenase-derived lipid electrophiles in mouse peritoneal
macrophages using omega-alkynyl fatty acid. ACS Chem
Biol 13, 887-893 (2018)
Invited Presentations
Arita M. “Genetics and lipidomics of omega-3 polyunsaturated fatty acid biology” The 3rd International Symposium on Lipids Science and Health (Qingdao, China)
November, 2018

Arita M. “The importance of LipoQuality in biologicalsystems (Keynote Lecture)” 8th Mind-Body Interface
International Symposium (Taichung, Taiwan) October,
2018
Arita M. “Genetics and Lipidomics of Omega-3 Polyunsaturated Fatty Acid Biology” Keystone Symposia
on Molecular and Cellular Biology, The Resolution of
Inflammation in Health and Disease (Dublin, Ireland)
March, 2018
Arita M. “The importance of LipoQuality in biologicalsystem” 7th International Singapore Lipid Symposium
2018 (iSLS7) (Singapore) March, 2018
Arita M. “Eosinophil polyunsaturated fatty acid metabolism and its potential control of inflammation andallergy” The 15th International Conference on Bioactive
Lipids in Cancer, Inflammation, and Related Diseases(Puerto Vallarta, Mexico) October, 2017

L

ipids are extremely diverse molecules; thus, the precise determination ofeach molecular species of lipid, termed Lipo-Quality (Quality of Lipids), is aprerequisite not only to understand their biological functions in physiology anddisease but also to discover novel bioactive lipids that may link lipid metabolism
and biological phenotypes. A powerful method for the analysis of lipid metabolites is liquid chromatography tandem mass spectrometry (LC-MS/MS). Our
research is aimed at elucidating the structure and function of endogenous lipid
metabolites that regulate inflammation and tissue homeostasis.
Polyunsaturated fatty acid (PUFA)-derived mediators are formed by enzymaticoxidation through the action of cyclooxygenases (COX), lipoxygenases (LOX),
and cytochrome P450 monooxygenases (CYP). By using LC-MS/MS-based lipidomics, we provided new insights into the molecular and cellular mechanisms ofinflammation resolution, especially the functional roles of 12/15-LOX-expressing
eosinophils and macrophages in controlling the process. Our research is also
focused on understanding the function of omega-3 PUFAs using genetic andlipidomic approaches, and we have identified a novel metabolic pathway, i.e., theomega-3 oxygenation pathway, and its bioactive metabolites that may be linked
to omega-3 PUFA’s anti-inflammatory actions in vivo. Identification of these endogenous mediators with potent anti-inflammatory properties could lead to thedevelopment of novel therapeutics for diseases in which sustained inflammation
is suspected as a key component of pathogenesis.
We also developed a new methodology, a non-targeted lipidomics platform, todiscover novel links between lipid metabolism and biological phenotypes. By taking advantage of Q-TOF (global lipid screening) and TripleQ (quantitative analyses) mass spectrometry, our new approach has a strong potential to search forlipids of interest globally and to identify unknown lipid species in a non-biased
fashion. In particular, we focus on developing an MS/MS library of oxidized phospholipids, skin barrier lipids such as acylceramides, and unique lipid metabolites
produced by the commensal microbiota. We also develop software that enable us
to more precisely and comprehensively search for lipid structures.

47

Lab activities

Laboratory for

Microbiome Sciences
Team Leader: Masahira Hattori

Recent Major Publications
Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T,
Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, RiceSA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK,Elinav E, Morita H, Xavier RJ, Hattori M*, Honda K*: Ectopic colonization of oral bacteria in the intestine drives
TH1 cell induction and inflammation. Science 358, 359365 (2017)

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A,
Levenez F, Tramontano M, Driessen M, Hercog R, Jung
FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E,
Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier
S, Daigneault M, Derrien M, Druesne A, de Vos WM,
Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna
RA, van Hylckama Vlieg J, Junick J, Klymiuk I, LangellaP, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C,
Morita H, O’Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP,
Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal
EG, Ehrlich SD, Dore J, Bork P: Towards standards for human fecal sample processing in metagenomic studies.
Nat Biotechnol 35, 1069-1076 (2017)
Takayasu L, Suda W, Takanashi K, Iioka E, Kurokawa R,
Shindo C, Hattori Y, Yamashita N, Nishijima S, Oshima K,
Hattori M: Circadian oscillations of microbial and functional composition in the human salivary microbiome.
DNA Res 24, 261-270 (2017)
Invited presentations
Hattori M. “Gut extrachromosomal genetic elements uncovered by long-read metagenomics” 69th International
Symposium and Annual Meeting, The Korean Society ofFood Science and Nutrition (Pusan, Korea) November,
2018

Hattori M. “Elucidation of the ecology and physiology ofhuman microbiomes by metagenomics” The 7th Japan
Food Research Laboratories Conference (Tokyo, Japan)
October, 2018
Hattori M. “The human microbiome and its association
with health and disease” The 61th Annual Meeting and
Symposium of the Japan Diabetes Society (Tokyo, Japan)
May, 2018
Hattori M. “Strategies and technologies for analysis of
the human microbiome” The 48th Annual Meeting ofJapanese Association for Anaerobic Infection Research(Hiroshima, Japan) March, 2018
Hattori M. “The Japanese bowels: its relation with gut
microbe” Public Symposium in the 71st Annual Meetingof the Anthropological Society of Nippon (Tokyo, Japan)
November, 201748

Figure: Long-read metagenomics provides an efficient approach for reconstructing complete chromosomes and extrachromosomal mobile genetic elements (eMGEs)T

he Laboratory for Microbiome Sciences engages in intensive research on
host-microbial interactions by elucidating the ecological, functional, andmedical features of various microbial communities, such as human gut, oral, andskin microbiomes. Our team also develops bioinformatic and statistical technologies for the analysis of metagenomic and genomic datasets from microbiomes
and microbes produced by next-generation sequencers. Currently, we are setting
up a long-read next-generation sequencer, PacBio Sequel, which generates much
longer and more accurate contigs than the standard short-read sequencers such as
Illumina HiSeq and MiSeq (Fig). This improvement is accomplished by assemblyof metagenomic reads of approximately 10 kb from microbiome samples, consequently providing efficient reconstruction of high-quality chromosomes and bins
as well as complete extrachromosomal mobile genetic elements, such as plasmids
and bacteriophages, in the community. Thus, metagenomic sequencing using
the long-read PacBio Sequel provides a powerful approach to elucidate not only
chromosomes/species and their genes but also extrachromosomal plasmids andbacteriophages in the community. In addition, the combined use of the long-read
PacBio Sequel and short-read sequencers will allow us to rapidly construct complete and near-complete genomes of individual microbial strains with high accuracy. We have also developed analytical pipelines for PacBio Sequel long reads,
which will be useful and helpful to facilitate analysis of microbial communities
and individual microbial genomes.

Lab activities

Drug Discovery Antibody
Platform Unit
Unit Leader: Toshitada Takemori

Figure: HBV entry into hepatocytes

Sinusoid

HBV particles circulate in the sinusoidal blood and enter
the space of Disse through gaps between endothelial
cells. After reversible attachment to heparan sulfate
proteoglycans on the hepatocyte, HBV particles contact
the integral membrane receptor NTCP and form an irreversible complex. NTCP is a sodium-dependent uptake
transporter expressed on the blood-side membrane ofhepatocytes and is primarily responsible for the uptakeof bile acids from the sinusoids. After HBV attachment
to the NTCP, the epidermal growth factor receptor (EGFR)
mediates HBV–NTCP internalization following fusion of
the viral and cellular membranes. Our established mAb
inhibits formation of the NTCP-virus complex, but does
not impair the normal NTCP-dependent uptake of bile
acids.

space of Disse

EGFR

NTCP

endocytosis

hepatocyte

Recent Major Publications
Tanaka M, Ishige A, Yaguchi M, Matsumoto T, Shirouzu M,
Yokoyama S, Ishikawa F, Kitabayashi I, Takemori T, Harada M. Development of a simple new flow cytometricantibody-dependent cellular cytotoxicity (ADCC) assay
with excellent sensitivity. J Immunol Methods 464, 7486 (2019)

Miyauchi K, Sugimoto-Ishige A, Harada Y, Adachi Y,
Usami Y, Kaji T, Inoue K, Hasegawa H, Watanabe T, Hijikata A, Fukuyama S, Maemura T, Okada-Hatakeyama
M, Ohara O, Kawaoka Y, Takahashi Y, Takemori T, Kubo
M. Protective neutralizing influenza antibody responsein the absence of T follicular helper cells. Nat Immunol
17, 1447-1458 (2016)
Kaji T, Hijikata A, Ishige A, Kitami T, Watanabe T, Ohara O,
Yanaka N, Okada M, Shimoda M, Taniguchi M, Takemori
T. CD4 memory T cells develop and acquire functional
competence by sequential cognate interactions andstepwise gene regulation. Int Immunol 28, 267-82(2016)

In order to conduct research and development of novel drugs and medical
technologies, RIKEN established the Drug and Medical Technology Basic Program (DMP) in December 2009. To achieve effective progress in this area, DMP
organizes various technological platform units to manage the program throughclose cooperation with the Drug Discovery Basic Unit established at each research
center. In this context, a Drug Discovery Antibody Platform Unit was establishedin IMS with budgetary support from the DMP. Our aim is to contribute to theidentification of new treatments for cancer and other diseases by promoting collaboration inside or outside RIKEN for the development of innovative new pharmaceuticals and medical technologies.
In response to proposals by researchers, this Unit creates new monoclonal antibodies (mAbs) that can be useful as immunotherapeutic drugs to meet medical
needs. During this process, we first review the proposal on the basis of clinicalusefulness and feasibility, frequently under discussion with clinical experts. In
accordance with the nature of the research, we then accumulate information andscientific background on the current state of the field and build up new experimental systems that can critically answer the requests as much as possible.
We have worked on several projects for creating new therapeutics, including
targeting human acute myeloid leukemia (AML) stem cells, development of novel
entry inhibitors for the treatment of acute and chronic hepatitis B virus infections
and for intervention in inflammatory bowel disease. In the process of this activity,
we have for the first time established a mAb against an HBV receptor that prevents viral infection in vitro (Figure).

49

Division of Cancer Immunology

Division of Cancer Immunology will explore novel principles of theimmune system, focusing on tumor cells, and promote research for theestablishment of novel therapeutics.

50

Lab activities

Laboratory for

Immunogenetics
Team Leader: Tadashi Yamamoto
A

B
immature hepatocytes

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Figures: Research projects in the laboratory

Recent Major Publications
Suzuki T, Kikuguchi C, Nishijima S, Nagashima T,
Takahashi A, Okada M. Yamamoto T. Postnatal liverfunctional maturation requires Cnot complex-mediateddecay of mRNAs encoding cell cycle and immature livergenes. Development 146, pii: dev168146 (2019)

Shirai Y, Mizutani A, Nishijima S, Horie M, Kikuguchi C,
Elisseeva O, Yamamoto T. CNOT3 targets negative cell
cycle regulators in non-small cell lung cancer development. Oncogene 38, 2580-2594 (2018)
Horie K, Kudo T, Yoshinaga R, Akiyama N, Sasanuma H,
Kobayashi TJ, Shimbo M, Jeon H, Miyao T, Miyauchi M,
Shirakawa M, Shiba D, Yoshida N, Muratani M, Takahashi
S, Akiyama T. Long-term hindlimb unloading causes a
preferential reduction of medullary thymic epithelial
cells expressing autoimmune regulator (Aire). Biochem
Biophys Res Commun 501, 745-750 (2018)
Invited presentations
Setoguchi R. “Chronic IFN-γ signals impair memory CD8
T cell maintenance” The 28th Molecular Immunology
Forum Tokyo (Tokyo, Japan) March, 2019

Yamamoto T. “Advanced Medicine & Bioengineering” STS
Forum (Kyoto, Japan) October, 2018
Yamamto T. “Cell death and CCR4-NOT, an mRNA decay
machinery” ZPM-RIKEN Symposium (Tubingen, Germany) July, 2018
Yamamoto T. “Biology of mRNA poly(A) tail” 2nd RIKEN
IMS-Stanford ISCBRM Joint Symposium (Yokohama,Japan) May, 2018

fetal liver genes
cell cycle-related genes

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liver function-related genes
others (house keeping genes etc.)

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DC

Hedgehog pathway: ON

Hedgehog pathway: OFF

Fortified IS

Weak IS

DC

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TCR

Hh

SMO

Gαi Gαi

T cell
Ca2+
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LFA-1

PTC

PTC

Gαq

T T

A. mRNA decay in liver functional maturation
Cnot complex degrades immature liver-related andcell cycle-related mRNAs during liver maturation. The
process influences a transcriptional induction of mature liver mRNAs. (Suzuki et al, Development 146, pii:
dev168146, 2019)
B. The critical factors for memory CD8 T cell persistence after the contraction of effector CD8 T
cells
The kinetics of antigen (Ag)-specific CD8 T cells andpathogen load in acute infection. The mechanisms involved with memory CD8 T cell maintenance still remain
elusive.
C. Hedgehog signaling in human naive lymphocytes at the immune synapse (IS) with DC
Upon TCR engagement, Hh ligand is secreted into theimmune synapse and initiates the Hh signaling cascadein the T cell. The SMO signal transducer competes for Gαi
coupling with CXCR4. It depletes a shared pool of available Gαi proteins, forcing CXCR4 to switch to a Gα11/q state.
This switch abrogates motility of the lymphocyte, consolidates inside-out signaling, and increases the affinityof integrins, thus fortifying immune synapse stability.

SMO

Gαq

adhesion
+++

Ca2+
+

Gαq GαqGαi Gαiadhesion+

T cellmotility+++

Targets and role in cancer and autoimmunity ?

1) One of the essential post-transcriptional mechanisms is regulation of mRNAstability. Suppression of mRNA deadenylase, an enzyme that triggers mRNA degradation by shortening their polyA tails, leads to abnormal tissue developmentconcomitant with loss of the ability to eliminate unnecessary mRNAs. We havebeen investigating how the deadenylase regulates tissue development and function. Furthermore, clinical studies have identified mutations in mRNA decayrelated genes in human diseases. Viruses also affect host mRNA stability by targeting mRNA decay molecules to create a cellular environment optimal for viral
amplification, resulting in virus-related diseases. We will understand the relationship of mRNA decay with extracellular stresses and virus infection. Our longterm goal is to develop novel therapeutics for human diseases caused by impaired
mRNA decay.
2) Memory CD8 T cells are long-lived antigen (Ag)-specific CD8 T cells that respond quickly, proliferate robustly, and exert effector functions faster than naïve
CD8 T cells upon reencounter with their cognate Ag. By such functions, memory
CD8 T cells protect our body from infectious agents and tumors. Pools of memory CD8 T cells are maintained at a stable size over a long period of time, but themechanisms that affect their long-term persistence still remain incompletely understood. One of the objectives of our study is to reveal how memory CD8 T cells
are maintained in vivo. Results of this research may provide new vaccination strategies for the induction of protective immunity to tumors and chronic infections.
3) Cancer immunotherapy has become an indispensable arm of cancer treatment
in recent years. Checkpoint inhibitors like CTLA4 or PD-1 antibodies have revolutionized the field, but had been shown to be more efficient when used in combination with other chemotherapeutic or biological agents, by providing more precision, reducing side effects, and improving efficiency. Thus, Hedgehog signaling,which is under investigation in the laboratory, could potentially be another target
for such a combinational therapy and needs to be evaluated in detail in health anddisease.

51

Lab activities

Laboratory for

Medical Science
Mathematics
Team Leader: Tatsuhiko Tsunoda

Figure: An international collaboration revealednine new asthma-related loci (left), and integrative omic-analysis applied with human GWAS
and mouse transcriptome identified new Alzheimer genes (right).

Recent Major Publications
Demenais F, Kubo M, Takahashi A, Tsunoda T, et al. Multiancestry association study identifies new asthma riskloci that colocalize with immune-cell enhancer marks.
Nat Genetics 50, 42-53 (2018)

Yamaguchi-Kabata Y, Morihara T, Ohara T, Ninomiya T,
Takahashi A, Akatsu H, Hashizume Y, Hayashi N, Shigemizu D, Boroevich KA, Ikeda M, Kubo M, Takeda M,
Tsunoda T. Integrated analysis of human genetic association study and mouse transcriptome suggests LBH
and SHF genes as novel susceptible genes for amyloid-β
accumulation in Alzheimer's disease. Hum Genet 137,
521-533 (2018)
Lysenko A, Sharma A, Boroevich KA, Tsunoda T. An
integrative machine learning approach for predictionof toxicity-related drug safety. Life Sci Alliance 1,e201800098 (2018)
Invited Presentations
Tsunoda T. “Omic Big Data Analysis Drives Precision
Medicine” The 8th Annual Translational Bioinformatics
Conference/2018 Annual Conference of Korean Society
for Bioinformatics (Seoul, Korea) November, 2018

Tsunoda T. “Public Big Data Accelerate Medical Science
Research” Symposium - Public database and application
for medicine in Japan and Asia, The 63rd Annual Meeting of the Japan Society of Human Genetics (Yokohama,Japan) October, 2018
Lysenko A. “Machine learning-driven analysis of biological networks for predictive modelling of drug toxicity”
14th International Symposium on Integrative Bioinformatics (Harpenden, UK) June, 201852

E

ffective utilization of rapidly developing omic profiling technologies and, inparticular, the introduction of personalized/precision/preventive medicine
have recently become major goals of medical research. This paradigm shift requires moving away from traditional approaches that do not adequately consider
the individual characteristics of each patient. Our laboratory develops strategies
to address these challenges by bringing the ideas and methods from mathematics
and computational sciences to the medical domain. The first part of our approachis driven by integrative analysis of clinical and omic data and aims to explore the
etiologies of intractable diseases such as cancer, common diseases such as coronary artery disease and type 2 diabetes, and neurodegenerative diseases. Next,
we classify each disease into finer categories using molecular profiles and clarify
underlying causal mechanisms with systems-based approaches. Lastly, we apply
mathematical and machine learning techniques to infer optimal therapy for eachpatient to guide treatment decisions by their hospital or clinic. Similar approaches
can be used for disease prevention based on an individual’s medical history. Our
past and current research projects include: (1) International collaborations forgenome-wide association studies (GWAS) with imputation, meta-analysis, andeQTL analysis techniques; (2) Development of new methodologies for increasing
GWAS statistical power and sample size estimation; (3) Integrating trans-omic
analysis with GWAS; (4) Accurate insertion/deletion calling from next-generation
sequencing (NGS) data, whole genome sequencing (WGS), and targeted-sequencing analysis; (5) Whole exome sequencing (WES) analysis to identify intractabledisease-causing genes; (6) Cancer WGS analysis; (7) Development of new clustering methods; (8) Development of cancer classification and prognosis prediction
methods based on gene expression data; (9) Development of original network/
pathway analysis methods for disease-causing genes; (10) Drug toxicity prediction
with machine learning; (11) Prediction of post-translational amino-acid modifications and protein structure; (12) Clarifying cancer immunology for therapy;and (13) Utilizing deep neural networks for image and omic data analyses.

Lab activities

Laboratory forCancer Genomics
Team Leader: Hidewaki Nakagawa

HBV

Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M,
Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor
RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M,
Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano
K, Tanaka H, Yamamoto Y, Kubo M, Kawakami Y, Aikata
H, Ueno M, Hayami S, Gotoh K, Ariizumi S, Yamamoto
M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A,
Hirano S, Nakamura T, Nakagawa H*. Genomic characterization of biliary tract cancers identifies their drivergenes and predisposing mutations. J Hepatol 68, 959969 (2018)
Invited presentations
Nakagawa H. “Whole genome sequencing and immunogenomic analysis for liver cancer” The 49th Princess
Takamatsu Cancer Research Fund International Conference (Tokyo, Japan) November, 2018

Nakagawa H, Miyano S. “Pan-cancer Whole Genome
Sequencing Project (PCAWG) in ICGC/TCGA” Symposium
10: Overview of cancer genome research and new challenges. The 77th Annual Meeting of Japanese Cancer
Association (Osaka, Japan) September, 2018
Nakagawa H. “Cancer Whole Genome Sequencing and
Immuno-genomic Analysis for Cancer” The 27th Korean
Genome Organization Annual Conference (Seoul, Korea)
September, 2018
Nakagawa H. “Genomic Landscape of Hepato-Biliary
Cancers and Forwarding to Precision Medicine” Molecular Analysis for Personalized therapy (MAP) Conference(Zurich, Switzerland) October, 2017
Nakagawa H. “Cancer Whole Genome Sequencing for
Precision Oncology and Cancer Immunology” The 2017
Cold Spring Harbor Asia Conference (Suzhou, China)
September, 2017

1

Y

HBV

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10 days

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Boot A, Huang MN, Ng AW, Ho SC, Lim JQ, Kawakami Y,
Chayama K, Teh BT, Nakagawa H, Rozen SG. In-depthcharacterization of the cisplatin mutational signaturein human cell lines and in esophageal and liver tumors.
Genome Res 28, 654-665 (2018)

Non-cancer 22 X
21
20
liver
19

Read depth

Recent Major Publications
Furuta M, Tanaka H, Shiraishi Y, Unida T, Imamura M,
Fujimoto A, Fujita M, Oku-Sasaki A, Maejima K, Nakano
K, Kawakami Y, Arihiro K, Aikata H, Ueno M, Hayami S,
Ariizumi S, Yamamoto M, Gotoh K, Ohdan H, Yamaue H,
Miyano S, Chayama K*, Nakagawa H*. Characterizationof HBV integration patterns and timing in liver cancerand HBV-infected liver. Oncotarget 9, 25075-25088(2018)

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Figure: HBV integration in human liver cancers, non-cancer HBV infected liver tissues and HBV-infected liver tissues in human-mice chimera model

Ultra-deep sequencing targeting HBV sequence identified 1684 HBV integration sites in 113 HBV-infectedliver tissues. In liver cancer, TERT and MLL4 genes werepreferential regions for HBV integration, and HBV
integration sites were significantly enriched in regions

annotated as exhibiting open chromatin and early replication timing in non-cancer liver tissues. In the HBVinfected human-mouse chimera model, HBV integration
occurred between 24-49 days after HBV infection andwas predominant in mitochondrial DNA.

C

ancer is essentially a “disease of the genome” that develops and evolves withthe accumulation of a variety of mutations in its genetically unstable background. Some somatic mutations of driver genes have been successfully targeted
for cancer treatment. Now, genotype-based personalized cancer therapy is in theclinical stage. Understanding of, and attention to the underlying genetic diversity in cancer is, therefore, likely to increase the success of new cancer treatment
modalities. Recent explosive advances in next-generation sequencing (NGS) andbioinformatics enable us to perform systematic, genome-wide identification of
all somatic abnormalities by whole genome sequencing (WGS), whole exome sequencing, and RNA sequencing (RNA-seq). Furthermore, cancer has been provento have a feature of “immune reaction”, and immune therapies targeting immune
checkpoints and neo-antigens derived from somatically mutated proteins are also
treatment realities. To explore whole genomic and immuno-genomic alterations
and their diversity in cancer, we have been addressing WGS and RNA-seq analyses for cancer. These approaches, combined with mathematical analysis and other-omics analyses, can clarify the underlying carcinogenesis and cancer immunology and achieve a molecular sub-classification of cancer, which will facilitate discovery of genomic biomarkers and personalized cancer medicine.

53Lab activities

Laboratory for

Immunotherapy
Team Leader: Shin-ichiro Fujii

Recent Major Publications
Shimizu K, Iyoda T, Okada M, Yamasaki S, Fujii S*. Immune suppression and reversal of the suppressive tumor
microenvironment. Int Immunol 30, 445-454 (2018)

Yamada D, Iyoda T, Vizcardo R, Shimizu K, Sato Y, Endo
TA, Kitahara G, Okoshi M, Kobayashi M, Sakurai M, Ohara
O, Taniguchi M, Koseki H, Fujii S*. Efficient regenerationof Human Vα24+ invariant NKT cells and their antitumor activity in vivo. Stem Cells 34, 2852-2860 (2016)
Shimizu K, Yamasaki S, Shinga J, Sato Y, Watanabe T,
Ohara O, Kuzushima K, Yagita H, Komuro Y, Asakura
M, and Fujii S*. Systemic DC activation modulates thetumor microenvironment and shapes the long-lived
tumor-specific memory mediated by CD8+ T cells. Cancer Res 76, 3756-66 (2016)
Invited Presentation
Fujii S. “Immunotherapy utilizing invariant NKT celllicensed dendritic cells in situ., Korean Association on
Immunologists meeting” KAI International Meeting
2018, Sejong University Convention Center (Seoul, Korea) November, 2018

Fujii S. “Novel type of cancer vaccine, artificial adjuvant
vector cells with multiple immunopotentiating effects
against melanoma” The 77th Annual Meeting of theJapanese Cancer Association, Osaka International Convention Center (Osaka, Japan) September 28, 2018
Fujii S. Multifunctional cancer vaccine “Artificial adjuvant vector cell” The 16th Annual Meeting of JapaneseSociety of Clinical Oncology (Kobe, Japan) July, 2018
Fujii S. “Development of new cellular vaccine systems
with synergistic immunopotentiating effects” The 46th
Japanese Society for Immunology (Sendai, Japan) December, 2017
Fujii S, Kanako Shimizu. “Systemic and Potent Dendritic
Cell (DC) Activation Modulates the Tumor Microenvironment and Shapes the Long-lived Tumor Specific Memory
CD8+T Cells” The 8th JSH International Symposium 2017
(Miyazaki, Japan) May, 2017544) Figure: Engineering nanoparticles for cancer therapy(A) Cytokine production by DCs after particle capture.
OVA antigen-encapsulated liposomes—small (200 nm)
and large (1,000 nm)—were fabricated to contain OVA
protein. IL-12p40 in culture supernatants from bonemarrow-derived DCs cultured with vehicle or each typeof liposome was measured by ELISA. DCs that took up
liposomes produced IL-12, but the large ones induced
higher levels and more rapid cytokine production. (B)Mice that had been inoculated subcutaneously withT

2×105 OVA-expressing lymphoma (EG7) cells (day0) were treated twice i.v. with OVA-containing large
liposomes and poly(I:C) (day 6 and 9) and then treated
twice i.t. with small or large liposomes and poly(I:C)(day 12 and 15). Tumor size was measured every 3 days.
(Significance of difference between vehicle and smallor large liposomes: *P<0.05, **P<0.01, ***P<0.001.
Significance of difference between small and large liposomes: #P<0.05, ##P<0.01, ###P<0.001.)

he laboratory conducts basic research in cancer immunology with a strongtranslational component in immunotherapy. The recent success of immune
checkpoint blockade (ICB) therapy represents a turning point in cancer immunotherapy. We have been studying cancer immunology and have developed an immunostimulatory immunotherapy against cancer. We have three ongoing projects
in basic cancer immunology. We have 1) identified KLRG1+ invariant (i)NKT
cells as having a memory-like phenotype with strong antitumor activity, and havecharacterized them in terms of intrinsic and extrinsic factors; 2) developed an immunotherapeutic strategy using tumor-derived neo-antigens; and 3) begun a bioengineering collaboration to develop a drug delivery system using nanoparticles.
We also have translational research (TR) projects that are related to iNKT cells
and are aimed toward clinical studies. We have established artificial adjuvant vector cells (aAVC) as a new type of drug delivery platform composed of an iNKT
cell ligand and tumor-associated antigens. We have completed the regulatory science consultation discussing the pharmaceutical quality and the design of a clinical study with the Pharmaceuticals and Medical Devices Agency. This project has
also been accepted by the RIKEN translational program and been reviewed by theInstitutional Review Board (IRB) of the Institute of Medical Science, the University of Tokyo (IMSUT). In July 2017, we launched a physician-initiated phase I
clinical trial for refractory or relapsed acute myelogenous leukemia (AML) at the
Department of Hematology/Oncology, the Institute of Medical Science, the University of Tokyo (IMSUT) hospital. In two other TR studies, we are engaged in theanalyses of iPS-iNKT cells in preclinical tumor models and also collaborated with
the National Hospital Organization (NHO) in a joint clinical phase I/IIa study of
NKT cell therapy for early-stage post-operative lung cancer patients.

Lab activities

Laboratory for

Human Disease Models
Group Director: Fumihiko Ishikawa
AC
AJCC stage

80%Tregs in CD4+ T cells

Recent Major Publications
Ono R, Watanabe T, Kawakami E, Iwasaki M, TomizawaMurasawa M, Matsuda M, Najima Y, Takagi S, Fujiki S,
Sato R, Mochizuki Y, Yoshida H, Sato K, Yabe H, Kato
S, Saito Y, Taniguchi S, Shultz LD, Ohara O, Amagai M,
Koseki H, Ishikawa F. Co-activation of macrophages andT cells contribute to chronic GVHD in human IL-6 transgenic humanised mouse model. EBioMedicine 41, 584596 (2019)%Tregs in CD4+ T cells

Tumorgrade

60
40
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T1

T3
T2
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T4

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B

Fujimoto H, Saito Y, Ohuchida K, Kawakami E, Fujiki S,
Watanabe T, Ono R, Kaneko A, Takagi S, Najima Y, Hijikata A, Cui L, Ueki T, Oda Y, Hori S, Ohara O, Nakamura M,
Saito T, Ishikawa F. Deregulated Mucosal Immune Surveillance through Gut-Associated Regulatory T Cells andPD-1+ T Cells in Human Colorectal Cancer. J Immunol
200, 3291-3303 (2018)
Saito Y, Mochizuki Y, Ogahara I, Watanabe T, Hogdal L,
Takagi S, Sato K, Kaneko A, Kajita H, Uchida N, Fukami
T, Shultz LD, Taniguchi S, Ohara O, Letai AG, Ishikawa F.
Overcoming mutational complexity in acute myeloid
leukemia by inhibition of critical pathways. Sci TransMed eaao1214 (2017)
Invited Presentations
Ishikawa F. “Overcoming genetically-complex leukemia
using humanized mouse” Regeneron (Tarrytown, USA)
November, 2018

Ishikawa F. “Finding targets and creating therapeutic
compounds for genetically-complex human hematological malignancies” JCA Morning Lecture (Osaka, Japan)
September, 2018
Ishikawa F. “Linking biological heterogeneity andgenetic complexity of human malignancies using thehumanized mouse” AACR: Meet-the-Expert session(Chicago, USA) April, 2018
Ishikawa F. “Understanding clonal complexity of humanhematologic malignancies by single cell genomics and
PDX modeling” AACR: PDX workshop (Chicago, USA)
April, 2018
Ishikawa F. “Functional single cell genomics for targeting genetically-complex acute myeloid leukemia” AACR:
Single cell workshop (Chicago, USA) April, 2018

Figure: Involvement of Tregs in human colorectal tumors(A) The proportions of Tregs among CD4+ T cells according to the (Left) TNM T classification and (Right) TNM
stage. The proportion of Tregs is significantly higher
in benign adenoma compared with normal mucosa,
and higher still in adenocarcinoma at each T grade
and TNM stage compared with benign adenoma. T3
adenocarcinoma shows significantly increased Treg frequency compared with T2. There is increase in the Treg
frequency between adenoma and stage I and between

stage I and stage II. (B) (Left) Heat map of genes highly
expressed in cancer Tregs compared with normal BM/
cord blood (CB) Tregs, Tconvs, and cancer Tconvs. (Right)
For cytokine and chemokine receptors, expression levelsof their ligands in normal and cancer stromal cells and inepithelial cells are presented as a heat map. (C) Foxp3+
Tregs were most abundant in the stroma-rich area ofcolon adenocarcinoma.

To understand in vivo behavior of normal and malignant human hematopoietic/immune cells, we have developed a system called “humanized mice”.
Although we have successfully achieved high chimerism of human hematopoietic cells in multiple immune organs of the humanized mice, the species barrier
between human cells and the mouse tissue microenvironment has been one of
the major obstacles. To overcome this caveat of humanized mice, we have been
making efforts to create next-generation humanized mice with a humanized
microenvironment. In collaboration with Drs. Koseki and Dr. Ohara at RIKEN
IMS and Dr. Shultz at the Jackson Laboratory, we have been developing immunecompromised mice expressing human MHCs, cytokines, and adhesion molecules.
We have also applied the humanized mouse system to a study of human hematologic malignancies. To date, we succeeded in recapitulating adult acute myeloid leukemia (AML) and infant acute lymphoblastic leukemia (ALL). Humanleukemias are heterogeneous in aggressiveness and genetic abnormalities. The
use of humanized mice for leukemia studies has enabled us to understand interpatient leukemia heterogeneity in terms of both biology and genomics. Further,by combining in vivo stem cell biology, immunology, and multi-omics, we are
currently attempting to discover therapeutic targets and to develop new and effective treatments against poor prognosis AML and ALL. In addition, we aim toanalyze interaction between human immunity and human leukemia by creating
HLA-expressing humanized mice. We hope to translate knowledge gained by humanized mouse research into the clinic in the near future.

55

Lab activities

Liver Cancer Prevention
Research Unit
Unit Leader: Soichi Kojima

Figure: Immunofluorescence staining of humanhepatocellular carcinoma (HCC) tissues.

Pictured is a fluorescent microphotograph of a sectionof HCC tissue stained for MYCN (red), a cancer stem cellmarker, EpCAM (green), and DNA (blue).

Recent Major Publications
Qin X-Y, Suzuki H, Honda M, Okada H, Kaneko S, Inoue I,
Ebisui E, Hashimoto K, Carninci P, Kanki K, Tatsukawa H,
Ishibashi N, Masaki T, Matsuura T, Kagechika H, Toriguchi
K, Hatano E, Shirakami Y, Shiota G, Shimizu M, Moriwaki
H, Kojima S. Prevention of hepatocellular carcinoma bytargeting MYCN-positive liver cancer stem cells withacyclic retinoid. Proc Natl Acad Sci U S A 115, 49694974 (2018)

Shrestha R, Shrestha R, Qin XY, Kou TF, Oshima Y, Iwatani
S, Teraoka R, Fujii K, Hara M, Li M, Takahashi-Nakaguchi
A, Chibana H, Lu J, Cai M, Kajiwara S, Kojima S. Fungusderived hydroxyl radicals kill hepatic cells by enhancing
nuclear transglutaminase. Sci Rep 7, 4746 (2017)
Tatsukawa H, Furutani Y, Hitomi K, Kojima S. Transglutaminase 2 has opposing roles in the regulation of cellularfunctions as well as cell growth and death. Cell Death &Disease 7, e2244 (2016)
Invited presentations
Kojima S. “Gut dysbiosis, nuclear transglutaminase andhepatocyte death” The 13th International Symposium
on ALPD and Cirrhosis (Kyoto, Japan) September, 2018

Kojima S. “Drug discovery researches at academia on
prevention, diagnosis, and treatment of liver diseases”
The 18th Meeting of the Kansai Society for Kinetics ofHepatic Blood stream and Imaging of Hepatic functions(Osaka, Japan) July, 2018
Kojima S. “Molecular mechanism by which acyclic
retinoid selectively kills MYCN-positive liver cancer
stem cells” FASEB the 4th International Conference on
Retinoids (Steamboat Springs, USA) June, 2018
Kojima S, Furutani Y. “Combinational treatment of CDM3008 and entecavir for suppression of HBV reactivation”
Taiwan-Japan-Korea Research Symposium on Hepatitis
B Virus (Taipei, Taiwan) April, 2018
Kojima S. “Genomic and nongenomic actions of acyclic
retinoid on deletion of MYCN+CD133+ liver cancer stem
cells” Xiamen University AFPS2017-The 104 Sciences
2017 (Xiamen, China) November, 2017

56

A

pproximately 250 million people worldwide are infected with hepatitis B
virus (HBV), which can progress to hepatitis, fibrosis, decompensated cirrhosis, and hepatocellular carcinoma (HCC). In infected hepatocytes, HBV forms
covalently closed circular DNA (cccDNA), from which pre-genomic RNAs andmRNAs are transcribed to sustain HBV replication. This process is suppressed by
nucleotide analogues (NAs) by inhibiting reverse transcriptase, but the cccDNA
is retained in the nucleus of the infected cells. Thus, inhibited cccDNA formationand its degradation are critical for eradication of the virus. Interferon (IFN)-αenhances the expression of the cytidine deaminase APOBEC (apolipoprotein B
mRNA editing enzyme, catalytic polypeptide-like) family, leading to cccDNA
degradation. Beginning from a structure-activity relationship study of compounds that mimic IFN-α, we found that these compounds had a strong antiHBV activity that was accompanied by a decrease in cccDNA, and thus renamed
them as cccDNA modulators (CDMs). CDMs bound to a novel pocket in the IFN
receptor and worked in vitro in combination with an NA.
We established a sensitive ELISA to quantify TGF-β latency-associated protein(LAP)-degradation products (DPs) at levels as low as 2 pM. The presence of theseDPs reflects plasma kallikrein-dependent TGF-β activation and an increase in activated hepatic stellate cells, which are responsible for liver fibrosis, thereby serving as a novel biomarker for liver fibrogenesis.
HCC is highly lethal, partly because of its high rate of recurrence, which is
caused by the presence of liver cancer stem cells (CSCs). Using a selective chemopreventive agent, acyclic retinoid (ACR), as a bioprobe, we identified MYCN as atherapeutic target of ACR in HCC through a selective deletion of MYCN+ liver
CSCs. We also demonstrated that the expression of MYCN in HCC served as aprognostic biomarker that positively correlated with the recurrence of HCC after
curative treatment. These findings highlight MYCN as a useful biomarker andan important therapeutic target in drug discovery for screening chemopreventive
agents against the recurrence of HCC.

Special Programs for
Young Leaders
RIKEN Hakubi Fellows Program
RIKEN offers junior Principal Investigator (PI) positions, the RIKEN
Hakubi Fellows, for exceptionally talented researchers for a maximum of
7 years. RIKEN Hakubi Fellows are expected to independently engage increative and ambitious research in natural and mathematical sciences,including research areas bordering the humanities and social sciences.
An important goal of the RIKEN Hakubi Program is to foster stimulatinginteractions among the Fellows with diverse backgrounds and to create
an intellectual hub of scientists with different disciplines within and beyond RIKEN.
“Hakubi” is a phrase derived from a classical Chinese story about five
siblings in ancient China, all gifted, but the most brilliant one had white(haku) eyebrows (bi).

Young Chief Investigator Program
The Young Chief Investigator Program (YCI) aims to provide a career
path for young investigators who conduct multidisciplinary research thatwill bridge immunology with other research fields. In this program, the selected Young Chief Investigator (age below 40) will head an independent
research laboratory but will have access to mentoring by multiple seniorspecialists in related research fields. Mentors provide guidance for experimental design, preparation of papers and presentations, promotion ofinternational visibility, and obtaining research funding. The YCI laboratory
will also share space, equipment, and facilities with a host laboratory in
IMS.

57

Lab activities

Genome Immunobiology
RIKEN Hakubi Research
Team
Team Leader: Nicholas Parrish

We hypothesize that viral sequences are integrated into
host genome loci that are transcribed and processed into
small RNAs. After integration into the genome, thesesequences are stable over time, even over generations
if integrated into the germline. Small RNAs produced
from these integrated viral sequences can guide RNAcleaving enzymes to silence the expression of viral proteins, blocking replication and/or pathogenesis. The goalof this laboratory is to test this hypothesis and thereby
reject the hypothesis or demonstrate that eukaryotes
have a heritable RNA-based immune system analogous
to CRISPR/Cas-mediated immunity in prokaryotes.

       Invited presentations
Parrish NF. “Interfering Small RNAs Derived from Ancient
Viral Sequences in Mammalian Genomes: a CRISPR/
Cas-like Eukaryotic Immune System?” RIKEN Center for
Biosystems Dynamics Research, internal seminar (Kobe,
Japan) October, 2018

Parrish NF. “Interfering Small RNAs Derived from Ancient
Viral Sequences in Mammalian Genomes: a CRISPR/
Cas-like Eukaryotic Immune System?” Tokyo University
Department of Neurochemistry, internal seminar (Tokyo,
Japan) August, 201858 

   

Recent Major Publications
Parrish NF, Feurer ID, Matsuoka LK, Rega SA, Perri R,
Alexopoulos SP. The Changing Face of Liver Transplantation in the United States: The Effect of HCV Antiviral Erason Transplantation Trends and Outcomes. Transplant
Direct (in press)





Figure: Central Hypothesis - Integrated Virus Sequences Enable Heritable RNA-based ImmunityW   

e are testing the hypothesis that viral sequences integrated into eukaryotic genomes can influence antiviral immunity, analogous to CRISPR/Casmediated immunity in prokaryotes. We hypothesize that small RNAs transcribedfrom integrated viral sequences can interfere with viral protein expression andthus block viral replication and/or pathogenesis. In humans and mice, we haveshown that a class of non-retroviral endogenous viral elements called endogenous
bornavirus-like nucleoprotein elements (EBLNs) often encode small RNAs called
Piwi-interacting RNAs (piRNAs). piRNAs can silence retrotransposons, fromwhich piRNAs are also transcribed, but this process has not been shown for infectious viruses.
We are using two complementary model systems to test this hypothesis andare collaborating to test a third model system: 1) knocking out EBLNs present in
the mouse genome, and knocking in viral sequences into functionally similar loci,2) characterizing immunity to human herpesvirus 6 (HHV-6) in ~1% of humans
in whom this virus has become endogenous, and 3) introducing arboviral genes
into mosquito genomes and testing arboviral vector competence. The three armsof the research program provide a balanced platform to test the high-risk, highreward concept that eukaryotes have an unrecognized immune system based on
virus-to-host gene transfer. If such a system is demonstrated, it would have practical applications for non-human germline and human somatic genome engineering for virus resistance.

Lab activities

YCI Laboratory for

Cellular Bioenergetic
Network
Young Chief Investigator: Toshimori Kitami

Combinatorial chemical screen

Figure: Schematic of activator-suppressor
screens for NLRP3 inflammasome, model building, and validation.

Activator screen
Suppressor screens
1280+1
chemicals

1

K+
?

2

3

X ROS Lysosome?

?

NLRP3‐PYCARD‐CASP1+2

pro‐IL‐1β

IL‐1β
IL‐1β

Model building
1

2

Ex vivo / in vivo analysis

3

K+

X ROS Lysosome

?

ATP

pH
K+

NLRP3‐PYCARD‐CASP1

K+

O2

pro‐IL‐1β

pro‐IL‐1β

IL‐1β
IL‐1β

Recent Major Publications
Tran UT, Kitami T. Niclosamide activates the NLRP3
inflammasome by intracellular acidification and mitochondrial inhibition. Commun Biol 2, 2 (2019)

Kaji T, Hijikata A, Ishige A, Kitami T, Watanabe T, Ohara O,
Yanaka N, Okada M, Shimoda M, Taniguchi M, Takemori
T. CD4 memory T cells develop and acquire functional
competence by sequential cognate interactions andstepwise gene regulation. Int Immunol 28, 267-282(2016)
Invited presentations
Kitami T. “Systematic dissection of mitochondrial functions via chemical genetics approach” Saitama Medical
University Research Center for Genomic Medicine(Saitama, Japan) October, 2018

Kitami T. “Systematic dissection of mitochondrial functions via chemical screening approach” Symposia:
Renaissance of the ‘Mitochondrial World’ unveiled by
cutting-edge technologies. The 91st Annual Meeting of
the Japanese Biochemical Society (Kyoto, Japan) September, 2018
Kitami T. “Mitochondrial chemical compendium version
2: detection of genotype-specific mitochondrial toxicity” The 1st Annual COCKPI-T (Co-Create Knowledge
for Pharma Innovation with Takeda) Presentation Day(Kanagawa, Japan) July, 2017

Lyso

pH

ATP

NLRP3‐PYCARD‐CASP1
IL‐1β
IL‐1β

Model refinementMitochondria are dynamic organelles central to energy homeostasis, intermediary metabolism, ion homeostasis, and cell death. Inherited defects inmitochondria cause the most common inborn errors of metabolism, and a growing body of evidence also links mitochondria to more complex diseases, including
type 2 diabetes, cardiovascular disease, and neurodegeneration. Despite our basic
understanding of mitochondrial functions, the precise mechanisms by whichmitochondria participate in disease pathogenesis remain largely unanswered. The
long-term goal of our laboratory is to use our expertise in chemical biology andgenomics to critically evaluate the role of mitochondria in disease pathways.
Toward our goal, we initiated a project focused on the role of mitochondria in
the NLRP3 inflammasome, which is one of the intracellular pattern recognition
receptors normally involved in the detection of pathogens and cellular damage.
However, recent studies also point to its involvement in age-associated diseases.
The NLRP3 inflammasome is activated by changes in cellular physiology, including mitochondrial damage, although the molecular players involved have notbeen fully elucidated. We therefore established a chemical screening platform todissect the inner wiring of the inflammasome activation pathway. We have successfully identified chemicals that activate or suppress the NLRP3 inflammasome
through mitochondria and revealed their mechanisms of action. These chemical
tools will be applied to ex vivo and in vivo disease models to critically evaluate therole of mitochondria in NLRP3 inflammasome activation.
In addition, we are also exploring the role of mitochondria in other complex
diseases through the use of large-scale datasets generated in our laboratory as wellas in RIKEN IMS. We hope that our genomic and chemical biology efforts will
not only help clarify the role of mitochondria in complex diseases but also point
to small-molecule therapies for treatment of mitochondria-related disorders.

59Lab activities

YCI Laboratory forTrans-Omics

Young Chief Investigator: Katsuyuki Yugi

Figure: Selective response of the global metabolic regulatory network to the low-dose (left,blue) and the high-dose insulin signal (right,
red)

The downregulated genes and metabolites in glycolysis
exhibited high sensitivity to insulin concentration,
whereas the upregulated genes and dicarboxylic acidsin the TCA cycle exhibited low sensitivity (†Kawata,†Hatano, †Yugi et al., iScience, 2018).

Recent Major Publications†Kawata K, †Yugi K, Hatano A, Kokaji T, Tomizawa Y, Fujii
M, Uda S, Kubota H, Matsumoto M, Nakayama KI, Kuroda S, Reconstruction of global regulatory network fromsignaling to cellular functions using phosphoproteomic
data. Genes Cells 24, 82-93 (2019) († These authors
contributed equally)†Kawata K, †Hatano A, †Yugi K, Kubota H, Sano T, Fujii
M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Suzuki Y,
Matsumoto M, Nakayama KI, Saitoh K, Kato K, Ueno
A, Ohishi M, Hirayama A, Soga T, Kuroda S. Trans-omic
analysis reveals selective responses to induced and basal
insulin across signaling, transcriptional, and metabolic
networks. iScience 7, 212-229 (2018) (Cover Article; †These authors contributed equally)
Yugi K, Kuroda S. Metabolism as a signal generator
across trans-omic networks at distinct time scales. Curr
Opin Syst Biol 8, 59-66 (2018)
Invited presentations
Yugi K. “Development of trans-omics technologies thatreconstruct molecular networks of psychiatric disorders”
Next Generation Brain Project Winter Symposium (Tokyo,
Japan) November, 2018

Yugi K. “Trans-omic analysis reveals fed and fasting
insulin signal across phosphoproteome, transcriptome,
and metabolome” The 1st International Symposium forTrans-Omics (Tokyo, Japan) November, 2017
Yugi K. “A trans-omic reconstruction of insulindependent regulatory networks for metabolism” The 4thInternational Symposium of Gunma University Initiative
for Advanced Research (Maebashi, Japan) November,
2017
Yugi K. “Reconstruction of insulin-dependent metabolic
regulatory networks from phosphoproteome andmetabolome data” RIKEN IMS-Japan Society for Immunology International Symposium on Immunology 2017
(Tokyo, Japan) June, 2017
Yugi K, Kubota H, Kuroda S. “Trans-omic reconstructionof insulin signal flow in global phosphorylation andmetabolic network” Institut Curie & SBI joint workshop:
Modeling and Data Analytics for Cancer Systems Biology(Tokyo, Japan) December, 201660

T

rans-omics is a discipline to reconstruct a global molecular network thatspans across multiple omic layers, not as a group of indirect statistical correlations but as chains of direct mechanistic interactions (Yugi et al., Trends Biotechnol., 2016; Yugi and Kuroda, Cell Syst., 2017; Yugi and Kuroda, Curr. Opin.
Syst. Biol., 2018). The network reconstruction is performed based on comprehensive measurement data of multiple omic layers not taken from heterogeneous
sources but measured under an identical condition. Our primary research interests are:
1. Developing methods for trans-omics
2. Reconstructing global metabolic regulatory networks in a trans-omic manner

We have developed methods for integration of metabolome, phosphoproteome, and transcriptome data. The methods have been applied to reveal the metabolic regulation by insulin in a global manner; insulin action on adipocytes, byintegrating phosphoproteome and 13C-labeled metabolome data (†Krycer, †Yugi
et al., Cell Rep, 2017), and on a rat FAO hepatoma cell line by integrating transcriptome, phosphoproteome, and metabolome data (Yugi et al., Cell Rep, 2014;†Kawata, †Hatano, †Yugi et al., iScience, 2018; †Kawata, †Yugi et al., Genes Cells,2019).
Our long-term goal is to extend the methodology of trans-omics in two senses:(1) extending the method to incorporate data from other omic layers, such as
genomic variants, so that global metabolic regulatory networks behind a broader
range of diseases and drug actions can be characterized, and (2) extending availability of trans-omic analysis to non-specialist researchers by development ofuser-friendly software.

Lab activities

YCI Laboratory for

ImmunologicalTranscriptomics

Young Chief Investigator: Hideyuki Yoshida

1.0

Pearson correlations were computed from RNA profiles
from 308 mTECs. Regulators and PTAs that showed significant correlations (q-val <= 0.05) were extracted andclustered by k-means clustering. Color-code indicates
Pearson’s correlation coefficient.

0.5

0.0

−0.5

Pearsonʼs correlation coeﬃcient

443 regulators (transcription factors and kinases)

Figure: Correlation of PTAs and their possible
regulators in mTECs.

−1.0

984 PTAs

Fig. correlations of PTAs and their possible regulators in TECs
Recent Major Publications
Hideyuki Y, Caleb L, Ricardo R, Samuel R, Barbara M,
Aleksandra W, Fiona D, Aleksey C, Arthur M, Claudia D,
Julie T, Edy K, Dan D, Susan S, Tsukasa N, YiLin Q, Bingfei
Y, Michelle R, Ki-Wook K, Amy W, Andrew R, Stephen N,
Brian B, Sara M, Jason B, Benoist C and the Immunological Genome Project. The cis-Regulatory Atlas of the
Mouse Immune System. Cell 176, 1–16 (2019)

Bansal K, Yoshida H, Benoist C and Mathis D. The transcriptional regulator Aire binds to and activates superenhancers. Nat Immunol. 18, 263-273 (2017)
Sara M, Hideyuki Y (Co-first author), Devapregasan M,
Hugo L, Katherine R, Towfique R, Chun-Jimmie Y, Nicolas
C, Shen-Ying Z, Ting F, Mark L, Jean-Laurent C, James C,
Martin H, Jean-Baptiste T, Nir H, Philip J, Aviv R, Diane M,
Benoist C and the Immunological Genome Project Consortium. Parsing the interferon transcriptional network
and its disease associations. Cell 164, 564-578 (2016)

Invited presentations
Yoshida H. “ATACseq, cool results, what next?” 2017
Workshop, Immunological Genome Project (Boston,USA) December, 2017

Yoshida H. “IFN response: analysis of transcriptional
network by an unbiased approach” The 11th International Symposium of The Institute Network Frontiers in
Biomedical Sciences (Tokushima, Japan) January, 2017

G

ene regulation is one of the most elemental mechanisms governing cell functions andbiological processes, including in immune cells and in the immune system, and has
been studied in many contexts. Recent advances in epigenome and transcriptome profiling, taking advantage of next-generation sequencing (NGS), enable us to investigate gene
regulation in an unprecedented manner and, hence, to explore uncharted mechanisms inbiology and immunology.
Our research aims to promote our understanding of gene regulation in immune cells
and the immune system by utilizing the techniques of cutting-edge transcriptomics forbetter understanding and treatment of immune disorders. Transcriptomics can be applied
to various studies in immunological settings, and we have been engaged in 1) a focused
subject and 2) a data-driven project with a systematic approach.

1) Focused subject: Gene regulation in immune tolerance
Negative selection of self-reactive T cells occurs in the thymus and is an essential mechanism for induction of immune tolerance. To achieve this, many peripheral tissue antigens(PTAs) are expressed in thymic medullary epithelial cells (mTECs) and the developing T
cells are eliminated if they respond too strongly to these PTAs. Since the disrupted expression of PTAs can lead to autoimmune disorders, understanding the mechanisms controlling their expression is important for understanding the pathogenesis of autoimmune
diseases and for developing new treatments. We are analyzing gene expression in mTECs
by single-cell RNA-seq to examine gene regulation in detail and to identify the regulators
involved. Candidate genes identified by RNA-seq will be validated using mouse models.

2) Data-driven project: Systematic analysis of various immune celltypes
Bioinformatics has already impacted research on gene regulation and is becoming evenmore powerful since we have begun dealing with big data analysis. To promote these datadriven studies, we are collaborating with the ImmGen group (www.immgen.org).

61

Lab activities

Laboratory for

Next-Generation
Proteomics
Young Chief Investigator: Yibo Wu

Figure: A mass spectrometry-based proteomics
analysis of preadipocytes and immune cell
populations in mouse visceral adipose tissue.

(A) The composition and activity of immune cells aredramatically different in the lean and obese state. (B)We perform mass spectrometry-based proteomics
analysis of preadipocytes and different types of immune
cells in mouse visceral adipose tissue. 11-week-old
C57BL/6N mice were fed a normal chow diet (CD) or ahigh-fat diet (HFD) for 8 weeks, and different cell populations were sorted from the visceral adipose tissue by
flow cytometry. We extracted and digested the proteinsfrom each sorted cell population and analyzed them byliquid chromatography-mass spectrometry (LC-MS/MS).
Then we performed computational analysis for precise
protein quantification. (C) Protein expression patterns
are clearly different in macrophages from CD or HFD-fed
mice. (D) Proteins that significantly change in macrophages from CD and HFD-fed mice. Right: up-regulatedin HFD-fed mice. Left: down-regulated in HFD-fed mice.
(E) Pathways that are significantly enriched in the macrophage proteome (top 19). Red: up-regulated in HFDfed mice. Blue: down-regulated in HFD-fed mice.
Recent Major Publications
Terfve C*, Sabidó E*, Wu Y*, Gonçalves E, Choi M, Vaga
S, Vitek O, Saez-Rodriguez J, Aebersold R. System-Wide
Quantitative Proteomics of the Metabolic Syndrome inMice: Genotypic and Dietary Effects. J Proteome Res
16, 831-841 (2017)

Williams EG*, Wu Y*, Wolski W, Kim JY, Lan J, Hasan M,
Halter C, Jha P, Ryu D, Auwerx J, Aebersold R. Quantifying and Localizing the Mitochondrial Proteome AcrossFive Tissues in A Mouse Population. Mol Cell Proteomics 17, 1766-1777 (2018)
Wu Y*, Williams EG*, Aebersold R. Application of SWATH
Proteomics to Mouse Biology. Curr Protoc Mouse Biol 7,
130-143 (2017) (*co-first author)
Invited presentations
Yibo Wu. “Quantifying and Localizing the Mitochondrial
Proteome” The 91st Annual Meeting of the Japanese
Biochemical Society (Kyoto, Japan) September, 2018

Yibo Wu. “Quantifying and Localizing the Mitochondrial
Proteome” IMS-JSI International Symposium on Immunology (Tokyo, Japan) June, 2018
Yibo Wu. “Quantifying and Localizing the Mitochondrial
Proteome” Conference on Mass Spectrometry and Proteomics (Osaka, Japan) May, 2018
Yibo Wu. “Systems proteomics of liver mitochondrial
activity” 2nd International Symposium of the Kyoto
Biomolecular Mass Spectrometry Society (Kyoto, Japan)
February, 2018
Yibo Wu. “Systems proteomics of liver mitochondrial
activity” The 1st International Symposium for TransOmics (Tokyo, Japan) November, 201762P

roteins are the functional molecules that play an essential role in determining the overall status of a cell or organ. The proteome is extremely multifaceted owing to alternate RNA splicing and posttranslational protein modifications,and this is further amplified by the interconnectivity of proteins into complexes
and signaling networks that are highly divergent in time and space. These physical and chemical properties of proteins and protein complexes make them moredifficult to analyze than their corresponding genes and transcripts. Proteome
analysis relies heavily on mass spectrometry.
Our lab applies state-of-the-art mass spectrometry and computational methods for proteome analysis in complex biological samples. Currently we have two
research topics: one focuses on the proteome changes associated with agingrelated diseases, another focuses on the protein networks established between adipocytes and immune cell populations during the development of obesity. In thefirst study, we analyze bulk tissues as well as isolated immune cell populations at
7 to 8 age time points and look for proteins that are significantly changed during
aging. We aim to identify the causative factors for age-associated defects in eachtissue, e.g., lung and liver. In the second project, we use visceral adipose tissue andisolate the (pre)adipocytes and various types of immune cells, e.g., macrophages,
CD4+ and CD8+ T cells, and B cells, from mice under control and high-fat diets
and analyze their respective proteomes. It has been reported that chronic inflammation is associated with obesity and that the immune cell populations and theiractivation status in the adipose tissue change dramatically during developmentof obesity. However, an omics view of these events is still missing. We expect that
our results will help elucidate the underlying mechanisms of the initial events
during obesity and provide targets to improve obesity immune therapy.

Lab activities

YCI Laboratory for

Metabolic Epigenetics
Young Chief Investigator: Azusa Inoue

Figure: Developmental dynamics of DNA methylation-mediated imprinting and H3K27me3mediated imprinting

H3K27me3 imprinting is established when oocytes,
but not sperm, are formed. Oocyte-derived H3K27me3
resists epigenetic reprogramming after fertilizationand is faithfully maintained during preimplantation
development. When genes with maternal allele-specific
H3K27me3 are expressed, they are expressed from thepaternal allele. At implantation, this imprinting is lost in
the embryonic cell lineage but maintained in the extraembryonic cell lineage that gives rise to the placenta,
etc. This dynamics is different from DNA methylationmediated imprinting, which is lost only in primordial
germ cells.
Recent Major Publications
Inoue A, Chen Z, Yin Q, Zhang Y. Maternal Eed knockout
causes loss of H3K27me3 imprinting and random X
inactivation in the extraembryonic cells. Genes Dev 32,
1525-1536 (2018)

Inoue A, Jiang L, Lu F, Zhang Y. Genomic imprinting ofXist by maternal H3K27me3. Genes Dev 31, 1927-1932(2017)
Inoue A, Jiang L, Lu F, Suzuki T, Zhang Y. Maternal
H3K27me3 controls DNA methylation-independent
imprinting. Nature 547, 419-424 (2017)
Invited presentations
Inoue A. “Genomic imprinting by maternal histones” The
9th meeting of Japanese Society for Quantitative Biology (Osaka, Japan) January, 2019

Inoue A. “Genomic imprinting by maternal histones” The
36th Annual Meeting of Japan Society of Fertilization
and Implantation (Chiba, Japan) July, 2018
Inoue A. “Genomic imprinting by maternal histones” The16th Stem Cell Research Symposium (Fukuoka, Japan)
June, 2018
Inoue A. “Genomic imprinting by maternal histones” The12th Japanese Epigenetic Symposium (Sapporo, Japan)
May, 2018
Inoue A. “The zygote world –Epigenetic reprogramming& Genomic imprinting–” Chinese Academy of Sciences
at Beijing (Beijing, China) April, 2018

O

besity is a growing social problem in the modern world and the obese population has been increasing worldwide. Since obesity is associated with anincreased risk of various diseases, including cancer, infertility, heart diseases, andtype 2 diabetes (T2D), and it greatly impacts national healthcare costs, development of preventive medicine for metabolic syndromes has been long awaited. Recently, intergenerational heritability of T2D has received much attention. Genetic
variants and mutations, however, are estimated to account for <30% of the heritability, suggesting the existence of a non-genetic, likely epigenetic, inheritancemechanism. Studies in animal models have suggested that gametes, at least inpart, mediate the inheritance. While significant progress has recently been madeon the mechanisms of sperm-mediated paternal inheritance, almost nothing is
known about the mechanisms of oocyte-mediated maternal inheritance.
Here we challenge the issue of oocyte-mediated inheritance of maternal
metabolic disorders by integrating developmental engineering and low-input
epigenome analysis technologies. The key to intergenerational epigenetic inheritance is resistance to epigenetic reprogramming that takes place after fertilization.
Namely, while most of epigenetic information in gametes is erased after fertilization, certain genomic loci can resist the reprogramming and carry epigenetic
information into the offspring. Our research has recently identified such locigenome-wide and revealed that a repressive histone modification, H3K27me3,
inherited from oocytes is critical for the resistance in a DNA methylation-independent manner. Consequently, maternally derived H3K27me3 enables maternalallele-specific gene silencing in preimplantation embryos, and this non-canonicalimprinting is maintained in the placenta (Figure, Nature 2017; Genes Dev 2017;
Genes Dev 2018). These results highlight an unexpected link between the oocyte
epigenome and the placenta, giving rise to the hypothesis that changes in the oocyte epigenome could influence the offspring’s metabolic traits via placental dysfunction. We are now trying to test this hypothesis by using a T2D mouse modeland a newly developed mouse model in which H3K27me3-mediated placental
imprinting is defective. In addition, we are trying to understand the functions,
regulatory mechanisms, and evolutional conservation of H3K27me3-mediatedimprinting.

63

Central facilities

Central facilities
C

entral Facilities in IMS provide all researchers in the Centerwith access to the most advanced equipment and technologies. Central Facilities consist of four sections; the FACS Laborato-

ry, the Confocal Laboratory, the Genomics/Proteomics Laboratory,
and the Animal Facility.

FACS Laboratory

The FACS Laboratory provides a range of support for flow
cytometry and cell sorting techniques that are essential fornearly all experiments in immunology, genome research, and disease studies. The Laboratory supports both population and singlecell analysis, and has upgraded all FACS Arias, including an Aria
Fusion for multi-color analyses. In addition to FACS instruments,
the lab possesses a CyTOF2, a mass-spectrometry-based cytometerthat has the potential to analyze more than 30 markers simultaneously with metal-labeled antibodies.
In 2018, 735 analytical and 1366 sorting experiments were
performed in the Laboratory. Two staff members offer various services for users of the FACS equipment (cell analyzers and cell sorters): (1) Technical support and training: In 2018, the facility offered
eight technical courses (four for cell sorting and four for cell analysis). The courses were held at three different levels, Calibur basic,
Canto II, and Aria basic. A total of 50 researchers participated inthese courses in 2018. (2) Cell sorting operation service: The FACS
Laboratory provides a cell sorting operation service, in which re-searchers can ask an experienced operator to conduct the sorting
experiment. In 2018, we provided 155 such services. Advanced
cell sorting techniques, such as single-cell sorting, have also been
performed. (3) Management and maintenance of FACS instruments:
FACS machines are available for registered users around the clock
and reservations are accepted up to one month in advance throughan internal website. In addition to the in-house FACS Laboratory
staff, engineers from Becton Dickinson visit once a week to provide maintenance and technical support.
Table: Instruments and their usage in the FACS Laboratory
Instrument types
FACS cell analyzer

Model

# of
machines

# of
users

# of training
sessions

Calibur

464

2

Canto II

2

735

16

FACS cell sorter

Aria II/III/Fusion

6

1,366

32

Mass cytometer

CyTOF2

1

49

2

Confocal LaboratoryThe Confocal Laboratory provides equipment for cell and tissue imaging and coordinates technical support. There areeight fluorescence microscopes available to researchers at IMS.
1. Inverted Leica SP5 system with a visible laser for single-photon
excitation and a 405 nm violet laser for UV excitation.
2. Inverted Leica SP8 system with two femtosecond Ti:Sa lasers for
multiphoton excitation. This system is equipped with two typesof scanners (resonant and galvano) and hybrid detectors withhigh sensitivity and low background noise. One of the two Ti:Sa
lasers is connected to an optical parametric oscillator (OPO)
that enables two-photon imaging by long wavelength excitation(Photo).
3. Upright Leica SP5 system with two femtosecond Ti:Sa lasers for
multiphoton excitation. This system utilizes resonant scanners
that enable high-speed acquisition of large z-stacks for live tissue imaging.
4. Inverted Olympus FV1200 system with a visible laser for singlephoton excitation.
5. Inverted Nikon N-SIM/N-STORM super-resolution microscope for dual color imaging (Photo).
6. GE Healthcare DeltaVision Elite system (Photo).
7. Keyence BZ-X700 all-in-one fluorescence microscope (Photo).

64

Photo: Leica SP8 multiphoton microscope (2), Nikon N-SIM/N-STORM superresolution microscope (5), GE Healthcare DeltaVision Elite system (6), andKeyence BZ-X700 microscope (7).

Central facilities

Genomics and related activitiesO

ne of the missions of the Laboratory for Integrative Genomics is to serve as a technical support service lab that provides
state-of-the-art genome- and proteome-wide analyses for researchgroups in IMS. We thus offer a variety of services to suit the needsof different labs. These include DNA sequencing, proteomics
analysis, multiplex suspension array, cDNA/genomic clone distribution, and primer/labeled probe distribution for qRT-PCR
analysis of immune cells (Table). In practice, next-generation DNA
sequencing on an Illumina HiSeq2500 (ver4) is supported both by
our laboratory and the Laboratory for Genotyping Development.
We also perform mass spectrometry-based quantitative proteome
analysis using an AB SCIEX TripleTOF 5600. Utilizing this support system, even researchers who are not familiar with such instrumental analyses can easily undertake genomics and proteomics
approaches when necessary.
Besides these support activities for conventional genomics andrelated technologies, it should be noted that IMS strongly encourages collaborations between experts and non-experts in genomics. Because the Division of Genomic Medicine at IMS has many
unique technologies and know-how in transcriptomics and genetics (e.g., CAGE technologies, GWAS, and whole genome sequencing), we expect that the intramural interactions among the Divi-

sions of Human Immunology, Disease Systems Biology, Cancer
Immunology, and Genome Medicine fostered by these technologies will greatly enhance research activities in IMS. In this respect,
the genomics support activity may serve as a gateway to initiate
efficient collaboration among the divisions in IMS.

Table: Central services provided by the Genomics Lab in 2018

Next-generation DNA sequencing
RNA sequencing
ChIP sequencing
Others (Exome etc)

# of samples
2,438
326
1,311

Proteomics# of samples

Mass spectrometry analysis
Multiplex suspension array

41
1,304

Sanger DNA sequencing# of samples

36 cm capillary
50 cm capillary

10,3122,304

cDNA clone delivery# of samples
37

Primer/labeled probe delivery# of samples
21# of teams
21
4
5# of teams
2
7# of teams
13
17# of teams
2# of teams
1

Animal FacilityW

e continue to maintain over 50,000 mice in the SPF areaand 1,500 mice in an isolated area. The SPF area also contains 550 germ-free or gnotobiotic mice in vinyl isolator rooms andin vinyl isolation bio-bubble rooms. The former are used by several
IMS research groups, in particular the mucosal immunologists,
and the latter are for “humanized mice”. We introduce mouse lines
into the SPF area via a combination of in vitro fertilization (IVF)
and embryo transfer methods, and have also generated cryostocks
of genetic resources (frozen embryos and sperms) for 737 lines.
We also maintain relatively large colonies of several commonlyused strains, such as Rag1 KO and Cre deleters, and provide themto users on demand. We have also provided technical assistance togenerate knockout and transgenic mice (54 lines). In addition, we
have made KO and KI mice (53 lines) using the CRISPR/Cas system and have created 21 lines of germ-free mice. We provide spacefor new experiments in the animal facility, e.g., the CRISPR/Cas
system using fertilized egg electroporation (Figure), and behavioral
testing for germ-free mice.

We have generated genetically modified mice to improve theefficacy of transplantation of human hematopoietic stem cells into
NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice by better “humanizing” the host strain. For this purpose, we have introduced large

genomic fragments containing human genes encoding MHC, cytokines, adhesion molecules, virus receptors, and others into the
NSG mice. We maintain such transgenic and knock-in mice withconfirmed expression of human genes on a C57BL/6 backgroundand have begun backcrossing them onto the NSG mouse background using the speed-congenic method.

+
1 mm

10 mm

Figure: Application of the CRISPR/Cas system by electroporation of fertilized eggs

65

Other programs

RIKEN International Program Associate (IPA)I

MS accepted eight international students as RIKEN International Program Associates (IPA). Under this IPA program, IMS
lab heads host international students from collaborating graduate
schools and supervise their Ph.D. program as Joint Supervisors.
The students receive a daily living allowance and housing costs for
up to a maximum of three years.
The IPA students who studied at IMS in 2018 were

Jiahui Ma (Peking University, China) in the Laboratory for Ge-

nome Information Analysis
Yan Jun Lan (ETH Zurich, Switzerland) in the Laboratory for Advanced Genomics Circuit

Shruti Bhagat (Karolinska Institute, Sweden) in the Preventive
Medicine and Applied Genomics Unit
Hsing-Fang Lu (Taipei Medical University, Taiwan) in the Laboratory for Bone and Joint Diseases
Jack Thomas Flanagan (The University of Liverpool, UK) in the
Laboratory for Endocrinology, Metabolism and Kidney Diseases
Michael Boettcher (Bielefeld University, Germany) in the Laboratory for Transcriptome Technology
Mengqian Li (Tokyo Medical and Dental University, from China)
in the Liver Cancer Prevention Research Unit
Daniela Kajihara (University of Sao Paulo, Brazil) in the Laboratory for Transcriptome Technology

RIKEN Junior Research Associate (JRA) ProgramT

he Junior Research Associate Program was launched in 1996
to encourage young scientists with fresh ideas and youthful
enthusiasm to collaborate with, and learn from, senior scientists
with years of experience. This program provides part-time positions at RIKEN for young researchers enrolled in university Ph.D.
programs. The JRA program serves the dual purpose of fostering
the development of these young scientists while also energizing
RIKEN with their innovative thinking.
This year, 24 JRA students studied in IMS.
Yosuke Ito (Preventive Medicine and Applied Genomics Unit)
Junichiro Takano (Laboratory for Developmental Genetics)
Yoshihiro Ito (Laboratory for Skin Homeostasis)
Eiichiro Watanabe (Laboratory for Gut Homeostasis)
Takaaki Kawaguchi (Laboratory for Gut Homeostasis)
Keiko Usui (Laboratory for Skin Homeostasis)
Mamoru Ogawa (Laboratory for Metabolomics)
Hiroki Sugishita (Laboratory for Developmental Genetics)

Hiroe Tetsu (Laboratory for Innate Immune Systems)
Manabu Nagayama (Laboratory for Gut Homeostasis)Ari Morimoto (Laboratory for Skin Homeostasis)
Yuki Ariyasu (Laboratory for Metabolomics)
Shohei Egami (Laboratory for Skin Homeostasis)
Shintaro Ono (Laboratory for Integrative Genomics)
Ryota Sato (Laboratory for Lymphocyte Differentiation)
Kyosuke Shishikura (Laboratory for Metabolomics)
Iori Motoo (Laboratory for Gut Homeostasis)
Tsuyoshi Yamane (Laboratory for Metabolomics)
Naoko Toki (Laboratory for Transcriptome Technology)
Makoto Iwasaki (Laboratory for Human Disease Models)Nao Otomo (Laboratory for Bone and Joint Diseases)
Akiko Oguchi (Laboratory for Transcriptome Technology)
Tomoaki Takahashi (Preventive Medicine and Applied Genom-

ics Unit)

Takahiro Matsunaga (Laboratory for Gut Homeostasis)

RIKEN Special Postdoctoral Researcher (SPDR)
Program

R

IKEN’s Special Postdoctoral Researcher Program was instituted to provide young and creative scientists the opportunity
to be involved in autonomous and independent research in linewith RIKEN objectives and research fields. The positions are competitive, but if selected, researchers receive salaries and researchbudgets (1 million yen) from RIKEN and they are able to conduct
their research at one of its laboratories.
This year, eight postdocs conducted their research at IMS
through the SPDR program.

66

Eiji Miyauchi (Laboratory for Intestinal Ecosystem)
Alexis Vogelzang (Laboratory for Mucosal Immunity)
Keiichiro Shiraga (Laboratory for Skin Homeostasis)
Xiaoxi Liu (Laboratory for Genotyping Development)
Callum Parr (Laboratory for Advanced Genomics Circuit)
Rei Nakano (Laboratory for Cellular Function Conversion Tech-

nology)Tsuyoshi Kiniwa (Laboratory for Innate Immune Systems)
Divya Mundackal Sivaraman (Laboratory for Advanced Genomics Circuit)Part 3
Research
Projects

Projects

The Human Cell Atlas projectO

ur bodies have 37 trillion cells, and for decades, scientists
have been sorting different types of cells, such as neurons,skin cells, liver cells, and tumors, in bulk. With this ‘averaged’ profiling, it is impossible to know which cells express particular genes,
making it challenging to fully understand diseases and develop effective and safe treatments for them. Now, new and powerful DNA
sequencing methods have emerged and they are finally allowing
us to determine which genes are expressed at single-cell resolution
across the entire human body.
To tackle this enormous yet meaningful challenge, an international team called the Human Cell Atlas (HCA) consortium wasrecently established, coming together to build an open “Google
Map of the human body”. The goal of the HCA is creating effective
diagnostics based on very precise molecular information on all thecells in the body. In the context of tumors, we expect to identify all
the key genes and cells and how they are related to each other, providing clinicians with a more precise understanding of the disease
and drug response status.
At RIKEN IMS, we are deploying a 5’-based single-cell genomics strategy to uncover gene regulatory mechanisms and bio-

markers of both coding and non-coding RNAs. Particularly, the5’-approach captures enhancer-derived RNAs that guide us to theprecise location of disease-associated regulatory elements. Building the Human Cell Atlas in Japan is necessary to provide a more
precise map of local genetics and environment. By focusing on themost relevant diseases, this approach will catapult effective healthcare for the Japanese people.
For this effort, RIKEN IMS is engaging with medical institutions across Japan to collect and process human samples to elucidate the mechanisms of health and disease. We envisage thatsingle-cell medical network in Japan will accelerate local researchand innovation, and initiate new engagements with industries (bothlife sciences and technologies) to positively impact the health andeconomy of Japan.
(A)(B)
Niigata
University(A) RIKEN is collaborating with various medical institutions in Japan to collect humansamples. (B) RIKEN will work with the global Human Cell Atlas to create the reference
map. (C) Samples from medical institutions will be processed by RIKEN using singlecell profiling techniques. Individual analysis will be processed and returned to sample
providers and integrative genomic analysis will be performed to construct a global mapof promoters and enhancers at single-cell resolution.

University of Tokyo
Toranomon Hospital

Keio University
National Cancer
Center

Ehime
University

Chiba University

Osaka
University

Figure. The Single Cell Medical Network in Japan   (C)

St. Marianna
Hospital
Kyoto University

Medical Institutions
Organ
donor

NRIKEN

Biopsies
5’5’5’5’-+ Post-mortem tissues+ Organoids/iPSC

5’5’5’5’-5’5’5’5’-Single cell
proﬁling

Imaging

Medical Single Cell
Database

Integrative Genomic
Analysis

Individual analysis

FANTOMT

he FANTOM project started in the year 2000 with a meeting,where it was decided to embark on an ambitious mission toannotate the function of mammalian genes by the analysis of fulllength cDNA collections. FANTOM has evolved over the years
through deciphering genomic regulatory elements and networks
that control the function of the genome. During the past 19 years,
we (1) constructed comprehensive catalogues of annotated protein coding genes, (2) found that the majority of the output of the
genome consists of lncRNAs, (3) comprehensively annotated promoters and enhancers and provided the most comprehensive mapof them, and (4) inferred the regulation of regulatory elements,
such as promoters, enhancers, and lncRNAs. These achievements
were made possible by international collaborative efforts, and thecurrent project, FANTOM6, includes more than 250 researchers
from over 60 research organizations.
The lncRNA collection produced by FANTOM5 has accurate
5’-end data, which allowed us to reliably recount the number oflncRNAs in mammalian cells. We estimated that at least 29,000
lncRNAs exist and inferred 19,175 potentially functional human
lncRNAs, either by examining conservation of promoters/exons,
overlap with GWAS or implication in eQTL databases (Hon et al,
Nature 2017). Currently, more than 96% of lncRNAs have no refer-

68

Photo: FANTOM6 NATSU Meeting (Aug 31-Sep 1, 2017)ence in PubMed (De Hoon et al. Mamm. Genome 2015), discouraging further investigation into their biology. To overcome thislimitation, FANTOM6 proposes to broadly screen for the functionof lncRNAs. We believe that a substantial fraction of the identified
lncRNAs will be revealed to have some sort of function.

Projects

Human genome analysis

In 2015, the Japanese government established priority disease
areas for the implementation of genomic information for actual
medical practice. Rare (hereditary) diseases, cancer, dementia,
infectious diseases, and pharmacogenomics were selected as thefirst priority areas because they were thought to be very close tobeing amenable to successful implementation of findings frombasic research. Common multifactorial diseases such as diabetes
and cardiovascular disease were positioned as the second priority
disease areas, because they need further basic genomic research toprecisely elucidate the relationships between genetic variants anddiseases.
Different laboratories in IMS have analyzed various diseases
by genome-wide association study and/or targeted- and wholegenome sequencing-based association studies: cancer (Momozawa& Nakagawa), pharmacogenomics (Mushiroda), bone & joint
diseases (Ikegawa), diabetes (Horikoshi), cardiovascular diseases(Ito), autoimmune diseases (Yamamoto K), and integrated analysisof all common diseases (Kamatani). In addition, we integrated
our results with knowledge of non-coding regions and single-cellsequencing approaches being done by laboratories for the FANTOM and Human Cell Atlas projects to better understand thedisease biology. We also have collaborations with large Japanesecohorts (BioBank Japan, Tohoku Medical Megabank, Japan MultiInstitutional Collaborative Cohort Study, and Japan Public HealthCenter-based Prospective Study) and various domestic and international universities, academic institutes, hospitals, and companies
to implement personalized medicine.

Figure: Genomic analyses reveal cell-type specific networks of complex
traitsSEAPharm for establishment of stratified medicine
in AsiaIt has been noticed that severe cutaneous adverse drug reactions (ADRs), including Stevens-Johnson syndrome (SJS) andtoxic epidermal necrolysis (TEN), occur at a considerably highfrequency in Asian populations. In the case of the anti-epileptic
drug carbamazepine, the US FDA now recommends preemptive
HLA-B*15:02 genetic screening for Han Chinese and other Asian
populations with a high prevalence of this allele, which is associated with SJS-TEN caused by carbamazepine therapy. To tackle thisproblem regionally, in 2012 we established the South East Asian
Pharmacogenomics Research Network (SEAPharm) together withfive other Asian countries (Korea, Indonesia, Malaysia, Taiwan,
and Thailand). Membership has been steadily increasing, with
Singapore joining in 2014, Vietnam in 2016, and Nepal, Laos, and
the Philippines in 2017. This year, SEAPharm has two newcomers,
Brunei and Myanmar, on the team.
The aims of the collaboration are to identify genomic biomarkers associated with ADRs, such as skin rash induced by antiepileptic drugs and antibiotics and hepatic injury induced by anti-

tuberculosis drugs, to provide technical assistance and training ofyoung researchers from the SEAPharm member countries, and to
hold international seminars and workshops. Recently, SEAPharm
has started a new project involving next-generation sequencing of
1,500 genomic DNA samples from 10 countries to clarify the genetic diversity of drug-metabolizing enzymes and drug transporters in individuals from Southeast Asia, Sothern Asia, Middle East,and Southern Europe. The discoveries from these collaborative efforts will lead to the establishment of stratified medicine based on
genotype-guided drug therapies.

Nepal – Swacon

International Hospital

Please visit http://www.pharmagtc.org/seapharm/index.php

Korea – Inje University
Taiwan – Academia Sinica
Laos – National Institute of Public HealthVietnam – Ho Chi Minh City International University
Philippines – University of Philippines Manila

Myanmar – Defence Services
Medical Research Centre

Figure: Members of the South East Asian Pharmacogenomics Research Network (SEAPharm)

RIKEN Center for
Integrative Medical Sciences (IMS)Brunei – Universiti Brunei Darussalam
Malaysia – University of Malaya

Thailand –Department of Medical Sciences,
Mahidol University,
Khon Kaen University,
Chulalongkorn University,
Thailand Center of Excellence
for Life Sciences (TCELS)

Singapore –Genome Instituteof Singapore (GIS)

Indonesia – YARSI University

69

Projects

International Cancer Genome Consortium (ICGC)
and PCAWG
Laboratory for Cancer Genomics

Laboratory for Medical Science Mathematics

The ICGC was established in 2007, and concluded its mission
to define the genomes of 25,000 primary untreated cancers(the 25K Initiative) in May 2018. The ICGC solved numerous data
governance, ethical and logistical challenges to make global genomic data sharing for cancer a reality, providing the international
community with comprehensive genomic data for many cancer
types. As the second ICGC initiative, the ICGC launched a “PanCancer” Whole Genome project (PCAWG) in 2014, in which
WGS data together with RNA-Seq of 2834 donors were analyzed
in uniform pipelines within the same computational environmentand cloud computing. RIKEN and IMUT (The Institute of Medical
Sciences, The University of Tokyo) are contributing to this project
as a member of a technical working group arranging ten cloud data
centers and PI/researchers in working groups for driver gene, mutational signature, germline, immuno-genomics, and mitochondrial genomics. RIKEN provided WGS data from 270 liver cancers
to the PCAWG (10% of the total), making us the most productive
group within the ICGC. In 2018, as a PCAWG-15 working group,

RIKEN and IMUT analyzed the immuno-genomic landscape fromPCAWG data, including mutations in HLAs and immune suppressor genes, neo-antigen profiles, and immune micro-environmental
signatures, and observed that tumors acquired many types of
immune escape mechanisms. As a PCAWG-10 working group,
RIKEN also analyzed PCAWG WGS data for genome-wide somatic mutations in microsatellite or repeat regions, one of the mostdifficult regions to analyze by NGS, and defined microsatellite
instability (MSI) cancers at a genome-wide level. They also identified highly mutated microsatellites that can be used to detect MSI
cancers with high sensitivity.

Figure: Mutation rate of 7M microsatellite regions in each type of cancer.

CR (colorectal), ST (stomach), and UT (Uterine) cancers showed a higher mutation rate(>0.3% of 7M) in microsatellite regions, indicating microsatellite instability (MSI).

eQTL project
Integration of genetic information and immune functions

R

ecently, many disease susceptibility variants have been identified by genome-wide association study (GWAS). Germline
genetic variations provide us with evidence into the causal relationship of an observed phenomenon and its pathogenesis. In thisregard, the majority of GWAS risk variants have been found tofunction as an expression quantitative trait locus (eQTL), regulating the expression levels of genes. Therefore, using genomic information, qualitative and quantitative analyses of transcriptomes
together with epigenomes, we will better understand the pathogenic components of immunocompetent cells in various immunemediated diseases.
We are now using a system to obtain various subtypes of leukocytes from peripheral blood mononuclear cells (PBMCs) fromhealthy individuals in order to obtain the utmost unbiased relationship between genotypes and gene expression. Cell separationis performed using fluorescence-activated cell sorting into about
20 different subsets. Cells are then analyzed in the steady state orunder stimulated conditions, such as with combinations of cytokines and cell surface receptor agonists to capture the dynamic responses of gene regulation. As the first step, genotyping as well as
RNA-seq are performed. Subsequently, we also perform epigenetic

Figure: Integration of genetic information and immune functions: The eQTL
project

70

analyses, specifically focusing on enhancers and promoters, as well
as long non-coding RNAs. We believe that cap analysis of gene expression (CAGE), assay for transposase-accessible chromatin using
sequencing (ATAC-seq), and analysis of several histone marks foreach subset will be powerful tools for identifying the causal relationship between genetic variation and gene expression.

Exact sites
for enhancers, promotors
and lncRNAs
Exact sites of risk SNPs
Epigenome conditions
Chromatin states

Fine mechanisms of
immunological reactionsin immune‐mediated diseases
and therapeutic strategies

Projects

Search for gut microbiota-associated biomarkers
involved in the pathogenesis of T2DT

2D is a highly prevalent metabolic disease worldwide, including in Japan. It has been estimated that approximately
20 million Japanese, as many as 1 out of 5 individuals, suffer fromdiabetic or prediabetic (medically defined as glucose intolerance)
conditions. Therefore, prevention of T2D is an urgent need bothsocially and economically. To identify T2D-preventive biomarkers
or factors involved in the pathogenesis of T2D, individuals withglucose intolerance should be carefully analyzed, instead of alreadydiagnosed and treated T2D patients. To this end, as an IMS center
project, we have been collaborating with the University of Tokyo
Hospital and recruited three groups (n = 100 each) of volunteers
from those undergoing a complete medical checkup: 1) no abnormal examination outcome (control), 2) obesity (BMI ≥ 25), and 3)
glucose intolerance (fasting blood glucose ≥ 110 mg/dl and HbA1c≥ 6.0%) (Fig). In addition to the thorough clinical examination
data taken during the medical checkup, the following have beencollected in RIKEN: fecal metagenomic and metabolomic data,
plasma and urine metabolomic data, CAGE-based RNAseq data of
peripheral blood mononuclear cells, and whole genome sequencing data. We are also collecting nutritional and physical activity

data using a brief self-administered diet history questionnaire andaccelerometry, respectively.
Correlation analysis of clinical data with fecal metabolome andmicrobiome data has revealed that insulin resistance and metabolic
syndrome are significantly associated with particular sugar derivatives, as are certain bacteria belonging to the family Lachnospiraceae among gut microbes.

Normal

Obese

n=107

n=99

Clinical data
ü Insulin resistance (HOMA-IR)
ü Metabolic syndrome (MetS)ü Fatty liver (NAFLD)

Impaired glucose tolerance
n=100
Multi-omics data
ü Gut microbiome
ü Fecal metabolomeü Serum metabolome

Correlation
analysis

Insulinsensitive

Fecal metabolite clusters+++ +++ +++ +++ ++++++ +++ +++ +++ ++++++ +++ +++++ +++ +++ + +++ ++ ++ + ++++++ + ++
+ ++
++ ++
+++ +
++
+ +
+++ ++ +++ +++ +++
++ ++
+

+
++

+

+++ +++ +++++ +++ +++ + +++ ++ ++ + ++++++ + ++
+ ++
++ ++
+++ +

FBG

HbA1c

LDL

SBP

HDL

ALT

TG

GGTP

HOMAIR

HOMAIRMetS
NAFLD

0.4 NAFLD+ ++ ME05#05: Monosaccharides,
amino sugars
ME06#06: Monosaccharides,
1 uronic acids++ ME08#08: Short-chain fatty acids
0
+++
ME03
#03: Amino 0.2
acid derivatives++
ME12#12: Purine derivatives−1+++ ++ ME09
#09: Amino acid derivatives+ + ME17#17: Miscellaneous
MetS
ME19
#19: Sugar 0alcohol+
ME18#18: Miscellaneous 1
ME07#07: Pyrimidine derivatives
0
ME10#10: Monosaccharides−1 and amino acid derivatives−0.2+++ +++ ME01
#01: Monocarboxylic acid
ME04
#04: Monocarboxylic acid derivatives
HOMAIR ketone bodies+ ME13#13: TCA cycle derivatives,+++
ME15#15: Miscellaneous1−0.4+++ + ME16
#16: Amino acid derivatives
0Z-score+ ME11#11: Amino acid derivatives+++ ++ ME02
#02: Amino acids−1
0.4 NAFLD+++ +++ +++ +++ ++++ ++ ME05++ +++
ME14#14:+++ ++++++Amino+++ +++acid derivatives ME06
1

++
+ +
+++ ++ +++ +++ +++
++ ++
+

+

FBG

HbA1c

LDL

SBP

HDL

ALT

TG

HOMAIR

HOMAIRMetS
NAFLD

The data in the bottom part of the figure are examples of fecal metabolome analyses.

GGTP

Figure: Correlating clinical and multi-omics data to identify biomarkers
involved in the pathogenesis of type 2 diabetes mellitus.

+++++ ME08
ME03
+++
ME12
++
+++ ++ ME09
+ + ME17
ME19
ME18
+
ME07
ME10
+++ +++ ME01
ME04
+ ME13ME15++++++ + ME16
+ ME11+++ ++ ME02++ +++ ME14

0.2

0
−1

Arabinose

Galacturonic acid

GlucoseGlucuronic acidRhamnose

Faecalibacterium

LyxoseFucoseAlloseXyloseAlistipes
Parabacteroides

SorboseMannoseN-Acetylmannosamine

Dorea

Blautia

Flavonifractor

Collinsella
Coprococcus

Galactose

Tagatose

Fructose

Arabinose

Galacturonic acid

GlucoseGlucuronic acidRhamnose

Faecalibacterium

LyxoseFucoseAlloseXyloseAlistipes
Parabacteroides

Sorbose

MetS
1
0
−1
−0.2

Subdoligranulum

Bacteroides
Lachnospira

Glucosamine

Insulinresistant0−0.4

Galactose

Tagatose

Fructose

MannoseN-Acetylmannosamine

Lachnospira

Glucosamine
Dorea

HOMAIR1
0−1

Subdoligranulum

Bacteroides

Blautia

Flavonifractor

Collinsella
Coprococcus

Medical Sciences Innovation Hub Program (MIH)W

e aimed to establish a pipeline for the modeling of pathogenetic processes of human diseases to facilitate discoveryof biomarkers and potential targets for therapeutic intervention.
Our strategy is to combine the comprehensive study of diseasemodel animals with multimodal data derived from patients. It istherefore necessary to gather, integrate, and analyze clinical data
and multimodal data from patient-derived materials. To initiate
this process, we have chosen atopic dermatitis (AD) as a model togenerate a platform for data collection and integration, and performed a comprehensive study to stratify AD patients based on
endophenotypes in collaboration with the RIKEN Medical Innovation Hub (RIKEN-MIH) program and Keio University Hospital.
Within this framework, we have so far collected transcriptomic
and histological data of skin tissue from approximately 60 AD patients and 25 healthy controls and will ultimately collect 200 and
50 samples from patients and healthy donors, respectively. These
data are stored in a fully isolated server installed in RIKEN-MIH
and are being integrated to facilitate our mathematical challenge

for patient stratification. This collaboration with RIKEN-MIH andexternal university hospitals will be continued and even expanded
to establish a seamless pipeline to collect, analyze, and store patient-derived materials and information in RIKEN.

Atopic dermatitis（58 patients, 121 samples）
Cluster１

Cluster２ Cluster３

Lesional skin sample

Cluster４

Healthy Control（26 persons, 26 samples）

Non-lesional skin sample

Figure: Unsupervised clustering analysis of skin transcriptomic data identifies four clusters of AD patients.

71

Projects

iPS projectVα24+iNKT cell-mediated head and neck cancer immunotherapy.
Differences in human leukocyte antigen class I (HLA-I) genes
can cause rejection in an allogeneic transplantation situation. To
address this concern, this year, the facility aimed to prepare Beta2-Microgloblin (B2M) gene-disrupted human iPS-Vα24+iNKT cells
using CRISPR/Cas9 and then they observed a distinct reduction inalloreactive CD8+ T cell-mediated killing (Figure 1). These results
suggest that B2M-disrupted iPS-Vα24+iNKT cells will be more
useful in allogeneic transplantation due to their longer half-life.
(A)

B2M KOHLA-ABCWTTCR Va24(B)

WT

B2M KOTCR Vb11

I

nduced pluripotent stem (iPS) cells possess tremendous therapeutic potential in many areas, including regenerative medicine and immune therapy. We have begun an activity to apply iPS
technology to both mouse and human immunology research andto develop therapeutics. On a collaborative basis with individual
RCAI-IMS research laboratories, the core facility for iPS researchis engaged in developing efficient protocols to reprogram various
types of lymphocytes into iPS cells, as well as to induce differentiation of iPS cells into a variety of lymphoid lineage cells. This activity is partly supported by the Research Center Network for Realization of Regenerative Medicine from the Japan Agency for Medical
Research and Development (AMED) and CREST, Japan Scienceand Technology Agency.
The facility has operated an IMS Cell Manufacturing Unit
(CMU) to produce iPS-Vα24 +iNKT cells under GMP (GoodManufacturing Practice)/GCTP (Good Gene, Cellular, and Tissuebased Products Manufacturing Practice) guidelines. The safety ofthese iPS-Vα24+iNKT cells was confirmed by preclinical studies.
The facility has been finishing PMDA (Pharmaceuticals and Medical Devices Agency) consultation for eventual clinical trials of iPS-TCR Va24

Figure: Minimization of alloreactive CD8+ T cell-mediated killing of HLAclass I depleted iPS-Vα24+iNKT cells in vitro.

(C)

60

Ratio % (Va24+/Vb11+ cells)(A) A representative flow cytometry plot of B2M-disrupted iPS-Vα24+iNKT cells(B2M KO) showing lack of cell surface expression of MHC class I. Wild type (WT) iPSVα24+iNKT cells are shown as a control. (B) A representative flow cytometry plot of acytotoxic assay of alloreactive CD8+ T cells against B2M KO or WT iPS-Vα24+iNKT cells
after 96 hours. The alloreactive CD8+ T cells were prepared from healthy donor-derived
PBMC, and they were cultured with B2M KO or WT iPS-Vα24+iNKT cells and analyzed
by flow cytometry. (C) Time-course analysis of B2M KO or WT iPS-Vα24+iNKT cells in acytotoxic assay of alloreactive CD8+ T cells. The frequency of the Vα24+iNKT cell specific
TCR (Vα24+ and Vβ11+) cells was calculated at the indicated time points.

50
40
30
20

B2M

10

WT

0

0h

24h

48h

96h

Humanized mouseWe have been developing “humanized mice” to study normal
human hematopoiesis and immunity as well as humanhematologic malignancies. When we transplanted purified humanhematopoietic stem/progenitor cells, we could detect multiple
human immune subsets in thymus, bone marrow, spleen, and intestinal mucosa. Therefore, the in vivo system is valuable to understand how stem/progenitor cells determine their in vivo fate andto what extent human immune cells are functional in each organ.
Using human immune cells and leukemic cells of humanized miceand those of human individuals, we have been taking a multiomics approach to measure expression of biologically relevant mol-ecules. By comparing normal and leukemic cells of human origin,
we aim to find therapeutic targets that are specifically expressed byleukemic cells. Through multi-faceted analyses, we hope to create
therapeutic modalities for poor prognosis leukemia and to find key
molecules determining stemness in human hematopoiesis.

Patients

Healthy donors

Clinical application
Hospital

Blood Bank

Basic understanding
Cell sorting
PBMC/BM

Understanding heterogeneity ofhuman systems and diseases

Figure: Connecting human blood/immune cell biology with multi-omics

Peripheral blood mononuclear cells (PBMCs), bone marrow cells, or cord blood are isolated from patients or healthy donors for creating mice recapitulating patient leukemic
status or reconstituting normal human blood/immune systems. The generated “humanized mice” have enabled us to study in vivo blood/immune cell behavior. Multi-omics
approaches and machine leaning also pave the way for a comprehensive analysis of thecellular heterogeneity of human hematopoiesis and drug development for leukemia.

72

Humanized mice
Pre-leukemic

Genomics

Leukemia

Epigenomics

Immune cells

Proteomics

Machine Learning & Bioinformatics

Connecting biology & omics

Projects

Cancer immunologyWe regard cancer immunology as an interdisciplinary branchof immunology, since cancer represents a failure of homeostasis of the immune system, involving many components. The
first goal of cancer immunology is to understand the role of immune system immunoediting in the development and progressionof cancer. An understanding of this process will lead to the stratification of cancer diseases by identification of the target molecules
or antigens for immune recognition of cancer. Several groups initiated the cancer immunology theme. Ishikawa’s and Fujii’s groups
recently demonstrated the important function of T cell subsets
and NKT/NK cells, respectively, in the regulation of progression ofsome cancers. The second goal of the cancer immunology group is
to develop a cancer immunotherapy strategy to treat cancer by enhancing the host protective response. We have several translational
research projects aiming at application of NKT cell therapy, including iPS-NKT and aAVC therapy. Among them, Koseki’s group has
almost completed an iPS-NKT cell preclinical trial. Fujii’s group
has launched a Phase I clinical trial of aAVC-WT1 therapy in acute
myeloid leukemia. These projects have been supported partly by

the Japan Agency for Medical Research and Development (AMED)
as well as the RIKEN Drug Discovery and Medical Technology
Platforms (DMP). In addition, as a clinical study, Fujii’s group has
been collaborating with 15 National Hospital Organization (NHO)
hospitals using autologous iNKT cell ligand-loaded DC therapy ina randomized phase IIa trial in early-stage lung cancer patients. In
this study, they have been performing immunological analyses ofthe patients.

New NKT
cell ligands(clinical
phase)

aAVC
therapy for
AML(Phase I)

Figure: NKT cell-mediated anti-cancer projects in IMS as translational research

Development ofanti‐cancer NKT
cell‐mediatedtherapy

iPS‐NKTfor Headand Neck
Cancer(preclinical)

DC/Galtherapy forlung cancer(Phase IIa)

We have four NKT cell-mediated anti-cancer projects underway. Three are cancer
therapy translational research projects and the fourth is the analysis of the patients in
the Phase II clinical study. All have progressed in this fiscal year.

Linkage to RIKEN Program for Drug Discovery andMedical Technology Platforms (DMP)I

MS collaborates with DMP to develop innovative new pharmaceuticals and medical technologies by facilitating the transfer ofbasic research within the institute. DMP was founded in RIKEN in2010 in order to support all phases of development of new therapeutics, from the discovery of promising targets to the identification of potential lead compounds, such as small molecules andantibodies, and the acquisition of intellectual property rights to
drugs and technologies that can then be brought to the development phase.
To achieve effective progress in this area, DMP established nine
Drug Discovery Basic Units, in which the types of studies being
performed are organized according to the expertise of each PI. IMS
contributes to this effort in several ways, including by setting up afacility for the development of antibody drugs, the Drug Discovery
Antibody Platform Unit. In addition, IMS now has seven collaborative programs with DMP: artificial adjuvant vector cells (Shinichiro Fujii), cancer therapy with iPS-derived NKT cells (Haruhiko
Koseki), cancer therapy with NKT cells (Hiroshi Ohno), drugs forallergic diseases (Masato Kubo), leukemia treatment mAb target-

ing leukemic stem cells (Fumihiko Ishikawa), neutralizing mAb for
HBV infection (Daiki Miki), and therapeutic mAb for IBD (Takashi
Saito). The preclinical study of the artificial adjuvant vector cellproject for cancer therapy has been completed and, therefore, Fujii
et al. are preparing for an investigator-initiated clinical trial.

identification& validationof targets

Seed/Lead
identification

Lead
optimizationpreclinicalpreclinicaldevelopment

clinicaldevelopment

1. Artificial adjuvant vector cells
2. Cancer therapy with iPS-derived
NKT cells
3. Cancer therapy with NKT cells
4. Drugs for allergic diseases
5. mAb targeting leukemic stem cells
6. A novel inhibitor for HBV infection
7. Ab drugs for IBD
In collaboration with pharmaceutical companies

Figure: Collaboration between IMS and DMP for the development of innovative new pharmaceuticals and medical technologies

73Obituary

In memory of Dr. Kimishige Ishizaka(Dec 3, 1925-Jul 6, 2018)

Photo: Dr. Kimishige Ishizaka(at the celebration party of his 80th birthday in 2006)

D

r. Kimishige Ishizaka passed away at 7:58 am on July 6th,2018. Dr. Ishizaka was born on December 3rd, 1925 and hewould have turned 93 years old in December of this year. He mademany invaluable contributions to the development of our research
center, RIKEN Center for Integrative Medical Sciences (IMS). Beginning in 2001, he was the Senior Advisor of our former Center,
RIKEN Research Center for Allergy and Immunology, and heldthat position for twelve years.
Dr. Ishizaka and his wife, Teruko, conducted their research in
the US for over 35 years and made several important discoveries
during that period, including the discovery of the long-elusive IgE
antibody isotype, which elicits allergic reactions. Dr. Ishizaka held
positions as Director of the Immunology Department at Johns
Hopkins University School of Medicine, President of La Jolla Institute of Allergy and Immunology (LJI), President of the American
Association of Immunologists, and Adjunct Professor at the University of California, San Diego. After his return to Japan, his presence at our research center as the Senior Advisor was an inspiration and helped us pull together for the Center’s research projects.
LJI and IMS, the two research institutions that Dr. Ishizaka supported during their establishment, continue to collaborate with thegoal of overcoming immune-related diseases. The collaborating
laboratory, led by Dr. Hilde Cheroutre, has been actively working
at IMS to understand the gut mucosal immune system.
Allergy continues to be one of the most important research topics in our Center. From the large-scale ENU mutagenesis project,launched in 2001, we successfully isolated an atopic dermatitis
mouse model, named the Spade mouse. Using this mouse model,
multiple laboratories in the Center and clinical dermatologists
at university hospitals collaborate for the elucidation of atopic
dermatitis pathogenesis. IMS allergy research has expanded to become a multidisciplinary project involving immunology, genomics,
epigenetics, neuroscience, informatics, and clinical medicine. In
addition, young researchers are pioneering new concepts for the
regulation of asthma and other allergic diseases by the innate immune system.
The scientific discoveries that Dr. Ishizaka left us, and his strict
but collaborative attitude toward science, will continue to remainin our hearts and inspire us forever.
Tadashi Yamamoto
Director,
RIKEN Center for Integrative Medical SciencesDr. Kimishige Ishizaka was an invaluable mentor for themembers of the RIKEN Center for Allergy and Immunology(RCAI), currently restructured as the RIKEN Center for Integrative Medical Sciences (IMS).
Approaching the end of the year in 2000, I received a facsimile
message on December 29th. It was announcing that the establishment of a research center for allergy and immunology had been
approved in the government budget for 2001, Dr. Ishizaka was appointed as the chairman of the establishment committee, and heasked me to cooperate for the creation of a basic research institution to contribute to allergy and immune regulation fields. Later,74

the President of RIKEN appointed me as the Director of the Centerand Dr. Ishizaka as the Senior Advisor. Thus, Japan’s first research
institution dedicated to allergy and immunology was founded withthe support of 300 million yen from the government. This could
not have been realized without Dr. Ishizaka.
In 1966, at the Children’s Asthma Research Institute and Hospital in Denver, Colorado, Dr. Ishizaka and his wife, Dr. Teruko
Ishizaka, discovered a novel antibody isotype that was associatedwith allergy (so-called “reagins”). At that time, researchers could
not isolate reagins by immunoprecipitation or other biochemical
techniques, and the nature of reagins had remained a mystery for
40 years. However, Dr. Ishizaka predicted the existence of extremely low concentrations of reagins in the “IgA fraction” of serum, bydemonstrating that reagin activity in the IgA fraction remained thesame after IgA neutralization. The only way to prove his hypothesis was to monitor the existence of reagin by intradermal tests.
After moving to the Children’s Asthma Research Institute andHospital in Denver, Dr. Ishizaka and his wife Teruko identified
reagins from a truck-load of atopic patients’ serum by using an intradermal test on the skin of their own backs to monitor the reagin
activity during purification. Further, by using radioisotope-labeled
antigens, they finally detected reaginic antibody by agarose-gel
immuoelectrophoresis. They named this novel class of immunoglobulin, IgE, which was unique from the already known immunoglobulins, IgG, IgM, IgA and IgD.
In 1989, Dr. Ishizaka became the Founding Director of the La
Jolla Institute for Allergy and Immunology (LJI), where he trained
many young investigators. In 1996, the Ishizakas returned to
Teruko’s hometown in Yamagata, Japan, but Teruko was hospitalized because of her illness. Dr. Ishizaka spent his time with Teruko
in her hospital room, but he still managed to attend the Japanese
government’s research council, monthly meeting of The Japan
Academy, research lectures, and Clinical Allergy Strategic Meetings held at the newly established RCAI every month. At RCAI, heparticipated as an active researcher in the development of an allergy vaccine that suppress IgE production.
I strongly believe that Dr. Ishizaka’s research attitude and his
research philosophy will be the best model for young scientists andthe future leaders in immunology.
Masaru Taniguchi
Senior Visiting Scientist,
Program for Drug Discovery and Medical Technology Platforms,
RIKEN Cluster for Science, Technology and Innovation Hub

Part 4
Events

Events

Human Genome Meeting 2018

T

he RIKEN Center for Life Science Technologies (CLST) cohosted the 22nd Human Genome Meeting (HGM) on March
12-15, 2018 at RIKEN’s Yokohama campus and the convention
center, Pacifico Yokohama. Marking the second time for Japan tohost the conference after it was held in Kyoto in 2005, it attracted
460 scientists and other professionals from 39 countries/regions,who presented and discussed a variety of topics related to genome
research.
The meeting, once dedicated to the human genome mapping
project, is now a major annual scientific conference on human genetics and genomics, genomic medicine, and genome biology andis organized by the Human Genome Organization. Dr. Piero Carninci, former deputy director of CLST and now deputy director of
the Center for Integrative Medical Sciences (IMS) chaired the localorganizing committee.
The theme of this year’s meeting was genome data and health.
Topics discussed included genome editing, single-cell biology,
and cancer genomics. RIKEN has played a vital role in the international efforts to sequence the human genome, and continues
to be a major contributor to developing next-generation genome
sequencing technologies, international genome-wide association

studies, and the International HapMap Project, a project to develop a haplotype map of the human genome that will describe thecommon patterns of human genetic variation. RIKEN also leads
the FANTOM project to identify the fundamental roles of the noncoding regions of the genome, including non-coding RNAs.

Japan Prize awarded to Dr. Max D. Cooper

On April 18th, 2018, the Japan Prize* was awarded to Dr. Max
D. Cooper and Dr. Jacques Miller for their discovery of B
and T cell lineages and its impact on understanding normal lymphocyte development and function as well disease pathology andon development of immunotherapeutics.
Dr. Cooper, Professor of Pathology and Laboratory Medicine
at Emory University School of Medicine in Atlanta, Georgia, is
known for his early work on the recognition of T and B lymphocytes as developmentally separate, functionally intertwined celllineages. Other research highlights of Dr. Cooper and his collaborators include the identification of B cell precursors and their
hematopoietic origin, demonstration that IgM-bearing B cells can
switch to produce other classes of antibodies and discovery of analternative adaptive immune system in jawless fish, such as lampreys and hagfish. Dr. Cooper studies immune system evolution,
development and function to gain insight into the pathogenesis ofblood cell malignancies, immune deficiencies, and autoimmune
diseases.
It was a happy surprise and also a big honor for IMS researchers that Dr. Cooper received the Japan Prize, because he has madesignificant contributions to RIKEN, specifically to the former Research Center for Allergy and Immunology (RCAI) and then IMS,
as Chair of the Advisory Council since 2004. He has visited IMS
10 times since 2004 and interacted with and advised many of theresearchers.
On April 23rd, 2018, a commemorative symposium, “Immune
system: the discovery of B/T lymphocytes and more,” was held at
IMS and attended by 110 people. After the opening remarks by

76

Group photo with Dr. Cooper and his wife Rosalie (first row, center)

IMS Director, Dr. Yamamoto, two IMS researchers gave presentations, “Lymphocytes with innate functions” by Dr. Koyasu and “Excessive T cell activation in the absence of PD-1 affects behavior” by
Dr. Fagarasan. After that, Dr. Kuratani from the RIKEN Center for
Biosystems Dynamic Research in Kobe introduced his research onmorphological evolution “Development of cyclostomes and early
evolution of vertebrates,” and then Dr. Cooper gave his special
lecture on “Evolution of T and B cells.” At the closing remarks, Dr.
Taniguchi, former RCAI Director, congratulated Dr. Cooper on
the award and gave special thanks for his long-time contributions
to IMS and RCAI.
*Japan Prize: https://www.japanprize.jp/en/index.html

Events

RIKEN IMS-Stanford ISCBRM Joint Symposium

R

IKEN IMS and the Stanford Institute of Stem Cell Biology
and Regenerative Medicine (ISCBRM) began their collaboration in 2017 when the first joint symposium was held at Stanford.
The second RIKEN IMS-Stanford ISCBRM Joint Symposium,“Bridging Immunology, Stem Cell Biology, and Regenerative
Medicine,” was held May 23-24, 2018, at the RIKEN Yokohama
Campus. The symposium was opened with introductory remarks
from RIKEN IMS Director Tadashi Yamamoto and Stanford ISCBRM Director Irv Weissman. Nine participants from Stanford
attended the symposium and presented their latest research alongwith 11 RIKEN IMS scientists. During the two-day symposium,
four sessions were held covering the topics of cancer immunology, developmental biology, hematopoietic stem cells, single-cell
analysis, and other genomic technologies. Closing remarks weredelivered by Drs. Weissman and Yamamoto, including a special
address by RIKEN Executive Director Shigeo Koyasu. During thecourse of the two days, both one-on-one and group discussions
were held among the participants to talk about ongoing collabora-

tions and the establishment of new ones. The symposium ended
with a closed lunch session at which the members discussed future
directions of the collaboration.

The IMS-JSI International Symposium on
Immunology 2018T

he IMS-JSI International Symposium on Immunology, hosted
by the RIKEN Center for Integrative Medical Sciences (IMS)
in conjunction with the Japanese Society for Immunology (JSI),
was held on June 7-8 at the Ito Hall, Ito International ResearchCenter, the University of Tokyo. The symposium, entitled “Checkpoint in medical science and its technology”, included nineteen
outstanding speakers presenting their research and attracted morethan 350 participants. There were four sessions: (1) Fundamental
aspects of immunology, (2) Functional genomics of lymphocytes,(3) Systems biology, and (4) Cancer immunology/Immunotherapy.
In addition, we invited several young investigators to present theirwork in each session. These broad research topics stimulatedparticipants and led to very active and provocative discussions.
New technologies such as single-cell gene expression profilingand metabolome analysis added a new research layer to this medical science field. Aided by such technologies, we have begun tounderstand better and more deeply the integrative nature of theimmune system and the networks governing immune responses.
Large combined datasets from genetic and epigenetic analyses will
help to explain the origins and features of various human diseases.
Furthermore, we have begun to explore the important connections
between the immune system, environmental factors, and other or-gans and tissues such as the brain and muscle. To our great honor,
we had Professor Tasuku Honjo of Kyoto University speaking inthis symposium about cancer immunotherapy by PD-1 blockade.
We are truly delighted that half a year later he received the 2018
Nobel Prize in Physiology or Medicine.

77Events

ZPM-RIKEN Symposium

R

IKEN and ZPM (Center for Personalized Medicine) in UKT(University Hospital Tübingen) have common interests inlife and medical sciences and are complementary to each otherin several fields. We held the first ZPM-RIKEN symposium on
July 16-17th, 2018, at Tübingen University, Germany. The goal ofthis symposium was to begin to establish international collaborations between these two groups and to exchange information andhuman resources.
At the opening session, Dr. Malek described the 3M Institute(microbiota-mice-mathematics or malignoma-metablome-microbiome) and large-scale patient registration in University Hospital
Tübingen, which can accumulate big health data. There were four
sessions that covered 3M concept research of both sides.
(1) Microbiome and regulation of inflammation
Microbiome, lipidome, and IBD models were discussed.
(2) Data integration and systems biology
Ideas were exchanged on systems medicine, as an expansion ofsystems biology, and the application of machine learning for biomedical data.
(3) Signaling and cancer therapy
Cell-cycle, cell death signaling, immunology, and kinase chemistry for new cancer therapies were discussed.

(4) Imaging and genomic technologies
In vivo imaging for immune cells and lipids, single-cell sequencing, whole genome sequencing, and liquid biopsy sequencing werediscussed.
In the breakout session, each subgroup discussed potential col-laboration projects for each field and an exchange program foryoung researchers or students.
(1) Data integration
The vision of joint systems biology approaches for prediction inpersonalized medicine to develop machine learning-based treatment recommendations was discussed.
(2) Microbiota/Inflammation
Several potential collaboration projects such as gastrointestinal
physiology and lipidomics were discussed.
(3) Signaling and Cancer Imaging
How to utilize various mouse models to develop imaging technologies for cancer and immunology were discussed.
(4) Genomics
As the first potential collaboration topic, the group decided tofocus on a longitudinal single-cell multi-OMICS study of glioma
patients.
In conclusion, this two-day joint symposium was quite productive. We found many topics in common and developed ideas for
future collaborations.

RIKEN-KI-SciLifeLab Symposium 2018T

his symposium series is organized between RIKEN and the
Karolinska Institutet/SciLifeLab in Sweden. The symposium
venue alternates between RIKEN and SciLifeLab. The overall main
goals of the symposia are a) to identify common scientific interests
between RIKEN and SciLifeLab, b) to identify complementaryskills and technologies for collaborations, and c) to encourage theexchange of PhD students and postdocs between RIKEN and SciLifeLab/KI.
Several collaborations between groups at SciLifeLab and RIKEN
started based on initial contacts during one of these symposia.
There are also several examples of PhD students from SciLifeLabvisiting RIKEN for a research stay.
The 5th Joint RIKEN-Karolinska Institutet/SciLifeLab Symposium was held on September 20-21, 2018, in Stockholm withthe title Artificial Intelligence Meets Life Science. Eighteen shortscientific presentations were given for 120 participants on the firstof two days, covering a range of research topics developing andemploying artificial intelligence (AI) at RIKEN, Karolinska Institutet, and SciLifeLab. On the second conference day, around 40 participants discussed their perspectives and the currently perceived

78

challenges in applying AI methods to life science data, including
biomedical data.
The 6th Joint RIKEN-Karolinska Institutet/SciLifeLab Symposium is planned for 2019 in Yokohama.

Events

RIKEN-Luxembourg Joint Symposium and WorkshopOn September 25-26, 2018, the second Joint RIKEN-Luxembourg Symposium and Workshop was held at the Universityof Luxembourg Belval Campus. Members from both RIKEN IMS
and the RIKEN Medical Sciences Innovation Hub Program (MIH)participated in the two-day event along with scientists from the
University of Luxembourg (UL) Luxembourg Centre for Systems
Biomedicine (LCSB) and Life Sciences Research Unit (LSRU), theLuxembourg Institute of Health (LIH), the Integrated BioBank of
Luxembourg (IBBL), the National Public Health Laboratory (LNS)and the Luxembourg National Research Fund (FNR). On the firstday of the symposium, after a brief welcome by Prof. Dr. Stéphane
Pallage, Rector of the University of Luxembourg, a ceremony washeld for the main conference room at the Luxembourg Centre for
Systems Biomedicine to be named the “RIKEN Conference Room.”This was followed by speeches from Ms. Lydia Mutsch, Luxembourg Minister for Health, and Mr. Shigeji Suzuki, the Japanese
Ambassador to Luxembourg. Members from Luxembourg thenbriefly explained their internationalization strategy in healthcare,science, and innovation. Representatives from both countries thenpresented an overview of current collaborations and plans for future expansion. This was followed by three scientific sessions on
the immune system and metabolism in ageing, barrier function
along the microbiome-gut-brain axis, and precision systems biomedicine. On the morning of the second day, the RIKEN members

were given tours of several of the Luxembourg institutes (i.e., LIH,
LNS, IBBL, and LCSB), and, in the afternoon, a joint workshop
was held on establishing a RIKEN Laboratory in Luxembourg
together with representatives from the FNR, Luxinnovation, theLuxembourg Ministry for Health, and the Ministry for Higher
Education and Research. The two-day event concluded with bothparties agreeing to further strengthen their relationship throughthe expansion of research activities, particularly focusing on therole of gut-brain interactions and barrier function in relation toneuro-inflammatory and neurodegenerative conditions, throughthe creation of a RIKEN outpost laboratory in Luxembourg that
could facilitate research stays for Japanese scientists.

Single Cell Symposium

T

he RIKEN Center for Integrative Medical Sciences (IMS) organized the Single Cell Science Symposium 2018 on October
9th, 2018 in Jiji Press Hall, located in Ginza, Tokyo. There wereover 200 attendees and 11 individuals who presented at the meeting.
Single-cell technologies are becoming increasingly important
tools in biological analysis. Complementing average measurements
on bulk populations of cells, single- cell measurements provide afiner-grained picture of complex biology and reveal heterogeneitythat is present in all tissues.
This one-day symposium, first held in 2017, is a series of meetings that address advanced technologies for single-cell analysis
in genomics. This year, the symposium also expanded their topic
coverage to include clinically relevant human tissues and computational approaches for analysis of single-cell data. This meetingbrought together a broad Japanese community of biologists, clinicians, technologists, physicists, computational scientists, software
engineers, and mathematicians who are involved in single-cellbiology and also discussed new projects as part of the Human Cell

Atlas Japan initiative. This community of scientists with diverse
expertise shares the common goal of creating a comprehensive reference map of all human cells as a basis for understanding humanhealth and diagnosing, monitoring, and treating diseases. Theirgoal is to meet the needs of medical communities in Japan. Detailsof the program can be seen at http://www.ims.riken.jp/?p=3539

79

Events

RIKEN - McGill Symposiums

S

ince 2016, the RIKEN IMS and the McGill University Facultyof Medicine have established close interactions to pursue research in the areas of genomics, immunology, and cancer across a
broad range of diseases, with the first comprehensive cooperationagreements/MOUs between the two institutes beginning as earlyas July 2010. The first symposium was held in May 2017 at McGill
University, Montreal, Canada. In 2018, two symposia were held.
The second symposium, “Immunology, Cancer, RNA & Genetics,” took place February 19-20 at the RIKEN Yokohama Campus.
Opening remarks were delivered by Dr. Ichiro Taniuchi, followedby special greetings from RIKEN Executive Director Shigeo
Koyasu and Luci Tremblay, representative from Québec’s Delegate
General in Japan. During the course of the two days, seven sessions covering the topics of infection and immunity, cancer, RNAbiology, and human genomics were held, including one session foryoung scientists. Eleven researchers from McGill University gave
presentations along with an equal number of RIKEN scientists.
The symposium ended with both open general and group discussions to exchange opinions, and a closed discussion for setting
collaborative projects and future planning. The third symposium,“Joint Initiatives in Genomics, Immunology and Cancer,” took
place November 12-13 at McGill University. During the first day,nine RIKEN scientists gave presentations in four sessions covering

the topics of genomic approaches and cohort studies for population health, genome biology and technologies, immunology anddisease, and other methodologies, and one session with talks frompostdoctoral fellows and students. The second day consisted ofa closed discussion session where members from both institutes
discussed potential funding opportunities and topics for further
collaboration, as well as future directions.

RIKEN -Tsinghua Joint SymposiumO

n November 16, 2018, IMS held the fourth RIKEN-Tsinghua
Joint Symposium “Towards the Integration of Basic andHuman Immunology”. There were 11 participants from the Institute for Immunology, Tsinghua University (IITU) in China and10 speakers from Japanese institutions, including 4 from Japanese
universities and 6 from IMS.
In the first session, Kazuhiko Yamamoto (IMS), Yun-Cai Liu(IITU), and Chung Chau Hon (IMS) discussed how recent genetic
and epigenetic studies have impacted contemporary biomedical research. In their talks, they showed examples of genetic andepigenetic regulation of normal immune cell development anddifferentiation, and their relationships with diseases, as well as thepotential involvement of long non-coding RNAs in both processes.
In the following sessions, Toshinori Nakayama (Chiba University) described the newly discovered fibrosis-inducing pathogenicTh2 cells, and he suggested the potential for new treatments offibrosis-induced allergic disorders based on these findings. Wataru
Ise (Osaka University) discussed a new model of germinal center(GC) B cells, in which the stability of contacts between T follicularhelper cells and GC B cells is the key for plasma cell-prone GC cell
formation. Heiichiro Udono (Okayama University) introduced his
recent discovery that metformin, an anti-diabetic drug, activates
CD8 T lymphocytes and shows significant tumor growth inhibition in vivo. Meng Michelle Xu (IITU) explained her discovery ofanti-tumor immunity controlled through an mRNA N6-methyl-

80

adenosine (m6A) methylation program and a new potential target
for anticancer immunotherapy. Finally, Akiharu Kubo (Keio University) introduced his research on skin biology, focusing on thespatiotemporal replacement of tight junctions, a mechanism thatmaintains skin barrier functions.
The second day was reserved for individual discussions among
the researchers. This joint symposium was supported by the JSPSNSFC bilateral program.
In 2019, the IITU-RIKEN Summer Program will be held at Tsinghua University in Beijing, and the fifth Tsinghua-RIKEN Joint
Symposium will be held in 2020. These joint activities will continue to enhance communication between Japan and China in thefield of biomedical sciences.

Events

Harvard Summer School 2018

I

MS offers a summer internship program for undergraduate
students from Harvard University. In this program, students
do a research internship in IMS laboratories, have basic biomedical science lectures given by PIs from IMS and other centers, andattend a Japanese language course. They also participate in the
RIKEN IMS-JSI International Symposium on Immunology. The
participants receive a letter grade from IMS and course credit from
Harvard. In 2018, we accepted four students, Gabriela Pelayo,
Shivani Aggarwal, Terzah Hill, and Eugene Oh, from Harvard University into the summer program, which was held from June 4th toAugust 13th.
Ms. Pelayo conducted her research on the theme of “Understanding in vivo dynamics of human leukemia and immunity” inthe Laboratory for Human Disease Models (Dr. Ishikawa). She
learned gene expression profiling and identified several potential
therapeutic targets for poor-prognosis acute myeloid leukemia. Ms.
Aggarwal studied “Pulmonary localization of ILC2s in asthma” inthe Laboratory for Innate Immune Systems (Dr. Moro). By using cKit-GFP reporter mice, she visualized that ILC2s localize near the
blood vessels with eosinophils under IL-33 stimulation. Ms. Hill
worked on “Dissecting roles of Cbfb2 isoform during immune cell
development” in the Laboratory for Transcriptional Regulation (Dr.
Taniuchi). She learned two techniques for measuring the expres-Photo: from the left in the front row, Director Yamamoto, Ms. Hill, Mr. Oh,
Ms. Aggarwal, and Ms. Pelayo.

sion level of a target protein: immunoblot and FACS analysis. Mr.
Oh studied “Identification of proliferating thymic epithelial cells
essential for preventing onset of autoimmunity” in the Laboratory
for Immune Homeostasis (Dr. Akiyama). He found a novel cellsubset in thymic epithelial cells essential for preventing autoimmunity. During their internships, the students had numerous discussions with IMS researchers, and at the end of the program, theygave oral presentations describing their research results.

International Conference on Innate Lymphoid Cells

T

he 3rd International Conference on Innate Lymphoid Cells(ILC2018) was held from November 29 to December 1,
2018, at the Ito International Research Center of the University ofTokyo under the auspices of RIKEN IMS. Since the discovery ofmultiple subsets of ILCs a decade ago, these cells have establishedthemselves as new and significant players in the field of immunology, contributing to tissue homeostasis as well as defense against
pathogens and inflammatory diseases. We set the theme of theconference as “Towards the next generation” and invited up-andcoming independent researchers, while senior researchers in thefield were asked to be members of the international programcommittee and session chairs. We covered several general topics
on innate lymphocytes, including NKT, MAIT, and γδT cells. We
received over 140 abstracts from 19 countries and welcomed about
300 participants. It was noteworthy that 75% of abstracts and 60%
of participants were from abroad, making the conference truly
international. Throughout the three-day conference, multiple topics, from developmental pathways of innate lymphocytes to theirpathophysiological roles in various diseases, were presented at bothoral and poster sessions and discussed with excitement in a warmand friendly atmosphere. As expected, the younger generation

certainly showed us their potential to contribute to the future development of the ILC research field. The conference was adjourned
after the announcement of the next conference, which will be heldin San Francisco in 2020.
http://www2.convention.co.jp/ilc2018/welcome.html

81Events

IMS Retreat 2018

T

he RIKEN IMS retreat is an annual event where membersof the center meet and share their scientific knowledge andskills. The IMS retreat 2018, the first such event as a newly reformulated center, featured “Team building” as the main theme,
aiming to facilitate new interactions between groups with different backgrounds. Around 230 people including PIs, researchers,
technical staff, and students gathered together on December 14 at
Yokohama Sambo Hall, about 40 minutes’ distance by public transport from the RIKEN Yokohama campus. In team building sessions, 27 teams of 8 members from various positions and with different scientific backgrounds competed against one another in two
group projects. The first was to build the tallest tower in 30 minutes using only newspapers. The winning team successfully built
a tower over 3 meters high, an achievement that was far beyond
the expectations of the organizers. The second group project was abrainstorming exercise to come up with crazy ideas about how tospend 5 quadrillion JPY for happiness and human well-being fora better future. After 50 minutes of discussion, all teams presented
many varieties of unique ideas, such as building a Moon-Earthtower, Global education for future happiness, In vitro reproduction

system, and Inventing a super robot. Finally, the grand prix wasawarded to a group who presented, while singing and dancing, aunique plan to save postdoctoral fellows.
In the afternoon poster session, each lab introduced its research and “Seeds and Needs” in science and technology, aiming
to explore future research collaborations within the new center.
Through their interactions at the retreat, the participants created
new personal exchanges and the event was successfully completed.

Adjunct professorship programs

I

MS collaborates with and accepts graduate students from 8
domestic university graduate schools. There are now a total of
32 adjunct professors/associate professors in IMS (Table), and 61
students studied at IMS in 2018. On September 1st, 2018, IMS helda briefing session on adjunct graduate school programs to provide
an opportunity for students to visit and talk directly with lab leaders and to consider their future directions.

Table: Joint graduate school programs
Graduate Program

Affiliated IMS Investigator

Graduate Program

Affiliated IMS Investigator

Graduate School of Medicine,
Osaka University

Takashi Saito (Visiting Professor),
Takashi Tanaka (Visiting Professor),
Kazuyo Moro (Visiting Professor)

Graduate School of Medical
Life Science,
Yokohama City University

Graduate School of Medicine,
Chiba University

Takashi Saito (Visiting Professor),
Haruhiko Koseki (Visiting Professor),
Hiroshi Ohno (Visiting Professor),
Ichiro Taniuchi (Visiting Professor),
Shin-ichiro Fujii (Visiting Professor),
Fumihiko Ishikawa (Visiting Professor)

Hiroshi Ohno (Visiting Professor),
Makoto Arita (Visiting Professor),
Takaharu Okada (Visiting Professor),
Kazuyo Moro (Visiting Professor),
Piero Carninci (Visiting Professor),
Yukihide Momozawa (Visiting Professor),
Hideya Kawaji (Visiting Associate Professor),
Hidehiro Fukuyama (Visiting Associate Professor)

Research Instituteof Biological Sciences,
Tokyo University of Science

Masato Kubo (Professor),
Takashi Saito (Visiting Professor)

Graduate School of Medicine,
Kyoto University

Fumihiko Ishikawa (Visiting Associate Professor)

Graduate School of Medicine,
Keio University

Masayuki Amagai (Professor),
Kenya Honda (Professor),
Shigeo Koyasu (Visiting Professor),
Haruhiko Koseki (Visiting Professor)

Graduate School of Medical
and Dental Sciences,
Tokyo Medical and
Dental University

Ichiro Taniuchi (Visiting Professor),
Soichi Kojima (Visiting Professor)

Graduate School of Medicine,
Yokohama City University

Shiro Ikegawa (Visiting Professor)
Hidewaki Nakagawa (Visiting Professor),
Taisei Mushiroda (Visiting Professor),
Yukihide Momozawa (Visiting Associate Professor),
Kaoru Ito (Visiting Associate Professor),
Momoko Horikoshi (Visiting Associate Professor)

82

Part 5
Data andStatistics

Award winners 2018
Name of the awardee

Name of the award

Date of theannouncement

Piero Carninci,
Team Leader, Laboratory for Transcriptome Technology

The Commendation for Science and Technology by the Minister of Education, Culture,
Sports, Science and Technology, Prizes for Science and Technology, Research Category

Apr 2018

Hiroshi Ohno,
Team Leader, Laboratory for Intestinal Ecosystem

The Commendation for Science and Technology by the Minister of Education, Culture,
Sports, Science and Technology, Prizes for Science and Technology, Research Category

Apr 2018

Haruhiko Koseki,
Team Leader, Laboratory for Developmental Genetics

55th ERWIN von BALZ PRIZE

Nov 2018

Hiroshi Ohno,
Team Leader, Laboratory for Intestinal Ecosystem

The Hideyo Noguchi Memorial Award for Medical ScienceNov 2018

Kazuyo Moro,Team Leader, Laboratory for Innate Immune Systems

The 8th Nagase Prize

Sep 2018

Masayuki Amagai,
Team Leader, Laboratory for Skin Homeostasis

Honorary Member of the Society for Investigative Dermatology (SID)

Nov 2018

Shin-ichiro Fujii,
Team Leader, Laboratory for Immunotherapy

RIKEN Eiho AwardJun 2018

Michiel de Hoon,
Team Leader, Laboratory for Applied Computational Genomics

RIKEN Baiho Award (RIKEN Excellent Achievement Award)

Jun 2018

Kenya Honda,
Team Leader, Laboratory for Gut Homeostasis

Highly Cited Researchers 2018 by Clarivate Analytics

Nov 2018

Kenya Honda,
Team Leader, Laboratory for Gut Homeostasis

The 87th Kitasato AwardJun 2018

Haruhiko Koseki,
Team Leader, Laboratory for Developmental Genetics

RIKEN Industry Partnerships Contribution Award FY2018

Nov 2018

Kaoru Ito,
Team Leader, Laboratory for Cardiovascular Diseases

Best Reviewer Award 2017, International Heart Journal

Mar 2018

Kosuke Miyauchi,
Deputy Team Leader, Laboratory for Cytokine Regulation2018 Academic Award, Japanese Society of Interferon & Cytokine Research

Jul 2018

Takashi Kanaya,
Senior Scientist, Laboratory for Intestinal Ecosystem

The 13th Japanese Society for Immunology (JSI) Young Investigator Award

Dec 2018

Yuuri Yasuoka,
Research Scientist, Laboratory for Comprehensive Genomic Analysis

Young Scientists' Excellent Oral Presentation Award, The 20th Annual Meeting of theSociety of Evolutionary Studies, JapanAug 2018

Senko Tsukuda,
Research Scientist, Liver Cancer Prevention Research Unit

Taisho Toyama Award, Liver Forum AwardJun 2018

Michio Miyajima,
Research Scientist, Laboratory for Mucosal Immunity

RIKEN Research Incentive Award

Mar 2018

Takahiro Suzuki,
Senior Scientist, Laboratory for Cellular Function Conversion Technology

RIKEN Research Incentive Award

Mar 2018

Hazuki Takahashi,
Special Fixed Term Contract Researcher, Laboratory for Transcriptome Technology

RIKEN Technology Incentive Award

Mar 2018

Marina Lizio,
Postdoctoral Researcher, Laboratory for Genome Information Analysis

RIKEN Technology Incentive Award

Mar 2018

Takahiro Suzuki,
Senior Scientist, Laboratory for Cellular Function Conversion Technology

RIKEN CLST Researcher Incentive Award

Mar 2018

Marina Lizio,
Postdoctoral Researcher, Laboratory for Genome Information Analysis

RIKEN CLST Technician Incentive Award

Mar 2018

Hazuki Takahashi,
Special Fixed Term Contract Researcher, Laboratory for Transcriptome Technology

RIKEN CLST Technician Incentive Award

Mar 2018

Yudai Iino,
Student Trainee, Laboratory for Metabolomics

Best Presentation Award, 17th Pharma-Bioforum of the Pharmaceutical Society ofJapan

Sep 2018

Mio Yoshida,
Student Trainee, Laboratory for Metabolomics

Presentation Award, 17th Pharma-Bioforum of the Pharmaceutical Society of JapanSep 2018

Joachim Luginbuehl,
Research Scientist, Laboratory for Advanced Genomics Circuit

Award for Oral Presentation, The 22nd Human Genome Meeting Trainee Symposium

Mar 2018

Jordan Ramilowski,
Research Scientist, Laboratory for Genome Information Analysis

Award for Best Poster Presentation, The 22nd Human Genome Meeting

Mar 2018

Hazuki Takahashi,
Special Fixed Term Contract Researcher, Laboratory for Transcriptome Technology

Award for Best Poster Presentation, The 22nd Human Genome Meeting

Mar 2018

Saumya Agrawal,
Postdoctoral Researcher, Laboratory for Applied Computational Genomics

Award for Outstanding Poster Presentation, The 22nd Human Genome Meeting

Mar 2018

Tsukasa Kouno,
Research Associate, Laboratory for Advanced Genomics Circuit

Award for Outstanding Poster Presentation, The 22nd Human Genome Meeting

Mar 2018

Yasutaka Motomura,Research Scientist, Laboratory for Innate Immune Systems

Poster Award, Medical Science Prize, FY2017 SPDR&FPR Presentation of research
results

Jan 2018

Yasutaka Motomura,Research Scientist, Laboratory for Innate Immune Systems

Immunity Poster Award, The 3rd International Conference on Innate Lymphoid Cells(ILC2018)

Dec 2018

Yudai Iino,
Student Trainee, Laboratory for Metabolomics

Poster Award, Lipoquality, JSPS Scientific Research on Innovative Area

Jun 2018

Sonoko Takahashi,Student Trainee, Laboratory for Tissue Dynamics

Poster Award, Symposium of the Division of Pharmacology and Drug Therapeutics,
Pharmaceutical Society of JapanAug 2018

XianYang Qin,
Research Scientist, Liver Cancer Prevention Research Unit

Federation of American Societies for Experimental Biology (FASEB), Travel AwardJun 2018

Tadashi Takeuchi,
Student Trainee, Laboratory for Intestinal Ecosystem

Ursula and Fritz Melchers Travel Award, Japanese Society for Immunology

Dec 2018

84

Guest lectures 2018
Table: Guest Lectures Jan-Dec 2018
Date

Speaker

Affiliation

Country

Title

15-Jan-18

Prof. Bing Zhu

Institute of Biophysics, Chinese Academy of Sciences

China

Establishment and maintenance of epigenetic
information

30-Jan-18

Prof. Yi Zhang

Harvard Medical School

USA

Epigenetic and chromatin reprogramming at the
beginning of mammalian life

2-Feb-18

Dr. Paola Laurino

Okinawa Institute of Science & Technology

Japan

A journey from an ancient finger print of Rossmann foldenzymes to cofactor engineering

6-Feb-18

Dr. Nicholas F. Parrish

Vanderbilt University Medical Center

USA

Interfering small RNAs derived from endogenous viralelements in mammals: a Eukaryotic CRISPR?

26-Feb-18

Dr. Sho Yamasaki

Research Institute for Microbial Diseases, Osaka
University

Japan

Regulation of immune responses via C-type lectin
receptors

19-Mar-18

Dr. Tomoki Nakashima

Tokyo Medical and Dental University

Japan

RANKL biology “Key of bone metabolism andimmunology”

23-Mar-18

Dr. Prim Singh

Nazarbayev University School of Medicine

Kazakhstan

Epigenetics, heterochromatin and age reprogramming

3-Apr-18

Dr. Tomohiko Okazaki

Graduate School of Pharmaceutical Sciences, The
University of Tokyo

Japan

Differential control of interferon and apoptotic
responses to viral infection

5-Apr-18

Dr. Catherine Porcher

The MRC Weatherall Institute of Molecular Medicine,
University of Oxford

UK

Transcriptional and epigenetic mechanisms of blood
cell specification

5-Apr-18

Dr. Paresh Vyas

The MRC Weatherall Institute of Molecular Medicine,
University of Oxford

UK

Human hemopoietic hierarchies in normal and leukemic
haemopoiesis

9-Apr-18

Prof. Roderic Guigo

Center for Genomic Regulation, University Pompeu
Fabra

Spain

Towards a molecular anatomy of the human body

11-Apr-18

Dr. Sungwhan F. Oh

Harvard Medical School and Brigham and Women’s
Hospital

USA

Dissecting “the holy trinity” of gut microbiome:
molecular-level investigation of host-microbiota-dietcomplex

16-Apr-18

Dr. Lev Becker

The University of Chicago

USA

Obesity and insulin resistance promote atherosclerosis
through an IFNg-macrophage pathway

18-Apr-18

Dr. Silvia Zucchelli

University of Eastern Piedmont

Italy

SINEUPs: a versatile tool to increase protein synthesis

19-Apr-18

Prof. Ferenc Krausz
Dr. Mihaela Zigman

Max Planck Institute of Quantum Optics

Germany

Molecular fingerprinting and cancer detection with
infrared light

24-Apr-18

Dr. Eswar P. R. Iyer

Harvard Medical School, Wyss Institute for Biologically
Inspired Engineering

USA

Barcoded oligonucleotides ligated on RNA amplified for
multiplex and parallel in-situ analyses

26-Apr-18

Dr. Ryohichi Sugimura

Center for iPS Cell Research and Application

Japan

Hematopoietic stem cells from human pluripotent stem
cells.

16-May-18

Dr. Alexej AbyzovCenter for Individualized Medicine, Mayo Clinic

USA

Somatic mosaicism in brain and other tissues

21-May-18

Dr. Ryo Nakaki

Rhelixa, Inc.

Japan

Starting epigenome analysis from scratch

21-May-18

Dr. Davide De Pietri Tonelli

Italian Institute of Technology

Italy

Emerging complexity of small noncoding RNA pathways
in mammalian neurogenesis: unconventional functionsof miRNA- and piRNA-biogenesis proteins in developing
and adult mouse brain

1-Jun-18

Dr. Francesca Buffa

University of Oxford

UK

miRNA aberrant regulation in cancer

4-Jun-18

Dr. Kyogo Kawaguchi

Harvard Medical School

USA

Fate coordination in the epidermal stem cell pool

6-Jun-18

Dr. Yusuke Hirabayashi

Columbia University Medical CenterUSA

ER-mitochondria tethering by PDZD8 regulates Ca2+
dynamics in mammalian neurons.

11-Jun-18

Dr. Mahesh Desai

Luxembourg Institute of Health and University ofSouthern Denmark

Luxembourg

Diet-driven interactions of the gut microbiome with theintestinal mucus barrier

10-Jul-18

Dr. Zheng Chao

SANE ASIA Pte. Ltd.

Singapore

Bioimaging with light-sheet microscopy –ultra gentle
imaging of live samples–

12-Jul-18

Dr. Charles Lecellier

The Institute of Molecular Genetics of Montpellier

FranceA strict combination of SINE enhancer RNAs is linked togene expression

21-Jun-18

Dr. Olivier Lantz

Center of Immunotherapy Institut Curie

FranceA surprising connection: invariant T cells, vitamins,
bacteria and wild mice

21-Jun-18

Dr. Iain Hrynaszkiewicz

Springer Nature

UK

Open research data: the future is now?

85

Date

Speaker

Affiliation

Country

Title

25-Jul-18

Dr. Takayuki Nojima

University of Oxford

USA

Noncoding transcription and genome maintenance

21-Aug-18

Dr. Patrick Matthias

Friedrich Miescher Institute for Biomedical Research

Switzerland

Acetylation is a novel regulator of stress granules
formation and phase separation

13-Sep-18

Dr. Hiroyuki Seimiya

Japanese Foundation for Cancer ResearchJapan

Telomere as the starting point of anticancer drug
discovery

14-Sep-18

Dr. Masayuki Horie

Institute for Frontier Life and Medical Sciences, Kyoto
University

Japan

Co-evolution of eukaryote genomes, retrotransposons
and RNA viruses

26-Sep-18

Prof. Zemin Zhang

Beijing Advanced Innovation Center for Genomics,
Peking University

China

Single cell RNA sequencing analysis of tumorinfiltrating immune cells

4-Oct-18

Dr. Keisuke Nimura

School of Medicine, Osaka University

Japan

How dysregulation of gene expression results indiseases

5-Oct-18

Dr. Xiaoyang Wu

Cancer Research University of Chicago

USA

Skin engineering with epidermal stem cells.

10-Oct-18

Dr. Ido Amit

Weizmann Institute of Scienc

IsraelThe Power of ONE: immunology in the age of single cell
genomics

12-Oct-18

Dr. Hirofumi Shintaku

RIKEN Hakubi Fellows Program

Japan

SINC-seq: dissecting nuclear and cytoplasmic RNA
expressions in single cells

16-Oct-18

Prof. Frank Brombacher

International Centre for Genetic Engineering andBiotechnology

South Africa

Immunology of tuberculosis: from genes to biomarkers& host directed therapy

16-Oct-18

Dr. Musa Mhlanga

University of Cape Town

South Africa

Immune genes are primed for robust transcription byproximal lncRNAs located in nuclear compartments

17-Oct-18

Dr. Kenneth Baillie

University of Edinburgh, Roslin Institute

UK

Understanding disease pathogenesis through functional
genomics

19-Oct-18

Dr. Sjef Verbeek

Leiden University Medical Cente

Netherlands

The role of FxCR and FxCR expressing immune cells in
the tumor microenvironment in antibody therapy incancer12-Nov-18

Dr. Saulius Klimašauskas

Life Sciences Center, Vilnius University

Lithuania

Catalytic plasticity of DNA methyltransferases: writers,
readers and erasers of epigenetic marks.

13-Nov-18

Dr. Jamey D. Young

Vanderbilt University

USA

13C flux analysis in metabolic disease research

27-Nov-18

Dr. Fumiyo Ikeda

Institute of Molecular Biotechnology Austria

Austria

Regulation of inflammatory responses by the ubiquitin
system27-Nov-18

Dr. Stephanie Houston

Journal of Experimental Medicine

USA

Scientific publishing: what, how and why?

6-Dec-18

Dr. Yurina Sekine

Japan Atomic Energy Agency, Materials Sciences
Research CenterJapan

Development of wearable sweat devices and their
future advancement

7-Dec-18

Dr. Daniel Kaplan

University of Pittsburgh

USA

Nociceptors are sufficient to initiate cutaneous type-17
inflammation

7-Dec-18

Dr. Brian Kim

Washington University School of Medicine

USA

Immune regulation of atopic dermatitis and itch

19-Dec-18

Dr. Takeshi Egawa

Washington University School of Medicine

USA

Tissue and cellular homeostasis during lymphocyte
immune responses

86

Publications 2018

1 Akiyama M, Takahashi A, Momozawa Y, Arakawa S, Miya F, Tsunoda T, Ashikawa K, Oshima Y,
Yasuda M, Yoshida S, Enaida H, Tan X, Yanagi Y, Yasukawa T, Ogura Y, Nagai Y, Takahashi K, Fujisawa K, Inoue M, Arakawa A, Tanaka K, Yuzawa M, Kadonosono K, Sonoda K, Ishibashi T, Kubo M.
Genome-wide association study suggests four variants influencing outcomes with ranibizumab
therapy in exudative age-related macular degeneration. J Hum Genet 63, 1083-1091 (2018)
2 Alhendi A, Patrikakis M, Daub CO, Kawaji H, Itoh M, De Hoon MJ, Carninci P, Hayashizaki Y, Arner
EA, Khachigian L. Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to
Fibroblast Growth Factor-2 or Interleukin-1β. Sci Rep 8, 13164 (2018)

Table: IMS Publications from January to December, 2018

Journal

Impact Factor(2017)

Number ofPapersChem Rev

52.6

1

Nature41.6

1

Science41.1

2

Nat Med

32.6

1

Cell

31.4

4

Nat Genet

27.1

4

Cell Stem Cell

23.3

2

Annu Rev Immunol

22.7

1

Gastroenterology

20.8

3

Immunity

19.7

3

Circulation

18.9

1

Lancet Psychiat

15.2

1

Blood

15.1

3

Mol Cell

14.2

1

Nat Microbiol

14.2

2

Nat Chem Biol

13.8

1

Nat Struct Mol Biol

13.3

1

J Allergy Clin Immun

13.3

3

J Clin Invest

13.3

1

Nat Protoc

12.4

1

Nat Commun

12.4

9

Ann Rheum Dis

12.4

3

Nucleic Acids Res

11.6

2

Jama Neurol

11.5

1

J Exp Med

10.8

6

J Thorac Oncol

10.3

1

Clin Cancer Res

10.2

1

Semin Cancer Biol

10.2

1

Genome Res

10.1

2

Dev Cell

9.6

1

ISME J

9.5

1
3

Proc Natl Acad Sci U S A

9.5

Gene Dev

9.5

2

Immunol Rev

9.2

2

Haematologia

9.1

1

Am J Hum Genet

8.9

1

Cell Rep

8.0

4

Curr Opin Immunol

7.92

Arthritis Rheumatol

7.9

1

Elife

7.6

2
1

J Autoimmun

7.6

Mucosal Immunol

7.4

1

Schizophrenia Bull

6.9

1

Oncogene

6.9

3

Clin Pharmacol Ther

6.5

4

J Invest Dermatol

6.4

1

Sci Signal

6.4

1
1

EBioMedicine

6.2

Plos Pathog

6.2

2

Anal Chem

6.0

1

Others

124

Total

223

3 Amare AT, Schubert KO, Tekola-Ayele F, Hsu Y, Sangkuhl K, Jenkins G, Whaley RM, Barman P,
Batzler A, Altman RB, Arolt V, Brockmöller J, Chen C, Domschke, Hall-Flavin DK, Hong C, Illi A, Ji
Y, Kampman O, Kinoshita T, Leinonen E, Liou Y, Mushiroda T, Shinpei N, Skime MK, Wang L, Kato
M, Liu Y, Praphanphoj V, Stingl JC, Bobo WV, Tsai S, Kubo, Klein TE, Weinshilboum RM, Biernacka
JM, Baune BT. Association of the Polygenic Scores for Personality Traits and Response to Selective
Serotonin Reuptake Inhibitors in Patients with Major Depressive Disorder. Front Psychiatry 6,
65 (2018)
4 Amininejad L, Charloteaux B, Theatre E, Liefferinckx C, Dmitrieva J, Hayard P, Muls V, Maisin J,
Schapira M, Ghislain J, Closset P, Talib M, Abramowicz M, Momozawa Y, Deffontaine V, Crins F,
Mni M, Karim L, Cambisano N, Ornemese S, Zucchi A, Minsart C, Deviere J, Hugot J, De Vos M,
Louis E, Vermeire S, Van Gossum A, Coppieters W, Twizere J, Georges M, Franchimont D. Analysisof Genes Associated With Monogenic Primary Immunodeficiency Identifies Rare Variants in XIAPin Patients With Crohn's Disease. Gastroenterology 154, 2165-2177 (2018)
5 Brainstorm Consortium, Anttila V, Bulik-Sullivan B, Finucane H, Walters R, Bras J, Duncan L,
Escott-Price V, Falcone G, Gormley P, Malik R, Patsopoulos N, Ripke S, Wei Z, Yu D, Lee P, Turley P,
Grenier-Boley B, Chouraki V, Kamatani Y, Berr C, Letenneur L, Hannequin D, Amouyel P, Boland A,
Deleuze J, Duron E, Vardarajan B, Reitz C, Goate A, Huentelman M, Kamboh M, Larson E, Rogaeva
E, St George-Hyslop P, Hakonarson H, Kukull W, Farrer L, Barnes L, Beach T, Demirci F, Head E,
Hulette C, Jicha G, Kauwe J, Kaye J, Leverenz J, Levey A, Lieberman A, Pankratz V, Poon W, Quinn
J, Saykin A, Schneider L, Smith A, Sonnen J, Stern R, Van Deerlin V, Van Eldik L, Harold D, Russo G,
Rubinsztein D, Bayer A, Tsolaki M, Proitsi P, Fox N, Hampel H, Owen M, Mead S, Passmore P, Morgan K, Nothen M, Rossor M, Lupton M, Hoffmann P, Kornhuber J, Lawlor B, McQuillin A, Al-Chalabi A, Bis J, Ruiz A, Boada M, Seshadri S, Beiser A, Rice K, van der Lee S, De Jager P, Geschwind
D, Riemenschneider M, Riedel-Heller S, Rotter J, Ransmayr G, Hyman B, Cruchaga C, Alegret M,
Winsvold B, Palta P, Farh K, Cuenca-Leon E, Furlotte N, Kurth T, Ligthart L, Terwindt G, Freilinger
T, Ran C, Gordon S, Borck G, Adams H, Lehtimaki T, Wedenoja J, Buring J, Schurks M, Hrafnsdottir
M, Hottenga J, Penninx B, Artto V, Kaunisto M, Vepsalainen S, Martin N, Montgomery G, Kurki M,
Hamalainen E, Huang H, Jie H, Sandor C, Webber C, Muller-Myhsok B, Schreiber S, Schreiber S,
Salomaa V, Gobel H, Macaya A, Pozo-Rosich P, Hansen T, Werge T, Kaprio J, Metspalu A, KubischC, Ferrari M, Belin A, van den Maagdenberg A, Zwart J, Boomsma D, Eriksson N, Olesen J, Chasman D, Nyholt D, Avbersek A, Baum L, Berkovic S, Bradfield J, Buono R, Catarino C, Cossette P, De
Jonghe P, Depondt C, Dlugos D, Ferraro T, French J, Hjalgrim H, Jamnadas-Khoda J, Kalviainen R,
Kunz W, Lerche H, Leu C, Lindhout D, Lo W, Lowenstein D, McCormack M, Moller R, Molloy A, Ng
P, Oliver K, Privitera M, Radtke R, Ruppert A, Sander T, Schachter S, Schankin C, Scheffer I, Schoch
S, Sisodiya S, Smith P, Sperling M, Striano P, Surges R, Thomas G, Visscher F, Whelan C, Zara F,
Heinzen E, Marson A, Becker F, Stroink H, Zimprich F, Gasser T, Gibbs R, Heutink P, Martinez M,
Morris H, Sharma M, Ryten M, Mok K, Pulit S, Bevan S, Holliday E, Attia J, Battey T, Boncoraglio
G, Thijs V, Chen W, Mitchell B, Rothwell P, Sharma P, Sudlow C, Vicente A, Markus H, Kourkoulis
C, Pera J, Raffeld M, Silliman S, Boraska Perica V, Thornton L, Huckins L, William Rayner N, Lewis
C, Gratacos M, Rybakowski F, Keski-Rahkonen A, Raevuori A, Hudson J, Reichborn-Kjennerud
T, Monteleone P, Karwautz A, Mannik K, Baker J, O'Toole J, Trace S, Davis O, Helder S, Ehrlich S,
Herpertz-Dahlmann B, Danner U, van Elburg A, Clementi M, Forzan M, Docampo E, Lissowska J,
Hauser J, Tortorella A, Maj M, Gonidakis F, Tziouvas K, Papezova H, Yilmaz Z, Wagner G, CohenWoods S, Herms S, Julia A, Rabionet R, Dick D, Ripatti S, Andreassen O, Espeseth T, Lundervold A,
Steen V, Pinto D, Scherer S, Aschauer H, Schosser A, Alfredsson L, Padyukov L, Halmi K, Mitchell
J, Strober M, Bergen A, Kaye W, Szatkiewicz J, Cormand B, Ramos-Quiroga J, Sanchez-Mora C,
Ribases M, Casas M, Hervas A, Arranz M, Haavik J, Zayats T, Johansson S, Williams N, Dempfle A,
Rothenberger A, Kuntsi J, Oades R, Banaschewski T, Franke B, Buitelaar J, Arias Vasquez A, Doyle A,
Reif A, Lesch K, Freitag C, Rivero O, Palmason H, Romanos M, Langley K, Rietschel M, Witt S, Dalsgaard S, Borglum A, Waldman I, Wilmot B, Molly N, Bau C, Crosbie J, Schachar R, Loo S, McGoughJ, Grevet E, Medland S, Robinson E, Weiss L, Bacchelli E, Bailey A, Bal V, Battaglia A, Betancur C,
Bolton P, Cantor R, Celestino-Soper P, Dawson G, De Rubeis S, Duque F, Green A, Klauck S, Leboyer
M, Levitt P, Maestrini E, Mane S, De-Luca D, Parr J, Regan R, Reichenberg A, Sandin S, Vorstman J,
Wassink T, Wijsman E, Cook E, Santangelo S, Delorme R, Roge B, Magalhaes T, Arking D, Schulze
T, Thompson R, Strohmaier J, Matthews K, Melle I, Morris D, Blackwood D, McIntosh A, Bergen
S, Schalling M, Jamain S, Maaser A, Fischer S, Reinbold C, Fullerton J, Guzman-Parra J, Mayoral
F, Schofield P, Cichon S, Muhleisen T, Degenhardt F, Schumacher J, Bauer M, Mitchell P, Gershon
E, Rice J, Potash J, Zandi P, Craddock N, Ferrier I, Alda M, Rouleau G, Turecki G, Ophoff R, Pato C,
Anjorin A, Stahl E, Leber M, Czerski P, Cruceanu C, Jones I, Posthuma D, Andlauer T, Forstner A,
Streit F, Baune B, Air T, Sinnamon G, Wray N, MacIntyre D, Porteous D, Homuth G, Rivera M, Grove
J, Middeldorp C, Hickie I, Pergadia M, Mehta D, Smit J, Jansen R, de Geus E, Dunn E, Li Q, Nauck
M, Schoevers R, Beekman A, Knowles J, Viktorin A, Arnold P, Barr C, Bedoya-Berrio G, Bienvenu O,
Brentani H, Burton C, Camarena B, Cappi C, Cath D, Cavallini M, Cusi D, Darrow S, Denys D, Derks
E, Dietrich A, Fernandez T, Figee M, Freimer N, Gerber G, Grados M, Greenberg E, Hanna G, Hartmann A, Hirschtritt M, Hoekstra P, Huang A, Huyser C, Illmann C, Jenike M, Kuperman S, Leventhal B, Lochner C, Lyon G, Macciardi F, Madruga-Garrido M, Malaty I, Maras A, McGrath L, MiguelE, Mir P, Nestadt G, Nicolini H, Okun M, Pakstis A, Paschou P, Piacentini J, Pittenger C, Plessen K,
Ramensky V, Ramos E, Reus V, Richter M, Riddle M, Robertson M, Roessner V, Rosario M, Samuels

87

J, Sandor P, Stein D, Tsetsos F, Van Nieuwerburgh F, Weatherall S, Wendland J, Wolanczyk T, Worbe
Y, Zai G, Goes F, McLaughlin N, Nestadt P, Grabe H, Depienne C, Konkashbaev A, Lanzagorta N,
Valencia-Duarte A, Bramon E, Buccola N, Cahn W, Cairns M, Chong S, Cohen D, Crespo-Facorro
B, Crowley J, Davidson M, DeLisi L, Dinan T, Donohoe G, Drapeau E, Duan J, Haan L, Hougaard D,
Karachanak-Yankova S, Khrunin A, Klovins J, Kucinskas V, Lee Chee Keong J, Limborska S, Loughland C, Lonnqvist J, Maher B, Mattheisen M, McDonald C, Murphy K, Nenadic I, van Os J, Pantelis C,
Pato M, Petryshen T, Quested D, Roussos P, Sanders A, Schall U, Schwab S, Sim K, So H, Stogmann
E, Subramaniam M, Toncheva D, Waddington J, Walters J, Weiser M, Cheng W, Cloninger R, Curtis
D, Gejman P, Henskens F, Mattingsdal M, Oh S, Scott R, Webb B, Breen G, Churchhouse C, Bulik C,
Daly M, Dichgans M, Faraone S, Guerreiro R, Holmans P, Kendler K, Koeleman B, Mathews C, Price
A, Scharf J, Sklar P, Williams J, Wood N, Cotsapas C, Palotie A, Smoller J, Sullivan P, Rosand J, Corvin A, Neale B, Schott J, Anney R, Elia J, Grigoroiu-Serbanescu M, Edenberg H, Murray R. Analysisof shared heritability in common disorders of the brain. Science 360, eaap8757(2018)
6 Baillie JK, Haley C, Gray A, Barrett J, Stahl E, Tenesa A, Brown B, Andersson R, Shaefer U, Zeggini
E, Asimit J, Faulkner GJ, Lizio M, Daub CO, Itoh M, Kondo N, Lassmann T, Kawai J, Bajic V, Heutink
P, Michael R, Kawaji H, Albin S, Suzuki H, Plenge R, Satsangi J, Wells C, Freeman TC, Hayashizaki
Y, Carninci P, Forrest AR, Hume DA. Shared activity patterns arising at genetic susceptibility locireveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol (2018)
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A, Miyagi S, Manabe I, Matsui H, Koseki H, Bardwell VJ, Iwama A. Bcor insufficiency promotes
initiation and progression of myelodysplastic syndrome. Blood 132, 2470-2483 (2018)

174 Suvichapanich S, Fukunaga K, Zahroh H, Mushiroda T, Mahasirimongkol S, Toyo-oka L, Chaikledkaew U, Jittikoon J, Yuliwulandari R, Yanai H, Tokunaga K. NAT2 ultra-slow acetylator and risk ofanti-tuberculosis drug-induced liver injury: a genotype-based meta-analysis. Pharmacogenet
Genomics 28, 167-176 (2018)

189 Tashiro Y, Murakami A, Hara Y, Shimizu T, Kubo M, Goitsuka R, Kishimoto H, Azuma T. Highaffinity IgM+ memory B cells are defective in differentiation into IgM antibody-secreting cellsby re-stimulation with a T cell-dependent antigen. Sci Rep 8, 14559 (2018)

175 Suzuki S, Endoh R, Manabe R, Ohkuma M, Hirakawa Y. Multiple Losses of photosynthesis andconvergent reductive genome evolution in the colourless green algae Prototheca. Sci Rep 8, 940(2018)

190 Tatsumi D, Hayashi Y, Endo M, Kobayashi H, Yoshioka T, Kiso K, Kanno S, Nakai Y, Maeda I, Mochizuki K, Tachibana M, Koseki H, Okuda A, Yasui A, Kono T, Matsui Y. DNMTs and SETDB1 function
as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonicstem cells. PLoS One 13, e0205969 (2018)

176 Tajima T, Morita H, Ito K, Yamazaki T, Kubo M, Komuro I, Momozawa Y. Blood lipid-related lowfrequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial
infarction in Japanese. Sci Rep 8, 8107 (2018)

191 Taylor J, Bongartz T, Massey J, Mifsud B, Spiliopoulou A, Scott I, Wang J, Morgan M, Plant D, Colombo M, Orchard P, Twigg S, McInnes I, Porter D, Freeston J, Nam J, Heather C, Isaacs J, Strathdee
J, Arnett D, de Hair, Tak P, Aslibekyan S, van Vollenhoven R, Padyukov L, Bridges L, Pitzalis C, Cope
A, Verstappen S, Emery P, Barnes M, Agakov F, McKeigue P, Mushiroda T, Kubo, Weinshilboum R,

93

Barton A, Morgan A, Barrett J. Genome-wide association study of response to methotrexate inearly rheumatoid arthritis patients. Pharmacogenomics J 18, 528-53 (2018)
192 Tenno M, Kojo S, Lawir D, Hess I, Shiroguchi K, Ebihara T, Endo TA, Muroi S, Satoh R, Kawamoto H,
Boehm T, Taniuchi I. Cbfβ2 controls differentiation of and confers homing capacity to prethymic
progenitors. J Exp Med 215, 595-610 (2018)
193 Teumer A, Chaker L, Groeneweg S, Li Y, Munno C, Barbieri C, Schultheiss U, Traglia M, Ahluwalia T,
Akiyama M, Appel E, Arking D, Arnold A, Astrup A, Beekman M, Beilby J, Bekaert S, Boerwinkle
E, Brown S, Buyzere M, Campbell P, Ceresini G, Cerqueira C, Cucca F, Deary I, Deelen J, Eckardt K,
Ekici A, Eriksson J, Ferrrucci L, Fiers T, Fiorillo E, Ford I, Fox C, Fuchsberger C, Galesloot T, Gieger C,
Gögele M, Grandi A, Grarup N, Greiser K, Haljas K, Hansen T, Harris S, Heemst D, Heijer M, Hicks
A, Hollander W, Homuth G, Hui J, Ikram M, Ittermann T, Jensen R, Jing J, Jukema J, Kajantie E,
Kamatani Y, Kasbohm E, Kaufman J, Kiemeney L, Kloppenburg M, Kronenberg F, Kubo, Lahti J,
Lapauw B, Li S, Liewald D, Cohort Study L, Lim E, Linneberg A, Marina M, Mascalzoni D, Matsuda
K, Medenwald D, Meisinger C, Meulenbelt I, Meyer T, Meyer zu Schwabedissen H, Mikolajczyk
R, Moed M, Netea-Maier R, Nolte I, Okada Y, Pala M, Pattaro C, Pedersen O, Petersmann A, Porcu
E, Postmus I, Pramstaller P, Psaty B, Ramos Y, Rawal R, Redmond P, Richards J, Rietzschel E,
Rivadeneira F, Roef G, Rotter J, Sala C, Schlessinger D, Selvin E, Slagboom P, Soranzo N, Sørensen
T, Spector T, Starr J, Stott D, Taes Y, Taliun D, Tanaka T, Thuesen B, Tiller D, Toniolo D, Uitterlinden A,
Visser W, Walsh J, Wilson S, Wolffenbuttel B, Yang Q, Zheng H, Cappola A, Peeters R, Naitza S, Völzke H, Sanna S, Köttgen A, Visser T, Medici M. Genome-wide analyses identify a role for SLC17A4
and AADAT in thyroid hormone regulation. Nat Commun 9, 4455 (2018)
194 Tsuchida Y, Sumitomo S, ota m, tsuchiya h, nagafuchi y, Shoda H, Fujio K, ishigaki k, Suzuki A,
Kochi Y. Reduction of CD83 Expression on B Cells and the Genetic Basis for Rheumatoid Arthritis:
Comment on the Article by Thalayasingam et al. Arthritis Rheumatol 70, 1695-1696 (2018)
195 Tsuchiya K, Tabe Y, Ohkawa T, Usui K, Yuri M, Ai T, Yang H, Matsushita H, Hanami T, Yamanaka Y,
Okuzawa A, Morishita S, Takaku T, Misawa S, Horii T, Hayashizaki Y, Ohsaka A. Eprobe mediated
RT-qPCR for the detection of leukemia-associated fusion genes. PLoS One 13, e0202429 (2018)
196 Tsukiji N, Osada M, Sasaki T, Shirai T, Satoh K, Inoue O, Umetani N, Mochizuki C, Saito T, Kojima S,
Shinmori H, Ozaki Y, Inoue K. Cobalt-hematoporphyrin inhibits CLEC-2-podoplanin interaction,
tumor metastasis, and arterial/venous thrombosis in mice. Blood Advances 2, 2214-2225 (2018)
197 Uchida N, Takahashi K, Iwasaki R, Yamada R, Yoshimura M, Endo TA, Kimura S, Zhang H, Nomoto
M, Tada Y, Kinoshita T, Itami K, Hagihara S, Torii KU. Chemical hijacking of auxin signaling with anengineered auxin-TIR1 pair. Nat Chem Biol 14, 299-305 (2018)
198 Ueda T, Tarui H, Kido N, Imaizumi K, Hikosaka K, Abe T, Minegishi D, Tada Y, Nakagawa M, Tanaka
S, Omiya T, Morikaku K, Kawahara M, Kikuchi-Ueda T, Akuta T, Ono Y. The complete mitochondrial
genome of Sarcoptes scabiei var. nyctereutis from the Japanese raccoon dog: prediction anddetection of two transfer RNAs (tRNA-A and tRNA-Y). Genomics S0888-7543(18)30414-2 (2018)199 Ueharaguchi Y, Honda T, Kusuba N, Hanakawa S, Adachi A, Sawada Y, Otsuka A, Kitoh A, Dainichi T,
Egawa G, Nakashima C, Nakajima S, Murata T, Ono S, Arita M, Narumiya S, Miyachi Y, Kabashima
K. Thromboxane A2 facilitates IL-17A production from Vγ4+ γδ T cells and promotes psoriatic
dermatitis in mice. J Allergy Clin Immunol 142, 680-683 e2 (2018)
200 Ujiie H, Muramatsu K, Mushiroda T, Ozeki T, Miyoshi H, Iwata H, Nakamura A, Nomoto H, Cho K,
Sato N, Nishimura M, Ito T, Izumi K, Nishie W, Shimizu H. HLA-DQB1*03:01 as a Biomarker for
Genetic Susceptibility to Bullous Pemphigoid Induced by DPP-4 Inhibitors. J Invest Dermatol
138, 1201-1204 (2018)
201 Umeyama T, Ito T. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions andNucleosome Centers. Curr Protoc Mol Biol 123, e60 (2018)202 Ürel-Demir G, Simsek-Kiper PO, Akgün-Doğan Ö, Göçmen R, Wang Z, Matsumoto N, Miyake N,
Utine GE, Nishimura G, Ikegawa S, Boduroglu K. Further expansion of the mutational spectrumof spondylo-meta-epiphyseal dysplasia with abnormal calcification. J Hum Genet 63, 10031007 (2018)
203 Ushijima M, Uruno T, Nishikimi A, Sanematsu F, Kamikaseda Y, Kunimura K, Sakata D, Okada T.
The Rac Activator DOCK2 Mediates Plasma Cell Differentiation and IgG Antibody Production.
Front Immunol 9, 243 (2018)
204 Ushijima T, Kawaguchi K, Matsumoto T, Takagi M, Kondoh T, Nishimura G, Iida A, Ikegawa S, Haga
N, Kato G. Double non-contiguous fractures in a patient with spondylo-epiphyseal dysplasia
with spinal ankylosis treated with open and percutaneous spinal fixation technique: a casereport. BMC Res Notes 11, 106 (2018)
205 Vacca A, Ito M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest A, Hayashizaki Y,
Aitken S, Semple C. Conserved temporal ordering of promoter activation implicates common
mechanisms governing the immediate early response across cell types and stimuli. Open Biol 8,180011 (2018)
206 VanderWeele DJ, Finney R, Katayama K, Gillard M, Paner G, Imoto S, Yamaguchi R, Wheeler D,
Justin L, Maggie C, Pontier A, Nguyen Y, Maejima K, Sasaki-Oku A, Nakano K, Tanaka H, Griend
D, Ratain MJ, Miyano S, Nakagawa H. Genomic heterogeneity within individual prostate cancer
foci impacts predictive biomarkers of targeted therapy. Eur Urol Focus S2405-4569(18)30007-5(2018)

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207 Vizcardo R, Klemen ND, Islam S, Gurusamy D, Tamaoki N, Yamada D, Koseki H, Kidder BL, Yu Z, Jia
L, Henning AN, Good ML, Bosch-Marce M, Maeda T, Liu C, Abdullaev Z, Pack S, Palmer DC, Stroncek DF, Ito F, Flomerfelt FA, Kruhlak MJ, Restifo NP. Generation of Tumor Antigen-Specific iPSCDerived Thymic Emigrants Using a 3D Thymic Culture System. Cell Rep 22, 3175-3190 (2018)
208 Vogelzang A, Guerrini MM, Minato N, Fagarasan S. Microbiota - an amplifier of autoimmunity.
Curr Opin Immunol 55, 15-21 (2018)
209 Wada H, Yasmin N, Kakugawa K, Ohno-Oishi M, Nieke S, Miyamoto C, Muroi S, Taniuchi I. Requirement for intron structures in activating the Cd8a locus. Proc Natl Acad Sci U S A 115, 34403445 (2018)
210 Wakabayashi T, Naito H, Suehiro J, Lin Y, Kawaji H, Iba T, Kouno T, Ishikawa-Kato S, Furuno M,
Takara K, Muramatsu F, Weizhen J, Kidoya H, Ishihara K, Hayashizaki Y, Nishida K, Yoder MC,
Takakura N. CD157 Marks Tissue-Resident Endothelial Stem Cells with Homeostatic and Regenerative Properties. Cell Stem Cell 22, 384-397 e6 (2018)
211 Wei W, Li X, Feng Q, Kubo, Kullo I, Peissig P, Karlson E, Jarvik G, Lee MM, Shang N, Larson E,
Edwards T, Shaffer C, Mosley J, Maeda S, Horikoshi M, Ritchie M, Williams M, Larson E, Crosslin D,
Bland S, Pacheco J, Rasmussen-Torvik L, Cronkite D, Hripcsak G, Cox N, Wilke R, Stein C, Rotter J,
Momozawa Y, Roden D, Krauss R, Denny J. LPA Variants are Associated with Residual Cardiovascular Risk in Patients Receiving Statins. Circulation 138, 1839-1849 (2018)
212 Xing S, Shao P, Li F, Zhao X, Seo W, Wheat J, Ramasamy S, Wang J, Li X, Peng W, Yu S, Liu C,
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213 Yakushiji-Kaminatsui N, Kondo T, Hironaka K, Sharif J, Endo TA, Nakayama M, Masui O, Koseki Y,
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214 Yamada M, Takahashi N, Matsuda Y, Sato K, Yokoji M, Sulijaya B, Maekawa T, Ushiki T, Mikami Y,
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215 Yamaguchi-Kabata Y, Morihara T, Ohara T, Ninomiya T, Takahashi A, Akatsu H, Hashizume Y,
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216 Yamashita A, Kondo K, Kunishima Y, Iseki S, Kondo T, Ota MS. Postnatal development of bitter
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217 Yazaki J, Galli M, Kim Y, Ecker JR. Profiling Interactome Networks with the HaloTag‐NAPPA In Situ
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218 Yoko-o T, Uemura M, Komatsuzaka A, Ikeda K, Ichikawa D, Takase K, Kanazawa N, Saito K,
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219 Yoshihama T, Fukunaga K, Hirasawa A, Nomura H, Akahane T, Kataoka F, Yamagami W, Aoki D,
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Budget, personnel and patent

IMS Budget FY2018

Personnel FY2018

IMS Budget FY2018

JPY Million

Category

Government funding for operations

3,064

Director

1

External competitive funding

2,046

Deputy Director

3

Total

5,110

Senior Advisor

1Team Leader

34

Unit Leader

5

Coordinator

5

Deputy Team Leader

9

Senior Scientist

28

Senior Research Scientist

3

Research Scientist

54

Postdoctoral Researcher

24

Special Postdoctoral Researcher

8

Research Fellow

2

Research Associate

15

Senior Technical Scientist

5Technical Scientist

22

Technical Staff I

74

Technical Staff II

49

International Program Associate

6

Junior Research Associate

24Intern2

Patents
There were 24 patents filed from January to December, 2018.

Patents
2018

Total
24

International
patents (PCT)21

Domestic patents(Japan)3Student Trainee

Number110

Research Administrator

4

Research Administrative Support Staff

3

Assistant

31

Part-time Staff

46

Senior Visiting Scientist

23

Visiting Scientist

170

Visiting Technical Scientist

23

Visiting Researcher

3

Temporary Staffing

15

Research Consultant

3

Consultant

1

Temporary Employee

1

Total

807

95

Original photos of the cover and front pages

Cover

Front page of Part 1

Credit to Dr. Masato Kubo

Credit to Dr. Taishin Akiyama

Laboratory for Cytokine Regulation

Laboratory for Immune Homeostasis

Front page of Part 2

Front page of Part 3

Credit to Dr. Joachim Luginbuehl

Credit to Dr. Xian-Yang Qin

Laboratory for Advanced Genomics Circuit

Liver Cancer Prevention Research Unit

Front page of Part 4

Front page of Part 5

Credit to Dr. Nanako Kadono

Credit to Animal Facility

Laboratory for Skin Homeostasis

96

Access to RIKEN Yokohama Campus

Local Access
By BusTake the #08 bus from Platform 8 at the East Exit of
Tsurumi Station (also accessible from the West Exit of
Keikyu Tsurumi Station) and get off at the RIKEN Shidai
Daigakuin Mae bus stop. The institute is across the street.
All buses from this platform are bound for Fureyu.
Buses depart Tsurumi every 5–15 minutes. It takes about
15 minutes to arrive at RIKEN Yokohama. The fare is 220
yen in cash.
By Train

A 15-minute walk from JR Tsurumi-Ono Station (JR Tsurumi Line), which is directly accessible by transfer from
JR Tsurumi Station.
Trains run about every 10 minutes during morning andevening rush hour, but less frequently at other times.
Searchable train timetables in English are available at
http://www.hyperdia.com/en/
By Taxi

Use the taxi stand at the East Exit of JR Tsurumi Stationor the West Exit of Keikyu Tsurumi Station. The trip takes
about 10 minutes and costs around 1,200 yen.

From the Airport
From Haneda Airport

From Narita Airport

Route 1

From Narita Airport Station take the JR Sobu Line (Rapid
Express), Airport Limousine Bus or JR Narita Express* to
JR Shinagawa Station. (JR Sobu Line is the most inexpensive option and takes about 1 hour and 15 minutes).
From JR Shinagawa Station take the JR Keihin Tohoku
Line (Yokohama direction) to JR Tsurumi Station (18minutes). Next, follow the Local Access directions above
to get to RIKEN Yokohama.

Take the Keikyu Railways Airport Express* (blue kanjisign) for Yokohama and get off at Keikyu Tsurumi Station(27–29 minutes). Airport Express trains run every 10-15
minutes between 9:30 a.m. and 9:30 p.m. Next, follow
the Local Access directions above to get to RIKEN Yokohama.
Route 2

Take any train marked with a green (express), red or
dark grey kanji sign to Keikyu Kamata Station. Transfer
to the Keikyu Main Line and take a local train* toward
Yokohama until Keikyu Tsurumi Station* (12 minutes).
*Only Airport Express (blue kanji sign) and local trains(dark grey kanji sign) stop at Keikyu Tsurumi Station.
Note that Keikyu Tsurumi Station and JR Tsurumi Station
are two different railway stations and are separated by abus rotary (the stations are about 150 meters apart).

* A reserved seat express that requires payment of asurcharge in addition to train fare.
Searchable train timetables in English are available at
http://www.hyperdia.com/en/

97

RIKEN Center for
Integrative Medical Sciences
http://www.ims.riken.jp/english/
RIKEN Yokohama Campus
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City,
Kanagawa, 230-0045, Japan
Tel : 045-503-9121
Fax : 045-503-9113
Email : ims-web@riken.jp

RIKEN IMS
Annual Report 2018

RIKEN 2019-038