Annual Reportof IFReC
2022 - 2023

Edit : Research Planning & Management Office, IFReC
Published in June, 2023

Osaka University

Copyright : Immunology Frontier Research Center (IFReC ), Osaka University

CO NTENTS
Message from the Director ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・1
Organization ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・3
Laboratories ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・9■ Immunology Groups ・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・10
■ Imaging Groups ・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・64
■ Bioinformatics Groups ・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・74
■ Units for Combined Research Fields ・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・
・78

Events & Outreach Activities ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・81
Information ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・93
Access Map ・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・110

Message from the Director
As the Director of the Immunology Frontier ResearchCenter (WPI-IFReC) at Osaka University, I am very pleased
to present the IFReC annual report for fiscal year 2022.
Since its inception in 2007, IFReC has established itself as ahigh-profile international research center for immunology
with the broad support of many people. Furthermore,since IFReC joined the WPI Academy in 2017, we havecontinued efforts to create history as a new research center
funded through a unique academic-industry partnershipagreement, which is paving the way for new possibilities incollaborative research.
After the start of the COVID-19 pandemic in late 2019,the major waves of COVID-19 in the past several years
led to a significant number of cases in Japan. However,as the COVID-19 pandemic began to subside in late 2022,
various regulations have been eased or lifted completely.
As a result, the activities in many regions have returned topre-COVID-19 levels and in-person classes and events haveresumed at the university.
Against this backdrop, the first “International School on
Advanced Immunology,” co-organized as a research retreat
by IFReC and ImmunoSensation2 (University of Bonn), washeld on Awaji Island in November 2022. It was the firstresearch retreat held in three years since the last “WinterSchool on Immunology" that IFReC jointly held in 2019with the Singapore Immunology Network as an annual
event starting in 2011. This "revived international school"provided an opportunity for young immunologists andsenior researchers from around the world to meet, discuss,and exchange ideas.

departments and between institutes. Our researchers
collaborate with the researchers at the Center for
Infectious Diseases Education and Research (CiDER), which
was established in response to the outbreak of COVID-19,
and the Center for Advanced Modalities and DDS (CAMaD),
which is a new vaccine research center established at
Osaka University.
IFReC welcomed two new female researchers in FY2022
as principal investigators. One is Dr. Sujin Kang, who
studies the regulation of metabolism and inflammationfrom an immunological perspective. The other is Dr. Yumi
Matsuoka, who is a researcher in infectious diseases andallergies as well as a clinician in dermatology. She aims
to elucidate the mechanisms of interaction between
host immunity and microorganisms in the skin of allergy
patients.
We continue our efforts to conduct basic research inimmunology and to seek ways to contribute to society,and through research and education, we will continue tocontribute to the advancement of science and grow tolead the world in immunology research.

Kiyoshi TAKEDA, MD/ PhD
Director
WPI Immunology Frontier Research Center

Internationalization is an important mission of IFReC,
and we made progress in our relationships with overseas
research centers in FY2022. We held joint symposia with
the University College of London and the University of
Melbourne in the UK and Australia, respectively. Also in
Osaka, "the International Symposium on Microbiology and
Immunology - The 12th International Symposium of IFReC"
was held, and we enjoyed discussions at a high level.
Although the COVID-19 pandemic appears to be
subsiding, there is still the possibility of another unknown
infectious disease causing another pandemic. IFReC playsa central role in the research of immunology and infectious
disease that transcends the boundaries between research

1Organization

Organization Chart
Organization

As of March 2023

MEXT

Osaka University

WPI Initiative Program Committee

International Advanced
Research Institute (IARI)

JSPS

Joint Research Chairs with the Pharmaceutical Companies
International
Scientific
Advisory
Board

Research
GroupsImmunology Groups• Innovative Drug Discovery in Immunology (Chugai Pharma)• Immune-Therapeutic Drug Discovery (Otsuka Pharma)• Innate Immunity• Innovative Drug Discovery in Host Defense

Imaging Groups
Informatics Groups
Core Instrumentation Facility

Unit for Combined Research Fields

Common Facilities

Animal Resource Center for Infectious Diseases
Network Administration OfficeDirector

Management
Committee

Board of Representatives

Administrative Office

DeputyDirectors

Administrative
Director

General Affairs Section
Administrative
Department• General Affairs Section• Accounting Section• Employment and acceptance procedures for researchers and staff• Social insurance (for part-time staff ), employment insurance• Various research support (MTA, patents, animal experiments, safety etc.)• Support for international researchers and students• IFReC Kishimoto Foundation Fellowship Program

Accounting Section
Research Planning and Management Office• Budget drafting / implementation / management• Acceptance and implementation of third-party funding• Purchasing and payment of payroll, travel expense and honorarium• Health insurance procedures• Management of facilities

Research Planning and Management Office

Cooperative Institutions• Institute for Frontier Life and Medical Sciences, Kyoto University, Japan• RIKEN Center for Integrative Medical Sciences, Japan• University College London, UK• ImmunoSensation2 , Cluster of Excellence, the Rheinische Friedrich-Wilhelms-University of Bonn, Germany

4• Research promotion and support (consultation for grants and patents, etc.)• Establishing research environments (facility and safety management, research agreement, etc.)• Fostering young scientists (Winter School, Advanced Postdoc Program, orientation, etc.)• Organizing scientific events (symposia, colloquia, seminars, etc.)• Public relations (publishing, website, outreach to citizens, etc.)5Committees & Advisory Board for IFReC● Program Director
Akira UKAWA

As of November 2022
WPI Program Director and Academy Director● Program Committee Members
Michinari HAMAGUCHI(Chairperson)

President, Japan Science and Technology Agency (JST)
Chairperson, The Japanese National Commission for UNESCO

Hiroshi AMANO

Professor, Nagoya University, Tokai National Higher Education and Research System Nobel laureate in
Physics (2014)

Mariko HASEGAWA

President, The Graduate University for Advanced Studies

Kazuhiko ISHIMURA

President, National Institute of Advanced Industrial Science and Technology

Maki KAWAI

Director General, Institute for Molecular Science (IMS)
National Institutes of Natural Sciences (NINS)WPI Academy
In 2017, MEXT established the WPI Academy to be the vanguard in internationalizing and further renovating Japan’s research
environment. The WPI Academy is a much-anticipated upgrade of WPI institutes, and is expected to position Japan as a hub at the
pinnacle of international researcher circulation. In the decade ahead, the research institutes of WPI and WPI Academy will work
together to hold public relations and outreach activities.

● Program Officer for IFReC
Kouji MATSUSHIMA

Professor, Research Institute for Biomedical Sciences, Tokyo University of Science

International Scientific Advisory Board for IFReC

Kiyoshi KUROKAWA

6

Lewis LANIER

University of California, San Francisco, USA

Anne O’GARRAThe Francis Crick Institute, UK

Jeffrey RAVETCH

Rockefeller University Immunology, USA

Art WEISS

University of California, San Francisco/Howard Hughes Medical Institute, USA

Joachim SCHULTZ

DZNE/LIMES Institute, University of Bonn, Germany

Kayo INABA

Japan Agency for Medical Research and Development, Japan

Kazuhiko YAMAMOTO

RIKEN Center for Integrative Medical Sciences, Japan

Osamu OHARA

Kazusa DNA Research Institute, Japan

Hiroshi KIYONO

Future Medicine Education and Research Organization at Chiba University, Japan

As of March 2023

Professor Emeritus, National Graduate Institute for Policy Studies

Hiroshi MATSUMOTO

President, RIKEN

Ryozo NAGAI

President, Jichi Medical University

Rita COLWELL

Distinguished University Professor, University of Maryland, USA

Richard DASHER

Organization

The World Premier International Research Center Initiative (WPI)

Director, US-Asia Technology Management Center, Stanford University, USA

Victor Joseph DZAU

President, National Academy of Medicine , USA

Klaus von KLITZING

Director, Max Planck Institute for Solid State Research, Germany
Nobel laureate in Physics (1985)

Chuan Poh LIM

Chairman, Singapore Food Agency (SFA)

Harriet WALLBERG

Professor, Karolinska Institutet, Sweden

Jean ZINN-JUSTIN

Scientific adviser, Institute of Research into the Fundamental Laws of the Universe (IRFU/CEA), France

7

Laboratories
As of March 2023

Host Defense

Professor

Shizuo Akira

Associate Professor

Kazuhiko Maeda

Assistant Professor

Hiroki Tanaka

producing chemokines that attract SatM and lead to lung fibrosis.
Thus, inhibition of RBM7 may be an effective therapy for fibrosis
in patients. We found that fibrosis-promoting macrophages
derived from different monocyte subsets closely interact withother immune and non-immune cells, releasing essential factorsthat maintain the fibrosis niche (Fukushima et al., Immunity 2020).
Our findings provide a comprehensive understanding of themechanisms involved in the development and maintenance offibrosis (Figure. 2).

Immunology

Shizuo Akira, MD/PhD

the pathogenesis is still poorly understood. We have identified a
new macrophage subset called SatM (segregated-nucleuscontaining atypical monocytes), which shares granulocyte
characteristics and is regulated by C/EBPβ). These cells play a
critical role in fibrosis. We have also identified Rbm7, a componentof the NEXT complex, whose increased expression in the fibrotic
phase leads to the suppression of fibrosis when lost in nonhematopoietic cells. Aberrant Rbm7 expression results in
apoptosis via nuclear degradation of non-coding RNA (ncRNA)
Neat1, which is involved in the development of fibrosis by

Kiyoharu Fukushima
Postdoctoral Fellow

2

Research Assistant

6

Visiting Scientist

5

Support Staff

5

Figure 1.
IL-17 induces Regnase-1 phosphorylation in an Act-1/TBK1/IKKi–dependent manner. Phosphorylation of Regnase-1 isreleased from the endoplasmic reticulum into the cytosols, resulting in loss of the mRNA degradation function.

The innate immune system, which has been conserved
throughout evolution, is activated by pattern recognition
receptors (PRRs) that identify specific structures on
microorganisms. Toll-like receptors (TLRs) are a class of PRRs thatcan detect a diverse range of microorganisms, including bacteria,
fungi, protozoa, and viruses. Each TLR recognizes different
components of microorganisms, leading to distinct patterns ofgene expression and activation of the innate immune system.
Our research aims to gain insight into host defense mechanisms
against various pathogens, including acquired immunity, in orderto develop effective therapeutic strategies against immunerelated diseases. Specifically, we are focusing on the RNA-binding
protein (RBP) Regnase-1, which is involved in the development of
autoimmune diseases, and Rbm7 (RNA-binding motif protein 7),
which is another RBP involved in pulmonary fibrosis.

The Role of Endoribonuclease Regnase-1 in Immune
and Non-Immune Cells
Regnase-1 is RBP with endonuclease activity (Maeda & Akira,Int. Immunol., 2018; Akira & Maeda, Annu. Rev. Immunol., 2021).
After Regnase-1 is deleted, mice develop autoimmune diseases
with enlarged spleens and lymph nodes. Our recent studies haveshown that when Regnase-1 is deleted in the NK cells of mice
(Regnase-1ΔNK mice), these mice produce more perforin andinterferon-γ, and as a result, show higher resistance to tumor
progression and metastasis. Furthermore, Regnase-1 regulates its
own expression by binding to its own 3'-untranslated region(3’UTR). To investigate the importance of this negative feedback
mechanism, we generated 3'UTR mutant mice that abolished10

Regnase-1-mediated self-regulation. Currently, we are analyzingthese mutant mice in various disease models.

Phosphorylation of Regnase-1
Phosphorylation of Regnase-1 by IKK at a DSGxxS motif resultsin βTrCP-dependent ubiquitination and degradation (Iwasaki etal., Nat. Immunol., 2011), but the role of other signal transduction
pathways to regulate Regnase-1 function remains largely
unknown. Phosphorylation of Regnase-1 after IL-17 stimulation
also occurs in Regnase-1 mutants that lack the IKK phosphorylationsite (Regnase-1AA/AA and Regnase-1ΔCTD/ΔCTD), which suggests that
other phosphorylation sites may post-translationally modify
Regnase-1 activities. We have shown that IL-17 induces Regnase-1
phosphorylation in an Act1-TBK1-IKKi-dependent manner,particularly in non-hematopoietic organs (Tanaka et al, J. Exp.
Med., 2019). Phosphorylated Regnase-1 is released from theendoplasmic reticulum into the cytoplasm, thereby losing its
mRNA degradation function and allowing IL-17 target genes tobe expressed (Figure. 1). Thus, Regnase-1 plays an important rolein the pathogenesis of IL-17-mediated inflammatory diseases via
the Act1-TBK1-IKKi axis, and blocking the phosphorylation site ofRegnase-1 may be a promising treatment for T helper 17-relateddiseases.

Diversity of Monocyte Subsets and their Role in Lung
Fibrosis in Humans and Mice
Fibrosis is a life-threatening disease with unknown causes, andeffective therapies are few. The activation of monocytes andmacrophages is associated with the development of fibrosis, but

Figure 2.
RBM-7 regulates fibrosis formation through ncRNA decay and cell death. RBM-7 destabilizes ncRNA NEAT1 and inducescell death in lung epithelial cells, resulting in recruitment of SatM and fibrocytes into the lung to promote lung fibrosis.

Recent Publications
1. Morisaka H, Takaishi M, Akira S, Sano S. Keratinocyte Regnase-1, a
downregulator of skin inflammation, contributes to protection
against tumor promotion by limiting cyclooxgenase-2 expression . J
Invest Dermatol. (2022).

4. Tanaka H, Arima Y, Kamimura D, Tanaka Y, Takahashi N, Uehata T,
Maeda K, Satoh T, Murakami M, Akira S. Phosphorylation-dependent
Regnase-1 release from endoplasmic reticulum is critical in IL-17
response. J Exp Med. 216:1431-1449 (2019).

2. Akira S and Maeda K. Control of RNA stability in immunity. Annu. Rev.
Immunol. 39:481-509 (2021).

5. Nagahama Y, Shimoda M, Mao G, Singh SK, Kozakai Y, Sun X, Motooka
D, Nakamura S, Tanaka H, Satoh T, Maeda K, Akira S. Regnase-1 controls
colon epithelial regeneration via regulation of mTOR and purine
metabolism. Proc Natl Acad Sci USA. 115:11036-11041 (2018).

3. Fukushima K, Satoh T, Sugihara F, Sato Y, et al. Dysregulated expressionof the nuclear exosome targeting complex component Rbm7 in nonhematopoietic cells licenses the development of fibrosis. Immunity
52:542-556 (2020).

11

Immunoglycobiology
Immunology

Taroh Kinoshita, PhD
Yoshiko Murakami, MD/PhD (Co-Pl)
Professor

Taroh Kinoshita
Yoshiko Murakami

Research Assistant

2

Visiting Scientist

2

Support Staff

2

Figure 1.
Model of GPI biosynthesis upregulation mechanism in cells defective in GPI transamidase and ERAD (Adopted from Liu
Y-S et al, J. Cell Biol., 2023).

Our major interest has been biosynthesis and deficiencies ofglycosylphosphatidylinositols (GPIs), which are a class of glycolipids
acting as membrane-anchors of more than 150 various cellsurface proteins and also being present as free glycolipids. In
FY2022, we made the following progress.

Mechanism of GPI biosynthesis up-regulation
It has been unclear how cells upregulate GPI biosynthesis
when needed. In cells defective in GPI transamidase that transfers
GPI to proteins, precursors of GPI-APs are usually degraded by ERassociated degradation (ERAD). We previously reported thatwhen both ERAD and GPI transamidase are defective in HEK293
cells, undegraded GPI precursors remain and GPI biosynthesis
increases 8- to 10-fold (Wang Y et al, Nat Commun, 2020). We
investigated mechanisms of this GPI biosynthesis up-regulationand found that accumulated precursors of specific GPI-APs, suchas CD55, CD48 and PLET1, upregulate GPI biosynthesis. We
showed that their C-terminal GPI attachment signal peptides arefunctional elements. We then found that ARV1, an ER-membraneprotein implicated in lipid homeostasis and GPI biosynthesis, isrequired for this GPI upregulation (Figure 1). There must be amechanism that senses the presence of specific GPI-AP precursors
that remain, which signifies GPI shortage and triggers
upregulation of GPI biosynthesis (Liu Y-S et al, J. Cell Biol., 2023).

Discovery of non-conventional mode of GPI-attachment
Until recently, it was believed that proteins are always attachedto GPI-anchors by making an amide bond with ethanolaminephosphate (EtN-P) linked to the third mannose (Man3), so-called

12“bridging EtN-P.” The core glycan of GPI precursor has threemannoses, which in mammals, are all modified by EtN-P. Whereas
EtN-P on Man3 acts as the bridge to the protein and EtN-P on
Man1 remains as a sidechain, EtN-P on Man2 is removed after
GPI-protein attachment. However, EtN-P on Man2 may not be
always transient, as mutations of PIGG, the enzyme that transfers
EtN-P to Man2, cause inherited GPI deficiency, characterized byneuronal dysfunctions. We showed in 2022 that EtN-P on Man2 is
the preferential bridge in some GPI-APs, such as ect-5’nucleotidase (NT5E) and netrin G2 (NTNG2) (Figure 2). We also
found that all CD59, a GPI-anchored complement regulator, in
PIGB-knockout cells, in which GPI lacks Man3, and a small fractionof CD59 in wild type cells are attached via EtN-P on Man2 to GPIanchors. Our findings modified the previous view of GPI
anchoring and provided a mechanistic basis of inherited GPI
deficiency caused by PIGG mutations (Ishida M et al, EMBO Rep.,
2022).

Gene therapy of inherited GPI deficiency model mice
To establish effective therapies for inherited GPI deficiency, we
generated model mice by knocking in pathogenic mutations into
the Pigo gene. The model mice had symptoms similar to some ofthose seen in human individuals with inherited Pigo deficiency.
Adeno-associated virus PHP.eB (AAV-PHP.eB)-based genetherapy that aimed to systemically restore normal Pigo mRNA in
the model mice was effective in ameliorating some symptoms(Kuwayama R et al, Nat. Commun., 2022).

Figure 2.
Ethanolamine-phosphate on the second mannose is a preferential bridge for some GPI-anchored proteins, such as NT5E
and NTNG2 (Adopted from Ishida M et al, EMBO Rep., 2022).

Recent Publications
1. Liu LS, Wang Y, Zhou X, Zhang L, Gao XD, Murakami Y, Fujita M andKinoshita T. Accumulated precursors of specific GPI-anchored proteins
upregulate GPI biosynthesis with ARV1. J Cell Biol. 222: e202208159(2023).
2. Kuwayama R, Suzuki K, Yoshioka Y, et al. Establishment of a mousemodel of inherited PIGO deficiency and therapeutic potential of AAVbased gene therapy. Nat Commun. 13:3107 (2022).

4. Wang Y, Menon AK, Maki Y, et al. Genome-wide CRISPR screen reveals
CLPTM1L as a lipid scramblase required for efficient glycosylphosphatidylinositol
biosynthesis. Proc Natl Acad Sci USA., 119(14): e2115083119 (2022).
5. Hirata T, Kobayashi A, Furuse T, et al. Loss of the N-acetylgalactosamineside chain of the GPI-anchor impairs bone formation and brain
functions and accelerates the prion disease pathology. J Biol Chem.
298(3):101720 (2022).

3. Ishida M, Maki Y, Ninomiya A, et al. Ethanolamine-phosphate on thesecond mannose is a preferential bridge for some GPI-anchoredproteins. EMBO Rep., e54352 (2022).

13

Immunopathology
Immunology

Atsushi Kumanogoh, MD/PhD

Our team adopts a two-pronged approach to research: basic
immunology and clinical immunology. Our proposed study aims
to investigate the regulation of immune cell motility andmigratory behavior in vivo by soluble and membrane-bound‘immune guidance molecules,’ such as semaphorins and their
receptors. Semaphorins were originally identified as axonguidance molecules that function during neuronal development.
However, cumulative evidence indicates that semaphorins also
participate in immune responses, both physiological andpathological, and they are now considered to be potential
diagnostic and/or therapeutic targets for a range of diseases.
Beyond such basic implications, we are trying to apply thefindings from this proposed study to the diagnosis/therapy forhuman immunological disorders, such as autoimmunity, allergy,
immune deficiency, cancer/metastasis, and neurodegenerative
diseases. We recently focus on the crosstalk among neuronal,
immune and metabolic systems since some of the semaphorins’
expression are regulated by a metabolic sensor, mTOR, in which
we investigated the biological and pathological significance ofLamtor1/p18, an amino acid sensor localized at the lysosome.
Lamtor1 is an essential component of the Ragulator complex.
Although the Ragulator complex has a clearly established role asa regulator of cellular metabolic states by coordinating mTORC1
and AMPK activities, recent research has focused on its otherfunctions. The Ragulator complex is a platform for maintaining
cellular homeostasis, with roles in integrin signaling via Lamtor2–
MEK, acidification of lysosomes via V-type ATPase, lysosome
biogenesis by enhanced TFEB nuclear translocation, endomembrane

14

Professor

Atsushi Kumanogoh

Assistant Professor

Takahiro Kawasaki

Research Assistant5

Support Staff

5

damage repair or organelle homeostasis, and the regulation of
migration through interactions with the myosin phosphataseRho-interacting protein. In addition to these regulatory effects on
cellular functions, we have uncovered a variety of roles of the
Ragulagtor complex as an inflammatory signaling hub. However,the precise role of the Ragulator complex in NLRP3 inflammasome
activation requires elucidation. Here, we show the vital role of the
Ragulator complex in NLRP3 inflammasome activation. Deficiency
of Lamtor1 abrogated NLRP3 inflammasome activation in murine
macrophages and human monocytic cells. Myeloid-specific
Lamtor1-deficient mice showed marked attenuation of NLRP3associated inflammatory disease severity, including LPS-induced
sepsis, alum-induced peritonitis, and monosodium urate (MSU)induced arthritis.
Mechanistically, Lamtor1 interacted with both NLRP3 andhistone deacetylase 6 (HDAC6). HDAC6 enhances the interaction
between Lamtor1 and NLRP3, resulting in NLRP3 inflammasome
activation. DL-all-rac-a-tocopherol, a synthetic form of vitamin E,
inhibited the Lamtor1– HDAC6 interaction, resulting in diminishedNLRP3 inflammasome activation. Further, DL-all-rac-a-tocopherol
alleviated acute gouty arthritis and MSU-induced peritonitis.
These results provide novel insights into the role of lysosomes in
the activation of NLRP3 inflammasomes by the Ragulator
complex.

Figure.
How inflammasome activation is orchestrated by specific organelles remains unclear. Here, the lysosomal Ragulator
complex is shown to enhance NLRP3 inflammasome activation via histone deacetylase 6 (HDAC6). Deficiency of Lamtor1,
an essential component of the Ragulator complex, abrogated NLRP3 inflammasome activation in vitro and in mice. The
Ragulator complex interacted with HDAC6, which facilitated the interaction between the Ragulator complex and NLRP3,
and that both interactions were required for the activation of the NLRP3 inflammasome.

Recent Publications
1. Tsujimoto K, Jo T, Nagira D, Konaka H, et al. The lysosomal Ragulator
complex activates NLRP3 inflammasome in vivo via HDAC6. EMBO J.
42(1):e111389 (2023).
2. Nakatani T, Tsujimoto K, Park J, Jo T, Kimura T, Hayama Y, Konaka H,
Morita T, Kato Y, Nishide M, Koyama S, Nada S, Okada M, Takamatsu H,
Kumanogoh A. The lysosomal Ragulator complex plays an essential
role in leukocyte trafficking by activating myosin II. Nat Commun.
12(1):3333 (2021).

3. Tsuda T, Nishide M, Maeda Y, Hayama Y, Koyama S., et al. Pathologicaland therapeutic implications of eosinophil-derived semaphorin 4D ineosinophilic chronic rhinosinusitis . J Allergy Clin Immunol. 145(3):843854 (2020).
4. Kang S, Nakanishi Y, Kioi Y, Okuzaki D, et al. Semaphorin 6D reverse
signaling controls macrophage lipid metabolism and antiinflammatory polarization. Nature Immunol. 19:561-570 (2018).

15

Immunochemistry
Immunology

Hisashi Arase, MD/PhD

Professor

Hisashi Arase

Assistant Professor

Wataru Nakai
Hui JinA) Misfolded proteins complexed with MHC class II
molecules are targets for autoimmune diseases.
MHC class II allelic polymorphisms are associated withsusceptibility to many autoimmune diseases. However, it hasremained unclear how MHC class II molecules are involved in
autoimmune disease susceptibility. We found that misfolded
cellular autoantigens are rescued from protein degradation by
MHC class II molecules (Int. Immunol. 2013). Furthermore, we
found that misfolded proteins complexed with MHC class II
molecules are targets for autoantibodies in autoimmune diseases
such as rheumatoid arthritis, antiphospholipid syndrome, andANCA-associated vasculitis (PNAS 2014; Blood. 2015; Br. J.
Dermatol. 2017; Arthritis Rheumatol. 2017; Arthritis Rheumatol.
2021). Furthermore, autoantibody binding to misfolded proteinstransported to the cell surface by MHC class II molecules wasstrongly correlated with susceptibility to autoimmune diseases.
Further analyses revealed that self-antigens complexed withMHC II molecules abrogate self-tolerance to induce autoimmune
response (Science Advances 2022). In addition, we found that not
only misfolded protein but also DNA is presented on MHC class II
molecules with SLE-risk allele but not with SLE-protective allele(Arthritis Rheumatol. 2022). These findings demonstrated that
misfolded proteins, which normally would not be exposed to theimmune system, are involved in the pathogenicity of autoimmune
diseases as ‘neo-self’ antigens (Figure 1).

B) Studies on host-pathogen interaction
The immune system has evolved with infectious diseases,
indicating that studies on host-pathogen interaction are important
16

Postdoctoral Fellow

1

Research Assistant

2

Visiting Scientist

1

Support Staff

4

to understand the immune system. We found that PILRα, one of apair of receptors, plays an important role in the regulation of
immune response (Nat. Immunol. 2012; Int. Immunol. 2015; Eur. J.
Immunol. 2016) as well as HSV-1 infection (Cell 2008; J. Virol. 2009).
Similarly, Siglec-4 and Siglec-7, which are a pair of receptors, areinvolved in VZV infection (PNAS 2010; BBRC 2022). LILR is anothertype of paired receptor family. We found that activating LILRA2 isinvolved in the detection of immunoglobulin abnormalities in
microbial infection (Nature Microbiology 2016). Furthermore, we
found that RIFINs, products of multigene family of Plasmodium
falciparum, are involved in immune evasion through binding to
inhibitory LILRB1 and LILRB2 (Nature 2017; Nature 2020; BBRC
2021). These findings demonstrated that paired receptors play animportant role in immune regulation as well as viral infection.
SARS-CoV-2 causes severe pneumonia in some infectedindividuals. Therefore, it is important to elucidate the factors thatcause severe COVID-19. Antibodies against the receptor-binding
domain (RBD) of spike protein play an important role in the
defense against SARS-CoV-2 infection. However, we found thatsome antibodies against the N-terminal domain (NTD) of spike
protein cause conformational changes in spike protein andenhance infectivity. In particular, anti-NTD antibodies thatenhance infectivity were found more in severe patients,suggesting that the antibodies may be involved in thedevelopment of severe disease (Cell 2021, Figure 2). Thesefindings indicated that the infectivity-enhancing antibodies must
be considered in antibody response against SARS-CoV-2.

Figure 1.
Misfolded proteins transported to the cell surface by MHC class II molecules are targets for autoantibodies.
Misfolded cellular proteins are generally degraded in the cells and are not transported to outside the cells. Therefore,
misfolded proteins transported to the cell surface by MHC class II molecules may be recognized as ‘neo-self’ antigens by
the immune system, which initiates an aberrant immune response to self-antigens (Int. Immunol. 2013; PNAS 2014; Blood
2015, Br. J. Dermatol. 2017; Arthritis Rheumatol. 2017, Arthritis Rheumatol. 2020; Arthritis Rheumatol. 2022; Science
Advances 2022).

Figure 2.
SARS-CoV-2 infectivity enhancing antibodies.
Some antibodies against NTD of spike protein induces conformational change in spike protein to induce the open formof RBD and enhance the infectivity of SARS-CoV-2 (Cell 2021).

Recent Publications
1. Jin H, Kishida K, Arase N, Matsuoka S, Nakai W, Kohyama M, Suenaga T,
Yamamoto K, Sasazuki T, Arase H. Abrogation of self-tolerance by
misfolded self-antigens complexed with MHC class II molecules. Sci
Advances. 8:eabj9867. (2022).
2. Tsuji H, Ohmura K, Jin H, et al. Anti-Double-Stranded DNA Antibodies
Recognize DNA Presented on HLA Class II Molecules of Systemic
Lupus Erythematosus Risk Alleles. Arthritis Rheumatol. 74:105-111(2022).
3. Liu Y, Soh WT, Tada A, Arakawa A, Matsuoka S, Nakayama EE, Li S, Ono
C, Torii S, Kishida K, Jin H, Nakai W, Arase N, Nakagawa A, Shindo Y,
Kohyama M, Nakagami H, Tomii K, Ohmura K, Ohshima S, Okada M,
MatsuuraY, Standley DM, Shioda T, Arase H. An infectivity-enhancing
site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient
antibodies. Cell.184:3452-3466 (2021).

4. Saito F, Hirayasu K, Satoh T, Wang CW, et al. Immune evasion of
Plasmodium falciparum by RIFIN via inhibitory receptors. Nature.
552:101-105 (2017).
5. Hiwa R, Ohmura K, Arase N, Jin H, Hirayasu K, Kohyama M, Suenaga T,
Saito F, Terao C, Atsumi T, Iwatani H, Mimori T, Arase H. Myeloperoxidase/
HLA Class II Complexes Recognized by Autoantibodies in Microscopic
Polyangiitis. Arthritis Rheumatol. 69:2069-2080 (2017).
6. Hirayasu K, Saito F, Suenaga T, Shida K, Arase N, Oikawa K, Yamaoka T,
Murota H, Chibana H, Nagai H, Nakamura Y, Katayama I, Colonna M,
Arase H. LILRA2 is an innate immune sensor for microbially cleaved
immunoglobulins. Nat Microbiol. 1:1-7 (2016).

17

Immune Regulation

Endothelial gp130-HIF1α signaling on the onset ofcytokine release syndrom
Endothelial integrity is important for maintaining immune
homeostasis. Previously, we identified that interleukin (IL)-6trans-signaling induced endothelial activation in the context ofcytokine production and activation of the coagulation cascade.
Treatment with an anti-IL-6 Receptor (IL-6R) antibody, tocilizumab
inhibited endothelial activation and prevented the developmentof cytokine release syndrome (CRS). Thus, tocilizumab wasrecently approved by the United States Food and Drug
Administration for the treatment of SARS-CoV-2 infectioninduced pneumonia. In our lab, to clarify the downstream
pathway of IL-6 trans-signaling in endothelial activation, we
performed an RNA-seq analysis of primary human vascularendothelial cells (HUVECs). We found that expression of HIF1α
was substantially increased by IL-6 trans-signaling in HUVECs.
Additionally, inhibition of HIF1α activity in HUVECs decreased theexpression of IL-6, IL-8, MCP-1, and plasminogen activation
inhibitor-1 (PAI-1) in response to IL-6 trans-signaling. Moreover,knockdown of gp130 suppressed expression of glycolysis-related
enzymes including HK2 and PFKFB3, which are target genes of
HIF1α transcriptional activity, indicating that IL-6 signaling
induces vascular inflammation via glycolysis activation inendothelium. Next, we generated the endothelial-specific gp130
knockout mice (gp130ECKO) to delineate the role of gp130-HIF1α
signaling on endothelium during cytokine storm in vivo. At theonset of sepsis, gp130ECKO mice showed resistance to survival rate,and decreased inflammatory cytokines production andendothelial permeability. Consistently, lung endothelial cells
18

Professor

Tadamitsu Kishimoto

Associate Professor

Sujin Kang

Postdoctoral Fellow

1

Support Staff

5

from gp130ECKO mice displayed decreased levels of HIF1α
expression. Thus, our findings demonstrated that endothelial
gp130-HIF1α signaling promotes vascular inflammation andsepsis progression. However, the long-lasting and discriminatory
suppression of IL-6 signaling in the acute critical care setting
raises concerns about the increased risk of secondary infections.
To overcome the limitations of IL-6 signaling blockade in acuteinflammatory diseases, we generated an anti-IL-6R antibody(silent anti-IL-6R antibody) with a short half-life to reduce Fcmediated side effects. We found that the treatment of CRS mousemodels including thermal injury and sepsis models with the silent
anti-IL-6R antibody significantly improved the survival ratecompared with controls. Additionally, we found that silent antiIL-6R antibody treatment prevented endothelial damage byinhibiting glycocalyx degradation, increasing endothelial
permeability, and PAI-1 production. Consequently, treatment
with silent anti-IL-6R antibodies showed significant efficacy inseveral acute inflammatory diseases by controlling endothelial
injury (Fig. 1).

exhibited increased expression of JAK-mediated pTyr STAT1.
Tofacitinib, a JAK inhibitor, has been approved for the treatmentof patients with ulcerative colitis. A potential explanation of theseparadoxical findings is that the protective role of STAT1 inulcerative colitis is largely independent of the canonical JAKSTAT1 pathway. We evaluated the intestinal inflammation of
wild-type (WT) and STAT1T748A mice following DSS
administration. Notably, STAT1T748A mice exhibited severe
colitis compared to WT mice by weight loss, colon lengths, andhistopathological analysis. We assessed the intestinal inflammationof STAT1KO and their STAT1T748A littermates by DSS
administration. STAT1T748A mice phenotype completely
mimicked the detrimental phenotype of STAT1KO littermates.
We found that epithelial cells, not immune cells, are responsible
for the phenotype observed in T748A mice. Our data indicatethat threonine748 phosphorylation on STAT1 is a key driver for
STAT1 protective function against intestinal inflammation.
Consequently, we found that pThr STAT1 contributed to STAT1
functions to a different extent in vivo in various disease models,and our findings suggest that cell-dependent threonine kinase
pathways contribute to the specificity of STAT1 functions,especially those not driven by canonical JAK pathway (Fig. 2).

Figure 1.
Targeting of anti-IL-6R antibody for infectious diseases by inhibition of endothelial injuries.

Immunology

Tadamitsu Kishimoto, MD/PhD
Sujin Kang, PhD (Co-Pl)

Thr748 phosphorylation of STAT1 protects the host against
lipopolysaccharide (LPS)-induced septic shock: We generated
genetically engineered mice expressing a non-phosphomimetic
threonine748-to-alanine (T748A) mutant STAT1. We found that
STAT1T748A and heterozygous mice exhibited higher survival
compared with control mice against LPS-induced septic shock,suggesting pThr STAT1 promoted the host inflammatory
response in sepsis. Additionally, STAT1T748A mice were resistantto LPS-induced lethality, albeit to a lesser extent than their STAT1deficient littermates. Notably, expression of STAT1 and other
STAT proteins was unperturbed in STAT1T748A mice, suggestingthat threonine748 phosphorylation of STAT1 regulates inflammatory
response against LPS-induced septic shock. We found thatmonocytes derived macrophages (MDMs) from STAT1T748A
mice decreased expression of inflammatory cytokines including
IL-6, IL-12. In contrast, MDMs from STAT1T748A mice increased
expression of antiviral genes, RSAD2, IFIT2, and increased IL-10
expression. Our work indicates that T748A mutation of STAT1
may induce anti-inflammatory characteristics of macrophages,
which alleviates the inflammatory response against sepsis. 2)
Disruption of Thr748 phosphorylation of STAT1 promotes
colitis: A deficiency in STAT1 leads to severe DSS-induced colitis.
However, colon samples from patients with ulcerative colitis

Figure 2.
Role of novel phosphorylation site of STAT1 in vivo.

Threonine phosphorylation of STAT1 controls the hostinflammatory response
The STAT1 working paradigm has focused on interferon (IFN)
mediated JAK-Tyr701 phosphorylation. However, IFN-JAK
signaling does not explain the full spectrum of STAT1 functions
against inflammatory stimuli. Our recent work identified thenovel Thr749 (Thr748 in mouse) phosphorylation of STAT1, which
triggered distinct gene-regulatory functions of STAT1 independentof the canonical Tyr701 phosphorylation. 1) Disruption of

Recent Publications
1. Kishimoto T* and Kang S*. IL-6 Revisited: From Rheumatoid Arthritis to
CAR T Cell Therapy and COVID-19. Annu Rev Immunol. 40:323-348(2022). (*equally contributed).
2. Narazaki M, Kishimoto T. Current status and prospects of IL-6-targetingtherapy. Expert Rev Clin Pharmacol. 15(5):575-592 (2022).

3. Hashimoto S, Kishimoto T. Roles of RNA-binding proteins in immune
diseases and cancer. Semin Cancer Biol. 86(Pt 3):310-324 (2022).
4. Nyati KK, Kishimoto T. Recent Advances in the Role of Arid5a in
Immune Diseases and Cancer. Front Immunol. 19;12:827611 (2022).

19

Mucosal Immunology
Kiyoshi Takeda, MD/PhD

Professor

Kiyoshi Takeda

Associate Professor

Hisako Kayama

Assistant Professor

Ryu Okumura

Immunohistochemical evaluation of CD4 and CD103 doublepositive cells including CDpop in the lamina propria revealed thatthey localized adjacent to the epithelia. Coculture of humanderived spheroids with CDpop stimulated with a cytokine cocktail
resulted in the epithelial damage accompanied by the elevationof LDH levels in the culture supernatant that is comparable to thefindings observed when IFN-γ was added to the spheroids. In
contrast, coculture with CDpop without cytokine cocktail did not
disrupt the spheroid structure or induce LDH release. This
response was inhibited by the addition of a neutralizing antibody
against IFN-γ. Finally, the positive correlation between theabundance of CDpop in the gut biopsy samples and a clinicalactivity score suggests that the accumulation of this T-cell subset
is a pathological hallmark of CD.

Immunology

Cytotoxic effect of CD-predominant T cells on epithelial
layer is maximized by their localization properties

Mari Murakami
Taiki Sakaguchi

Inflammatory bowel disease (IBD), which consists of Crohn’sdisease (CD) and ulcerative colitis (UC), involves chronic
inflammation of digestive tract. Despite a plethora of studies
emphasizing the involvement of T cells in the pathogenesis of
IBD, no disease-specific T-cell subset that plays an essential role in
the progression of IBD has been identified. In this study, we
performed deep profiling of T cells in the intestinal mucosa of IBD
and identified a particular subset of CD4+ tissue-resident memory
T cell (Trm) subset that is prevalent in CD showing uniqueinflammatory properties. Our results highlight the importance of
CD4+ Trm in the pathogenesis of CD, which can be applicable tothe development of T cell-directed strategies.

CD and UC are characterized by distinct T-cell subsets
To explore the specific molecular properties of each subtype of
IBD, we applied mass cytometry panels using antibodies against
28 cell surface markers, which allow us to capture various types ofT-cell subsets. We profiled the intestinal lamina propria
mononuclear cells isolated from inflamed gut mucosa of patientswith CD, UC, and unaffected mucosal regions of colon cancer
patients as a control. Overall, landscape of adaptive immunity in
CD and UC were clearly distinguished from each other by themarked changes in the specific clusters. CD4+ Trm weresignificantly increased in CD, whereas follicular helper T cells
were significantly increased in UC. Heatmaps of the mean
expression levels of T-cell markers revealed that a particular
fraction of CD4+ Trm abundant in the gut of CD (CD-enriched
population: CDpop) exhibited high expression of CD103, CD161
and CCR5 compared with other T-cell fractions. Furthermore,

20

Postdoctoral Fellow

1

Research Assistant

9

Visiting Scientist

1

Support Staff

4

CD4+ Trm expressing CCR5 or CD161 produced significantly
higher IFN-γ levels upon phorbol 12-myristate 13-acetate (PMA)/
ionomycin stimulation than their negative counterparts that did
not express these markers.

CD4+ Trm are reprogrammed in CD gut to initiate
effector and innate functions
To identify the transcriptional landscape of IBD gut, single-celltargeted RNA-sequencing (scRNA-seq) analysis of CD3+ T cells
was performed. Multi-resolution Reconciled Tree, which reflect
the extent of transcriptional distinctions among cell groups,
applied to scRNA-seq datasets revealed that the transcriptionalsignature of CD4+ CD8- Trm is more closely related to that of CD8+
T cells rather than other CD4+ T cell subsets and enriched ininnate immune-like cytotoxic pathways. Notably, a particularsubset of CDpop is highly specific to CD patients. This CD-specificCD4+ Trm highly expressed genes associated with cytotoxicity,such as NKG6, GZM, and GNLY, and also significantly upregulated
Th1-related genes, such as IFNG and TBX21. In vitro evaluation of
CDpop revealed that it secretes IFN-γ by cytokine stimulation
without exogenous TCR ligation, implicating the innate aspect of
this subset. Cytokines that stimulated CDpop includes IL-12, IL18, IL-7, and IL-15, which are known to be elevated in the intestinal
mucosa of IBD patients. Thus, the effector function of CDpop canbe maximally enhanced by the unique cytokine milieu in IBD gut.
Furthermore, CDpop was the predominant producer of type-1
inflammatory cytokines upon stimulation by both cytokine
cocktail and PMA/ionomycin stimuli among all CD4+ T cellsubsets.

Figure.
In the lamina propria of Crohn's disease (CD) patients, CD4+ CD103+ CCR5+ CD161+ tissue resident memory T
cells (Trm), which localize adjacent to the gut epithelial cells are expanded. These Crohn’s disease-specificTrm are stimulated by cytokines which are abundant in the gut of CD patients, and secrete IFN-γ and GZM.
This in turn activate inflammatory immune cells and damage adjacent epithelial cells, exacerbating thedisease.

Recent Publications
1. Nii T, Maeda Y, Motooka D, et al. Genomic repertoires linked withpathogenic potency of arthritogenic Prevotella copri isolated fromthe gut of rheumatoid arthritis patients. Annals Rheum. Dis. In press.
2. Yokoi T, Murakami M, Kihara T, et al. Identification of a unique subset oftissue resident memory CD4+ T cells in Crohn's disease. Proc. Natl.
Acad. Sci. USA 120, e2204269120 (2023).

4. Tani H, Li B, Kusu T, Okumura R, et al. The ATP-hydrolyzing ectoenzyme
E-NTPD8 attenuates colitis through modulation of P2X4 receptordependent metabolism in myeloid cells. Proc. Natl. Acad. Sci. USA118,
e2100594118, (2021).
5. Morita N, Umemoto E, Fujita S, Hayashi A, et al. GPR31-dependent
dendrite protrusion of intestinal CX3CR1+ cells by bacterial
metabolites. Nature 566,110-114 (2019).

3. Otake-Kasamoto Y, Kayama H, Kishikawa T, et al. Lysophosphatidylserines
derived from microbiota in Crohn's disease elicit pathological Th1
response. J. Exp. Med. 219, e20211291 (2022).

21

Experimental Immunology

long-lasting memory and without deleterious autoimmunity.
Cancer immunotherapy with cell-depleting anti-CCR8 mAb isenvisaged in the clinic.

Immunology

Treg depletion, which eradicated tumors but induced severe
autoimmune disease. Thus, specific removal of clonally expanding
Tregs in tumor tissues for a limited period by cell-depleting antiCCR8 mAb treatment can generate potent tumor immunity with

Shimon Sakaguchi, MD/PhD

Professor

Shimon Sakaguchi

Associate Professor

Kenji Ichiyama

Assistant Professor

Yusuke Takeshima
Kelvin Chen Yigene

This laboratory studies: (i) the cellular and molecular basis of
immunologic self-tolerance, in particular the roles of regulatory T
cells (Tregs); (ii) the strategy for eliciting effective immune
responses to autologous tumor cells, or inducing immunologic
tolerance to organ transplants, by manipulating the mechanismof immunologic self-tolerance; and (iii) the cause andpathogenetic mechanism of systemic autoimmune diseases,
such as rheumatoid arthritis, by utilizing an animal model
established in our laboratory.
Tregs, which specifically express the transcription factor Foxp3,
are actively engaged in the maintenance of immunological selftolerance and homeostasis. They are abundant in tumor tissues,
hampering effective anti-tumor immune responses; and theirdepletion is indeed able to evoke/enhance tumor immunity.
However, one of the difficulties to specifically eliminate tumor
Tregs by targeting a molecule expressed by Tregs is that amajority of such candidate molecules are commonly shared bytumor-infiltrating Tregs and activated conventional T cells. For
example, CTLA-4 and PD-1 are both expressed by Tregs and CD8+
CTLs in tumor tissues. We have previously shown that highADCC/ADCP anti-CTLA-4 mAb treatment effectively evoked antitumor immune responses in tumor-bearing mice only when mAbadministered first to deplete Tregs and then tumor antigen
vaccination several days later to spare activated CD8+ CTLs fromcell depletion by the mAb treatment (Ha et al., PNAS 2019). In
contrast, anti-PD-1 blocking mAb not only activate PD-1+ CD8+
CTLs, but also occasionally drive PD-1+ Tregs to proliferate andenhance their suppressive activity, hindering tumor immunityand even causing rapid cancer progression called hyper-

22

Postdoctoral Fellow

4

Research Assistant

3

Visiting Scientist

16

Support Staff

3

progressive disease (HPD) (Kamada et al., PNAS 2019).
These findings have prompted us to search for a molecule thatis more specifically expressed by Tregs but not by activated CD8+
CTLs in tumor tissues, enabling specific depletion of tumor Tregs
but not activated CD8+ CTLs. In 2022, assuming that tumor Tregs
would clonally expand when they were activated by tumorassociated antigens to suppress anti-tumor immune responses,
we performed single-cell analysis on tumor Tregs to characterizethem by T-cell receptor (TCR) clonotype and gene expression
profiles. We found that multi-clonal Tregs present in tumor
tissues predominantly expressed the chemokine receptor CCR8.
In mice and humans, CCR8+ Tregs constituted 30-80% of tumor
Tregs in various cancers and less than 10% of Tregs in othertissues, whereas most tumor-infiltrating conventional T cells(Tconvs) were CCR8–. CCR8+ tumor Tregs were highly
differentiated, functionally stable, and potently suppressive.
One-time administration of cell-depleting anti-CCR8 mAb indeed
selectively eliminated multi-clonal tumor Tregs, leading to cureof established tumors in mice. The treatment resulted in the
expansion of CD8+ effector Tconvs, including tumor-antigenspecific ones, that were more activated and less exhausted thanthose induced by anti-PD-1 immune checkpoint blockade. AntiCCR8 mAb treatment also evoked strong secondary immune
responses against the same tumor cell line inoculated several
months after tumor eradication, indicating that elimination oftumor-reactive multi-clonal Tregs was sufficient to induce
memory-type tumor-specific effector Tconvs. Despite inductionof such potent tumor immunity, anti-CCR8 mAb treatment
elicited minimal autoimmunity in mice, contrasting with systemic

Figure.
(A) Search for the genes specifically expressed by clonally expanding tumor Tregs. Tumor-infiltrating CD3+ T cells in CT26bearing mice on day18 after tumor cell inoculation were analyzed for gene expression by single-cell RNA-seq. The Treg
population defined by the expression of Treg function-associated genes was divided into the clonally expanded population (i.e.,
more than two Tregs commonly expressing a particular TCR clonotype) (red dots) and the clonally non-expanded one (i.e., every
Treg expressing a non-replicated unique TCR) (blue dots) by TCR clonotyping. Volcano plot shows gene expression profiles of
the two cell populations. (B) CCR8 protein expression by CD3+CD4+ T cells in LNs, draining LNs (DLNs) and tumors. (C) Tumor
growth in tumor-bearing mice treated with anti-CCR8 or control mAb. Antibodies were administered on day 5 to mice with CT26
colon tumor.

Recent Publications
1. Tanaka A, Maeda S, Nomura T, et al. Construction of a T-cell receptor
signaling range for spontaneous development of autoimmune
disease. J. Exp. Med. 220(2):e20220386 (2023). doi: 10.1084/
jem.20220386.

4. Kawakami R, Kitagawa Y, et al. Coordinated activation of distinct
Foxp3 enhancer elements for Treg development, maintenance, andimmunological self-tolerance. Immunity. 54(5):947-961.e8 (2021). doi:
10.1016/j.immuni.2021.04.005.

2. Kidani Y, Nogami W, Yasumizu Y, et al. CCR8-targeted specific depletionof clonally expanded Treg cells in tumor tissues evokes potent tumor
immunity with long-lasting memory. Proc Natl Acad Sci USA.
119(7):e2114282119 (2022). doi: 10.1073/pnas.2114282119.

5. Ohkura N, Yasumizu Y, Kitagawa Y, Tanaka A, Nakamura Y, Motooka D,
Nakamura S, Okada Y, Sakaguchi S. Regulatory T cell-specificepigenomic region variants are a key determinant of susceptibility tocommon autoimmune diseases. Immunity. 52(6):1119-1132.e4 (2020).
doi: 10.1016/j.immuni.2020.04.006.

3. Tekguc M, James Badger Wing JB, Osaki M, Long J, Sakaguchi S. Tregexpressed CTLA-4 depletes CD80/CD86 by trogocytosis, releasing free
PD-L1 on antigen-presenting cells. Proc Natl Acad Sci USA.
118(30):e2023739118 (2021). doi: 10.1073/pnas.2023739118.

23

Cell Signaling
Immunology

Takashi Saito, PhD

Professor

The objective of our team is to determine the molecularmechanisms of T cell activation, differentiation and function.
Ultimately, we wish to elucidate the onset of and to modulate T
cell function/activation to prevent immune diseases such as
autoimmunity and allergic inflammation. For this purpose, we
analyzed the regulation of T cell activation/function from asignaling perspective.

1. Regulation of T cell function by innate signaling.
We found that Receptor-interacting serine/threonine-protein
kinase 1 (RIPK1) plays a critical role in T cell function andparticularly on cellular senescence and following systemic
inflammation during the analyses on the modulation of T cellfunction by innate-like signals. RIPK-1 has been known to function
both on cell death – apoptosis and necroptosis - and cell survival.
We generated and analyzed T cell-specific RIPK1-deficient (tKO)mice to analyze its function in T cells on metabolism and aging.
RIPK1-tKO mice induces various inflammatory diseases withageing (inflammaging) such as opacity, sarcopenia, cardiovascularinflammation, anemia, hypoglycemia, lymphopenia, and early
death. T cells in KO mice show senescence phenotype from earlylife through constitutive activation of Caspase-8, RIPK3 andmTORC1. Inhibition of mTORC1, or caspase-8/RIPK3 restored T
cell senescence and age-related diseases. Therefore, caspase-8/
RIPK3 induced basal activation of mTORC1 and senescenceprogram, which leads to inflammaging (Figure). Since it has beensuggested that senescent cells influence neighbor cells to induce
senescence, when senescent T cells were transferred into normal
mice, transferred senescence T cells returned to normal, whereas

24

Takashi Saito

normal T cells become senescent when transferred into RIPK1-KO
mice.

2. Negative regulation of T cell activation
Our finding that TCR-microclusters (MC) initiate T cell activation
led us to analyze the dynamics of signaling molecules at theimmune synapse. Similar to our previous studies on negative
regulation of T cell activation through CTLA4 and PD-1, we haveanalyzed the dynamic regulation of another inhibitory costimulator, LAG3. LAG3 was also colocalized with the TCR-MC
upon TCR stimulation to mediate inhibition of T cell activation.
Since the association between TCR-MC and LAG3 cluster is critical
for the inhibitory function, anti-LAG3 Ab induced separation of
LAG3 cluster from TCR-MC and consequently enhancement of T
cell activation. Our analyses provide a dynamic view of signal
regulation to define inhibitory mechanism. Furthermore, wehave also analyzed negative regulation of T cell activation by
autoimmune-related PTPN22. Its deficiency resulted in enhanced
activation and an increase in effector/memory T cells. Analysis of
the associated proteins revealed that PTPN22 was recruited to
the TCR-MC to comprise an “inhibitory complex” with otherinhibitory molecules to inhibit activation. A PTPN22 mutant
causing susceptibility to autoimmune diseases was defective inrecruitment to the TCR-MC. These studies help define theautoimmune susceptibility caused by the mutation.

Figure.
Regulatory mechanism of T cell senescence and consequent inflammation and age-related diseases by RIPK1
RIPK1 inhibits excess activation of mTORC1 by inhibiting RIPK3 and Caspase-8. Overactivation of mTORC1 induces expression ofsenescence-related genes, promotes T cell senescence which produce various cytokines, chemokines, and senescenceassociated secretory phenotype (SASP), which promote tissue senescence and induces age-related diseases. Senescent tissue
environmental signals enhance mTORC1 activation, exacerbates ageing and age-related diseases. On the other hand, normal
tissue environmental signals inhibit mTORC1 activation and T cell senescence and inflammaging.

Recent Publications
1. Imanishi T, Unno M, Yoneda N, Motomura Y, Mochizuki M, Sasaki T.,
Moro K., Pasparakis M. and Saito T.: RIPK1 blocks T cell senescentregulated by RIPK3 and caspase-8. Sci Advances. 25(9): eadd6097(2023).

3. Kumagai A, Nara T., Uematsu M, Kakinuma Y, Saito T,Masuda.
Development and characterization of a unique anti-IgE monoclonal
antibody cross-reactive between human and canine IgE. Immun.
Inflamm. Dis. 9:1740-1748 (2021).

2. Takemori T, Sugimoto-Ishige A, Nishitsuji H, Futamura Y, Harada M,
Kimura-Someya T, Matsumoto T, Honma T, Tanaka M, Yaguchi M, Isono
K, Koseki H, Osada H, Miki D, Saito T, Tanaka T, Fukami T, Goto T,
Shirouzu M, Shimotohno K, Chayama K. Establishment of a monoclonal
antibody against human NTCP that blocks HBV infection. J Virology
96:e0168621(2022).

4. Imanishi T, Unno M, Kobayashi W, Yoneda N, Akita S and Saito T.
mTORC1 signaling controls TLR2-Mediated T-cell activation by
inducing TIRAP expression. Cell Reports. 32:107911-107911 (2020).
5. Imanishi T and Saito T. T Cell co-stimulation and functional modulation
by innate signals. Trends lmmunol. 41:200-212 (2020).

25

Lymphocyte Differentiation
Immunology

Tomohiro Kurosaki, MD/PhD

Since the outbreak of COVID-19 in late 2019, several SARSCoV-2 variants of concern have continuously emerged in the past
years. Among them, the Omicron BA.1 (B.1.1.529) variant,harboring ~15 mutations in the spike receptor-binding domain(RBD), showed a profound effect on evading the neutralizing
antibody responses in those received 2-dose of mRNA vaccination(Pfizer-BioNTech BNT162b2 or Moderna mRNA-1273). In fact,epidemiologic data suggested that weak or undetectableneutralizing antibodies against Omicron variant were induced inserum IgG after a 2-dose of mRNA vaccination. In contrast,
individuals boosted with a third dose of mRNA vaccine encoding
the original Wuhan spike protein induced potent neutralizing
serum activity against Omicron, and were highly protected from
infection.
In addition to the antibody induction, mRNA vaccination elicits
the generation of SARS-CoV-2-specific memory B cells which
represent a second layer of immune protection through quick
differentiation into antibody-secreting plasma cells upon reencountering antigens. Indeed, a recall response from memory B

Professor

Tomohiro Kurosaki

Associate Professor

Takeshi Inoue

Postdoctoral Fellow

1

Research Assistant

1

Visiting Scientist

1

Support Staff

5cells was highlighted as a key factor for the protection fromsevere pathology in the lungs of nonhuman primates.
Furthermore, memory B cells can persist for a long period andevolve due to the progressive acquisition of somatic
hypermutations (SHM) through germinal center (GC) reaction. In
fact, SARS-CoV-2 mRNA vaccination induced a robust andpersistent GC response in humans. Hence, memory B cells areable to possess a diverse antibody repertoire, allowing for an
adaptive response against the pathogen upon re-infection,
particularly in the case of variant pathogen infections.
We have addressed the underlying mechanism of thedifferential neutralizing antibody responses against the Omicron
variant between the second and the third vaccine dose. For thispurpose, we analyzed memory Our results suggest that acutely
produced Omicron-non-cross-reactive antibodies help skew the
memory B cells towards more Omicron-cross-reactivity during a
2-dose immune response, thereby at least partly, contributing to
the generation of Omicron-neutralizing antibodies upon a third
vaccine dose.

Figure.
Model for antibody feedback regulation of B cell responses upon mRNA vaccination. Before or just after the 2nd vaccination, B
cells specific for immunodominant epitopes are preferentially selected for antibody production. Antibodies induced by the 2nd
vaccine dose diversifies the immunogenicity of memory B cells during the sustained GC responses, likely by epitope masking, sothat immuno-subdominant epitope-specific memory B cells are generated more frequently and can produce Omicronneutralizing antibodies upon the 3rd vaccine dose.

Recent Publications
1. Inoue T, Kurosaki T. Memory B cells. Nat. Rev. Immunol. in press.
2. Koike T, Fujii K, Kometani K, Butler NS, Funakoshi K, Yari S, Kikuta J, Ishii
M, Kurosaki T, Ise W. Progressive differentiation toward the long-lived
plasma cell compartment in the bone marrow. J Exp Med.
220(2):e20221717 (2023).

4. Tanaka S, Ise W, Baba Y, Kurosaki T. Silencing and activating anergic B
cells. Immunol. Rev. 307(1):43-52 (2022).
5. Yeh CH, Finney J, Okada T, Kurosaki T, Kelsoe G. Primary germinal
center-resident T follicular helper cells are a physiologically distinct
subset of CXCR5hiPD-1hi T follicular helper cells. Immunity 55(2):272289.e7 (2022).

3. Inoue T, Shinnakasu R, Kawai C, Yamamoto H, Sakakibara S, Ono C, Itoh
Y, Terooatea T, Yamashita K, Okamoto T, Hashii N, Ishii-Watabe A, Butler
NS, Matsuura Y, Matsumoto H, Otsuka S, Hiraoka K, Teshima T,
Murakami M, Kurosaki T. Antibody feedback contributes to facilitating
the development of Omicron-reactive memory B cells in SARS-CoV-2
mRNA vaccinees. J Exp Med. 220(2):e20221786 (2023).

26

27

Malaria Immunology

Immunology

related signaling events involved in B differentiation. Importantly,
these findings were not only specific to malaria infection but
rather general, and even during vaccination. We currently follow
these studies to understand the role of TBK1 in B cells in a tissuespecific manner.

Cevayir Coban, MD

Our lab focuses on the elucidation of host-pathogen
interactions. We mainly work on malaria disease but cover various
infectious organisms such as Leishmania parasites, andrespiratory viruses, to be able to understand their way of causing
pathology and eventually create successful vaccines against
them. Our recent topics include how to bolster B cell memory
responses against pathogens.

Elucidation of malaria-mediated pathologies:
Malaria is caused by Plasmodium parasites which often lead tosevere complications such as cerebral malaria and death.
According to a recent WHO report (WHO Malaria Report, 2022),
Covid19 pandemic brought many challenges to malariaintervention services including diagnostics and treatment. In
2021, the global malaria cases reached 247 million with 619,000
deaths (50% more child death than the previous year). Why andhow malaria infection causes severe outcomes have been
intensely researched in our laboratory. We have investigated thespatial distribution of the Plasmodium berghei ANKA (PbANKA)
parasites in the whole-brain microvessels by utilizing the newtissue-clearing method CUBIC (Clear, Unobstructed, Brain/Body
Imaging Cocktails and Computational analysis) with light-sheet
fluorescent microscopy (LSFM). We reported that parasites
significantly accumulated in the olfactory bulb (OB) of mice(Matsuo-Dapaah et al., Int Immunology, 2021). With ongoingstudies, we have further discovered several important genes
involved in olfactory pathology with the same experimental
cerebral malaria model (manuscript in preparation).

28

Professor

Cevayir Coban

Assistant Professor

Michelle S.J. Lee

Postdoctoral Fellow

1

Research Assistant

3

Visiting Scientist

2

Novel adjuvant discovery and development:
Adjuvants are known as must-have vaccine components forthe potentiation of vaccine responses. As a member of IMSUTInternational Vaccine Design Center (https://vdesc.ims.u-tokyo.
ac.jp/en/), we have been involved in the screening of herbal
medicine extracts as safe and ready-to-use adjuvants for current
human vaccines (Hioki et al., Frontiers Immun., 2022). We havebeen systematically screening innate and adaptive immune
signaling molecules taking part in the mode of action (MOA) of
adjuvants and vaccines. One of the recent findings involves
understanding how the combination of TLR9 and STING agonists
synergistically induce innate and adaptive responses to become
an advantageous type 1 adjuvant while suppressing type 2
immunity which leads to the generation of robust anti-tumor
responses (Temizoz et al., Int. Immunol., 2022).
Our recent projects focus on the investigation of B cell
development and pathways involved in the germinal center (GC)
formation for the generation of potent antibody responses. We
found that TANK-binding kinase-1 (TBK1), the famous innate
immune signaling kinase for controlling anti-viral immune
responses and nucleic-acid mediated type-I interferon responses,
is very important for the generation of GC which confers sterile
immunity to reinfections. In the absence of TBK1 in B cells, B cells
failed to form GC despite normal T-follicular helper (Tfh) celldifferentiation. Notably, memory B cells generated from TBK1deficient B cells fail to confer sterile immunity upon malaria reinfection, suggesting that TBK1 determines B cell fate to promote
long-lasting humoral immunity (Lee et al., J Exp. Medicine, 2022).
Figure 1 depicts the current mechanistic understanding of TBK1-

Figure.
Mechanistic insights into the role of TBK1 in B cells (Lee et al., J Exp. Medicine, 2022).
TBK1 drives the fate decision of B cell differentiation into either germinal center (GC) B cell or short-live plasmablast through theregulation of CD40 and BCR signaling. TBK1 phosphorylation increases as naïve B cell differentiates into GC B cell. TBK1 isinvolved in CD40-induced TRAF2 phosphorylation in B cell and negatively regulates downstream non-canonical NFκB signaling
to limit IRF4 expression. TBK1 also negatively regulates the downstream of BCR activation-induced AKT phosphorylation at T308
site to suppress c-Myc expression. In the absence of TBK1, high c-Myc and IRF4 expressions driven by activated BCR and CD40
signalings drive plasmablast differentiation, while on the other hand suppress BCL6, which is the master regulator of GC B celldifferentiation.

Recent Publications
1. Hioki K, Hayashi T, Natsume-Kitatani Y, Kobiyama K, Temizoz B, Negishi
H, Kawakami H, Fuchino H, Kuroda E, Coban C, Kawahara N, Ishii KJ.
Machine learning-assisted screening of herbal medicine extracts asvaccine adjuvants. Front Immunol. 13:847616 (2022). doi: 10.3389/
fimmu.2022.847616.
2. Temizoz B, Hioki K, Kobari S, Jounai N, Kusakabe T, Lee MSJ, Coban C,
Kuroda E, Ishii KJ. Anti-tumor immunity by the transcriptional synergy
between TLR9 and STING activation. Int Immunol. 34(7):353-364(2022). doi: 10.1093/intimm/dxac012.

4. Matsuo-Dapaah J, Lee MSJ, Ishii KJ, Tainaka K, Coban C. Using a new
three-dimensional CUBIC tissue-clearing method to examine thebrain during experimental cerebral malaria. Int Immunol. dxab060(2021). doi: 10.1093/intimm/dxab060.
5. Coban C. The host targeting effect of chloroquine in malaria. Curr
Opin Immunol. 66:98-107 (2020). doi: 10.1016/j.coi.2020.07.005.

3. Lee MSJ, Inoue T, Ise W, Matsuo-Dapaah J, Wing JB, Temizoz B,
Kobiyama K, Hayashi T, Patil A, Sakaguchi S, Simon AK, Bezbradica JS,
Nagatoishi S, Tsumoto K, Inoue JI, Akira S, Kurosaki T, Ishii KJ, Coban C.
B cell intrinsic TBK1 is essential for germinal center formation during
infection and vaccination in mice. J Exp Med. 219(2):e20211336(2022). doi: 10.1084/jem.20211336.

29

3. Machine Learning-Assisted Screening of Herbal
Medicine Extracts as Vaccine Adjuvants

Vaccine Science

Primary goal of our laboratory is to understand theimmunological mechanisms of the intra- and inter-cellularsignaling pathways that mediate the immunogenicity ofsuccessful vaccines, as well as biological responses to adjuvants.
Such knowledge will enable us to develop novel concepts,
modalities and next generation immuno-preventive and/or
therapeutic agents against infectious diseases, cancer and allergy
as well as other non-communicable diseases.

1. Making innate sense of mRNA vaccine adjuvanticity.
Successful vaccines contain two essential immunologicalcomponents: a protective antigen and an adjuvant. Adjuvants
are essential for optimal antigen-specific immune responses, theso-called ‘immunogenicity’, but are often a cause of reactogenicity(even toxicity) that results in local and systemic inflammation.
Therefore, to ensure vaccine efficacy and safety, it is critical tounderstand the molecular and cellular mechanism(s) by which
adjuvants provoke the immune system. By introducing papers,
we describe that there seems to be more room to improve theimmunogenicity and reduce the reactogenicity of LNP-mRNA
vaccine formulations by further study of immunization methods(including delivery systems and devices) and their built-in
adjuvanticity.

2. Anti-tumor immunity by transcriptional synergy
between TLR9 and STING activation
Agonists for TLR9 and stimulator of IFN genes (STING) offer
therapeutic applications as both anti-tumor agents and vaccine
adjuvants, though their clinical applications are limited; the30

Professor

Ken J. Ishii

Associate Professor

Kouji Kobiyama

Assistant Professor

Burcu Temizoz

Postdoctoral Fellow

2

Research Assistant

3

Visiting Scientist

3

Support Staff

2clinically available TLR9 agonist is a weak IFN inducer and STING
agonists induce undesired type 2 immunity. Yet, combining TLR9and STING agonists overcame these limitations by synergisticallyinducing innate and adaptive IFNγ to become an advantageous
type 1 adjuvant, suppressing type 2 immunity, in addition toexerting robust anti-tumor activities when used as amonotherapeutic agent for cancer immunotherapy. Here, wesought to decipher the immunological mechanisms behind thesynergism mediated by TLR9 and STING agonists and found that
their potent anti-tumor immunity in a Pan02 peritoneal
dissemination model of pancreatic cancer was achieved only
when agonists for TLR9 and STING were administered locally, andwas via mechanisms involving CD4 and CD8 T cells as well as the
co-operative action of IL-12 and type I IFNs. Rechallenge studiesof long-term cancer survivors suggested that the elicitation of
Pan02-specific memory responses provides protection against
the secondary tumor challenge. Mechanistically, we found that
TLR9 and STING agonists synergistically induce IL-12 and type I
IFN production in murine APCs. The synergistic effect of the TLR9and STING agonists on IL-12p40 was at protein, mRNA andpromoter activation levels, and transcriptional regulation wasmediated by a 200 bp region situated 983 bp upstream of the IL12p40 transcription initiation site. Such intracellulartranscriptional synergy may hold a key in successful cancer
immunotherapy and provide further insights into dual agonism
of innate immune sensors during host homeostasis and diseases.

Immunology

Ken J. Ishii, MD/PhD

Adjuvants are important vaccine components, composed of avariety of chemical and biological materials that enhance thevaccine antigen-specific immune responses by stimulating the
innate immune cells in both direct and indirect manners to
produce a variety cytokines, chemokines, and growth factors. It
has been developed by empirical methods for decades andconsidered difficult to choose a single screening method for an
ideal vaccine adjuvant, due to their diverse biochemical
characteristics, complex mechanisms of, and species specificity
for their adjuvanticity. We therefore established a robust adjuvant
screening strategy by combining multiparametric analysis ofadjuvanticity in vivo and immunological profiles in vitro (such as
cytokines, chemokines, and growth factor secretion) of various
library compounds derived from hot-water extracts of herbal
medicines, together with their diverse distribution of nano-sized
physical particle properties with a machine learning algorithm.
By combining multiparametric analysis with a machine learningalgorithm such as rCCA, sparse-PLS, and DIABLO, we identified
that human G-CSF and mouse RANTES, produced upon adjuvant
stimulation in vitro, are the most robust biological parametersthat can predict the adjuvanticity of various library compounds.
Notably, we revealed a certain nano-sized particle populationthat functioned as an independent negative parameter toadjuvanticity. Finally, we proved that the two-step strategy
pairing the negative and positive parameters significantly
improved the efficacy of screening and a screening strategy
applying principal component analysis using the identified
parameters. These novel parameters we identified for adjuvant
screening by machine learning with multiple biological andphysical parameters may provide new insights into the future
development of effective and safe adjuvants for human use.

4. A-910823, a squalene-based emulsion adjuvant,induces T follicular helper cells and humoral immune
responses via α-tocopherol component
A-910823 is a squalene-based emulsion adjuvant used for
S-268019-b, a novel vaccine against severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) that is currently in clinicaldevelopment. Published evidence has demonstrated that
A-910823 can enhance the induction of neutralizing antibodies
against SARS-CoV-2 in humans and animal models. However, thecharacteristics and mechanisms of the immune responses
induced by A-910823 are not yet known. Here, we found that thenovel adjuvant A-910823 is capable of robust Tfh cell andhumoral immune response induction, even when used as abooster dose, and we also emphasized that the adjuvant activityof A-910823 is driven by α-tocopherol.

Figure.
How TLR9 and STING agonists synergize to protect against cancer
Agonists of TLR9 and STING can induce anti-tumor responses and, in combination, they appear to be much more effective than individually. To delineate themechanisms, we use the Pan02 peritoneal dissemination model of pancreatic cancer. Local (i.p.) K3 CpG (TLR9 agonist) or c-di-AMP (STING agonist) generate antitumor responses; the combination is even more effective, prolonging host survival compared with single treatments or systemic (i.v.) inoculation of the combination.
This antigen-free therapy allows 100% of mice to survive and even protects them from rechallenge with this aggressive tumor. Levels of IL-12 and type I interferons(IFNs) are increased by the combination, which is required for induction of potent anti-tumor CD4+ and CD8+ T cell responses along with robust NK cell activity. IL-12
is crucial and synergistically coordinates with type I IFNs to regulate the anti-tumor effect of the combination. The synergism operates within individual antigenpresenting cells and is regulated at the level of promotor activation, transcription and translation of IL-12.

Recent Publications
1. Yoshioka Y, Kobiyama K, Hayashi T, et al. A-910823, a squalene-based
emulsion adjuvant, induces T follicular helper cells and humoral
immune responses via α-tocopherol component. Front Immunol.
14:1116238 (2023). doi: 10.3389/fimmu.2023.1116238.
2. Temizoz B, Hioki K, Kobari S, et al. Anti-tumor immunity bytranscriptional synergy between TLR9 and STING activation. Int
Immunol. 34(7):353-364 (2022). doi: 10.1093/intimm/dxac012.

3. Hioki K, Hayashi T, Natsume-Kitatani Y, et al. Machine LearningAssisted Screening of Herbal Medicine Extracts as Vaccine Adjuvants.
Front Immunol. 13:847616 (2022). doi: 10.3389/fimmu.2022.847616.
4. Koiyama K, Ishii KJ. Making innate sense of mRNA vaccine
adjuvanticity. Nat Immunol. Apr;23(4):474-476 (2022). doi: 10.1038/
s41590-022-01168-4.

31

Immunoparasitology

Toxoplasma gondii is an obligatory protozoan parasite that can
infect cells with nuclei from virtually all warm-blooded animals.
Although it is estimated that one-third of the world’s population
is infected with T. gondii, most infections are asymptomatic.
Infection with T. gondii, however, can lead to life-threatening
toxoplasmosis in immunocompromised humans and animals.
Moreover, T. gondii is ranked among the top five humanpathogens that cause economic loss and life impairment via
foodborne illness in the United States. Thus, T. gondii is an
important human and animal pathogen.
T. gondii forms parasitophorous vacuoles (PVs) in infected cells,
which are membranous structures originating from host cell
plasma membranes and are generated during invasion by theparasite. T. gondii can proliferate only inside the PV membrane(PVM), which is an interface between the host and the parasite.
During infection, T. gondii secretes various molecules fromsecretory organelles such as rhoptry and dense granules into thehost cell cytoplasm and nucleus, onto the PVM, and within the PV
space. An important function of rhoptry proteins (ROPs) anddense granule proteins (GRAs) is to downregulate the hostimmunity that is dependent on interferon gamma (IFN-γ). IFN-γ
robustly stimulates expression of hundreds of genes encoding avariety of proteins related to anti-T. gondii cell-autonomous
immunity. IFN-γ-stimulated nitric oxide production andtryptophan degradation are important for suppression of T.
gondii growth. IFN-inducible GTPases such as p47 immunityrelated GTPases (IRGs) and p65 guanylate-binding proteins(GBPs) are required for disruption of PVM of avirulent type II T.
gondii to kill the pathogen in a cell-autonomous fashion. IRGs and32

Professor

Masahiro Yamamoto

Associate Professor

Miwa Sasai

Assistant Professor

Fumiaki Ihara

Postdoctoral Fellow

1

Support Staff

2

GBPs are coordinately accumulated on the T. gondii PVM. Amongthem, Irgb6 has been shown to act as a pioneer that detects T.
gondii PVM, subsequently leading to recruitment of other IRGs
such as Irga6 and Irgb10, GBPs, and effectors, including p62/
Sqstm1 and ubiquitin. Irgb6-deficient mice are susceptible totype II T. gondii to the same extent as IFN-γ-deficient mice. Thus,
Irgb6 plays a fundamental role in IFN-γ-dependent anti-T. gondii
cell-autonomous host defense.
Targeting Irgb6 is one of the most effective virulencemechanisms of virulent type I T. gondii. Rhoptry kinases such as
ROP17 and ROP18, and a pseudokinase ROP5 are secreted into
the host cell cytoplasm and localized at the PVM to directly
phosphorylate and inactivate IFN-inducible GTPases to inhibit
their accumulation on the T. gondii PVM. Loss of ROP18 from avirulent type I T. gondii strain results in decreased virulence inmice. Thus, targeting host Irgb6 via ROP18 is an important
counter-defense system for virulent T. gondii in IFN-γ-activatedcells. However, little is known about the mechanism of how
ROP18 is prepared at the transcriptional, translational, and posttranslational levels inside type I T. gondii itself.
A genome-wide loss-of-function screen in a type I T. gondii
strain identified >350 genes that determine fitness in IFN-γactivated murine macrophages. Some of the highly ranked
genes, such as GRA45, TGGT1_263560 and TGGT1_269950(encoding putative GRAs), were characterized to determine thefitness-related mechanisms. However, most of the remaining
genes remain uncharacterized. Here, to explore mechanisms bywhich T. gondii-derived molecules target host Irgb6-dependentcell-autonomous immunity, we tested the involvement of several

ROP18 overexpression in IWS1-deficient T. gondii reduced
recruitment of IFN-inducible GTPases to the PVM and resulted in
restoration of in vivo virulence in wild-type mice. Taken together,
this study demonstrates that the T. gondii transcription factor
IWS1 is important for ROP18 mRNA expression in the virulent
parasite to subvert host IFN-inducible GTPase-mediated cellautonomous immunity; this determines the fitness of the parasite
in IFN-γ-activated cells and mice.

Immunology

Masahiro Yamamoto, PhD

type I T. gondii proteins encoded by uncharacterized genes insuppression of Irgb6-depedent host defense. We found that aputative transcription factor called IWS1 is important for ROP18mediated virulence of type I T. gondii. Loss of IWS1 from type I
parasites led to markedly increased accumulation of Irgb6 as wellas other IFN-inducible GTPases at the PVM, and severely
decreased the virulence of the parasite in mice. Global geneprofile analysis revealed that IWS1 deficiency resulted in
downregulation of various genes, including ROP18. Moreover,Figure.
Transcriptional regulation of a key Toxoplasma virulence gene by IWS1.

Recent Publications
1. Hashizaki E, Sasai M, Okuzaki D, Nishi T, Kobayashi T, Iwanaga S,
Yamamoto M. Toxoplasma IWS1 Determines Fitness in Interferon-γActivated Host Cells and Mice by Indirectly Regulating ROP18 mRNA
Expression. mBio. 14(1):e0325622 (2023). doi: 10.1128/mbio.0325622.
2. Sasai M, Ma JS, Okamoto M, Nishino K, Nagaoka H, Takashima E,
Pradipta A, Lee Y, Kosako H, Suh PG, Yamamoto M. Uncovering a novelrole of PLCβ4 in selectively mediating TCR signaling in CD8+ but not
CD4+ T cells. J Exp Med. 218:e20201763 (2021). doi: 10.1084/
jem.20201763. PMID: 33970189.

4. Sakaguchi N, Sasai M, Bando H, Lee Y, Pradipta A, Ma JS, Yamamoto M.
Role of Gate-16 and Gabarap in Prevention of Caspase-11-Dependent
Excess Inflammation and Lethal Endotoxic Shock. Front Immunol.
11:561948 (2020). doi: 10.3389/fimmu.2020.561948.
5. Bando H, Pradipta A, Iwanaga S, Okamoto T, Okuzaki D, Tanaka S,
Vega-Rodríguez J, Lee Y, Ma JS, Sakaguchi N, Soga A, Fukumoto S,
Sasai M, Matsuura Y, Yuda M, Jacobs-Lorena M, Yamamoto M. CXCR4
regulates Plasmodium development in mouse and humanhepatocytes. J Exp Med. 216:1733-1748 (2019). doi: 10.1084/
jem.20182227.

3. Pradipta A, Sasai M, Motani K, Ma JS, Lee Y, Kosako H, Yamamoto M.
Cell-autonomous Toxoplasma killing program requires Irgm2 but not
its microbe vacuolar localization. Life Sci Alliance. 4:e202000960(2021). doi: 10.26508/lsa.202000960.

33

Biochemistry & Immunology
Immunology

Shigekazu Nagata, PhD

34

Phospholipids are asymmetrically distributed between the
inner and outer leaflets of plasma membranes with exclusive
phosphatidylserine (PtdSer) localization in the inner leaflet. Thisasymmetrical distribution of phospholipids is maintained by ATPdependent flippases, which translocate PtdSer from outer toinner leaflets. When cells undergo apoptosis, the asymmetrical
distribution of phospholipids is disrupted by a scramblase(s) that
non-specifically scrambles phospholipids between the twoleaflets, leading to PtdSer-exposure.
We previously identified two P4-type ATPases (ATP11A and11C) and their subunit CDC50A as flippases at plasma membranes(Segawa et al. Science 2014) and TMEM16F as Ca2+-dependent
scramblases (Suzuki et al. Nature 2010). The TMEM16F gene ismutated in human Scott syndrome, a congenital bleeding
disorder, indicating that TMEM16F is responsible for exposing
PtdSer in the platelets to activate blood clotting factors (Suzuki etal. Nature 2010). We also found that XKR8 forms a binary complex
with Basigin or Neuroplastin, an Ig-super family protein andworks as a caspase-dependent scramblase in apoptotic cells invarious cells (Suzuki et al. Science 2013; PNAS 2016). The PtdSer,
thus on the dead cell’s surface, serves as an “eat me” signal. The
null mutation of Xkr8, thus, causes inefficient engulfment of
apoptotic cells leading to the activation of autoimmunity andmale infertility (Kohno et al. PNAS 2019; Yamashita et al. MCB2019), as found in the lack of the PtdSer-recognition system(Hanayama et al. Science 2004).
A high concentration of ATP (~ 4 mM) is present in the cells,
while its extracellular concentration is low (less than 30 nM).
However, it increases by several hundred μM in the inflamedtissues or tumour environment, where a large amount of ATP isreleased from the cells undergoing necrosis. ATP rapidly induces

Professor

Shigekazu Nagata

Assistant Professor

Takaharu Sakuragi

Postdoctoral Fellow

2

Research Assistant

4

Visiting Scientist

3

Support Staff

1

PtdSer-exposure in CD25+CD4+ T cells and macrophages bybinding to its receptor, P2X7, followed by necrotic or pyroptosis
and releasing inflammatory cytokines. During CRISPR/Cas9
screening for the molecules involved in ATP-induced PtdSerexposure in mouse T cells, we found that XK, a paralogue of XKR9,and the VPS13A cytosolic lipid transporter, is required for the
ATP-induced PtdSer-exposure downstream of P2X7. An
unidentified signal from the ATP-engaged P2X7 receptor seems
to activate the XK-VPS13A complex to scramble phospholipids inthe plasma membranes (Figure 1). Patients of neuroacanthocytosis,
a disorder that affects erythrocytes and the central and peripheral
nervous system, carry a defect in Xk or Vps13a, indicating that the
XK- and VPS13A-mediated scrambling of phospholipids plays an
inevitable role in maintaining the homeostasis in hematopoietic
and nervous systems.
Cell fusion occurs in various biological systems, such as
myoblasts to myotubes, and trophoblasts into syncytiotrophoblasts.
Before the fusion, PtdSer is exposed on the cell surface, andblocking PtdSer inhibits cell fusion, indicating that the PtdSer
exposed on the cell surface is essential for cell fusion. The ATP11A
and ATP11C flippases in the plasma membrane are present
ubiquitously in most types of cells except for the placenta, which
expresses only ATP11A. Accordingly, the Atp11a-null mice areembryonic lethal, while the epiblast-specific deletion of the
Atp11a gene did not affect the development, confirming that
ATP11A has a non-redundant essential role in the placenta.
Syncytiotrophoblasts were not well developed in the Atp11a-nullplacenta probably due to the constitutive PtdSer-exposure introphoblasts (Figure 2). These results indicated that the PtdSer
exposed at the pre-fusion state must be withdrawn during thefusion process.

Figure 1.
Association of XK with VPS13A at the plasma membrane to scramble phospholipids.
VPS13A, a giant cytoplasmic protein (human VPS13A: 3174 aa), is associated with XK in the plasma membrane. P2X7 is a receptor for extracellular ATP
and serves as a cation transporter. The binding of ATP to P2X7 activates the XK-VPS13A complex to scramble phospholipids by an unknown mechanism(s),leading to PtdSer-exposure and cell lysis.

Figure 2.
Embryonic lethality of Atp11a-/- mice due to poor placenta development. Top panels: Atp11a-/- mouse embryos died at E14.5. However, epiblast-specific
Atp11a deletion did not affect mouse development, suggesting the inability of Atp11a-/- placentas to support the embryos. Bottom panel: Two
syncytiotrophoblasts (SynT-I and SynT-II) tightly adhere and separate the maternal and fetal blood compartments in the wild-type placenta labyrinth
layer. In the Atp11a-/- placenta, the two syncytiotrophoblasts were not well developed, and the labyrinth was sparse.

Recent Publications
1. Sakuragi T. and Nagata S. Regulation of phospholipid distribution in
the lipid bilayer by flippases and scramblases. Nat Rev Mol Cell Biol.
(2023). https://doi.org/10.1038/s41580-023-00604-z.
2. Ochiai Y, Suzuki C, Segawa K, Uchiyama Y, and Nagata S. Inefficientdevelopment of syncytiotrophoblasts in the Atp11a-deficient mouseplacenta. Proc Nat Acad Sci USA. 119, e2200582119 (2022).

4. Segawa K, Kikuchi A, Noji T, et al. A sublethal ATP11A mutation
associated with neurological deterioration causes aberrant
phosphatidylcholine flipping in plasma membranes. J Clin Invest. 131:e148005 (2021).
5. Sakuragi T, Kanai R, Tsutsumi A, et al. The tertiary structure of thehuman Xkr8-Basigin complex that scrambles phospholipids at plasma
membranes. Nat Struct Mol Biol. 28: 825-834 (2021).

3. Ryoden Y, Segawa K, and Nagata S. Requirement of Xk and Vps13a for
the P2X7-mediated phospholipid scrambling and cell lysis in mouse T
cells. Proc Nat Acad Sci USA 119: e2119286119 (2022).

35

Molecular Neuroscience
Immunology

Toshihide Yamashita MD/PhD
Professor

Toshihide Yamashita

Associate Professor

Takahide Itokazu

Assistant Professor

Hiroshi Nakagawa
Oluwaseun Fatoba
Hiroshi Tsujioka
Iyo Yorifuji
Yosuke Ohtake
Toru Nakanishi
Nao Shibuya
Abdellatif Abbaoui

Disorders of the central nervous system, such as cerebrovasculardiseases, cerebrospinal trauma, and encephalomyelitis, oftencause spatiotemporal changes in the nervous system and invarious biological systems, such as the immune system andvascular system. We have analyzed disorders of the neuralnetworks in the central nervous system and the subsequent
restoration process from the perspective of the functional
network of biological systems (Fig. 1). Further, we have analyzed
the mechanism by which the spatiotemporal dynamics in thosebiological systems control a series of processes (Fig. 2).
Particularly, the ultimate goal of this study is to elucidate themanner in which the control mechanism is affected by the
associations among the nervous system, immune system, andvascular system. Additionally, we aim to elucidate the processes
involved in the functioning of living organisms with neuralnetwork disorders within the central nervous system by observing
such disorders and their functional recovery process with respect
to the dynamics of the entire biological system and by conducting
a comprehensive analysis of the association between eachsystem.

Postdoctoral Fellow

1

Research Assistant

2

Visiting Scientist

6

Support Staff

2

Figure 1.
The mechanism of spontaneous functional recovery.

We observe the central nervous system as a single organ withina biological system. Further, studies from the perspective of how
the entire biological system is involved in disorders and recoveryof neural networks are scarce. By observing disorders in neuralnetworks and the biological reactions during the subsequent
recovery process as a “scrap-and-build” strategy, we aim toelucidate the mechanisms behind a series of reactions as well as
their significance that may potentially lead to a new and original
trend in Life Sciences.
Figure 2.
Biological systems that regulate rewiring of neural network after CNS injury.

Recent Publications
1. Iwamoto S, Itokazu T, Sasaki A, et al. RGMa signal in macrophages
induces neutrophil-related astrocytopathy in NMO. An Neurol. 91:532547 (2022).
2. Ito M, Muramatsu R, Kato Y, Sharma B, Uyeda A, Tanabe S, Fujimura H,
Kidoya H, Takakura N, Kawahara Y, Takao M, Mochizuki H, Fukamizu A& Yamashita T. Age-dependent decline in myelination capacity is
mediated by apelin-APJ signaling. Nat Aging 1:284-294 (2021).
3. Fujita Y, Nakanishi T, Ueno M, Itohara S & Yamashita T. Netrin-G1
regulates microglial accumulation along axons and supports thesurvival of layer V neurons in the postnatal mouse brain. Cell Rep.
10:107580 (2020).

36

4. Tanabe S & Yamashita T. B-1a lymphocytes promote oligodendrogenesis
during brain development. Nat Neurosci. 21:506-516 (2018).
5. Kuroda M, Muramatsu R, Maedera N, Koyama Y, Hamaguchi M,
Fujishima H, Yoshida M, Konishi M, Itoh N, Mochizuki H & Yamashita T.
Promotion of central nervous system remyelination by peripheral
FGF21. J Clin Invest. 127:3496-3509 (2017).
6. Fujita Y, Masuda K, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K,
Miyakawa T, Shirahige K & Yamashita T. Cohesin regulates formation ofneuronal networks in the brain. J Exp Med. 214:1431-1452 (2017).

37

Molecular Immunology

Immunology

further show the crystal structure of the TCR expressed by Traj33+
T cells expanded in Bcl11bΔiThy mice. Overall, we establish that
MR1-reactive T cells have pathogenic potential.

Sho Yamasaki, PhD

Professor

Sho Yamasaki

Assistant Professor

Masamichi Nagae
Eri Ishikawa

Postdoctoral Fellow

3

Research Assistant

5

Visiting Scientist

6

Support Staff

5

Figure 1.
A model for generating distinct dendritic responses through FcRγ signaling.

Timing matters for dendritic cell signaling
The common Fc receptor γ (FcRγ) chain is a signaling subunit
common to several immune receptors, but cellular responses
induced by FcRγ-coupled receptors are diverse. We investigatedthe mechanisms by which FcRγ generates divergent signals
when coupled to Dectin-2 and Mincle, structurally similar C-type
lectin receptors that induce the release of different cytokines
from dendritic cells. Chronological tracing of transcriptomic andepi- genetic changes upon stimulation revealed that Dectin-2
induced early and strong signaling, whereas Mincle- mediatedsignaling was delayed, which reflects their expression patterns.
Generation of early and strong FcRγ-Syk signaling by engineered
chimeric receptors was sufficient to recapitulate a Dectin-2–likegene expression profile. Early Syk signaling selectively stimulated
the activity of the calcium ion–activated transcription factor
NFAT, which rapidly altered the chromatin status and transcriptionof the Il2 gene. In contrast, proinflammatory cytokines, such as
TNF, were induced regardless of FcRγ signaling kinetics. These
results suggest that the strength and timing of FcRγ-Syk signaling
can alter the quality of cellular responses through kineticssensing signaling machineries.

β-GlcCer-induced phagoptosis of neurons by microglia
causes Gaucher disease
Gaucher disease (GD) is the most common lysosomal storage
disease caused by recessive mutations in the degrading enzymeof β-glucosylceramide (β-GlcCer). However, it remains unclear
how β-GlcCer causes severe neuronopathic symptoms, which are
not fully treated by current therapies. We herein found that38

β-GlcCer accumulating in GD activated microglia throughmacrophage-inducible C-type lectin (Mincle) to induce
phagocytosis of living neurons, which exacerbated Gaucher
symptoms. This process was augmented by tumor necrosis factor(TNF) secreted from activated microglia that sensitized neurons
for phagocytosis. This characteristic pathology was also observedin human neuronopathic GD. Blockade of these pathways in micewith a combination of FDA-approved drugs, minocycline(microglia activation inhibitor) and etanercept (TNF blocker),effectively protected neurons and ameliorated neuronopathic
symptoms. In this study, we propose that limiting unrestrained
microglia activation using drug repurposing provides a quickly
applicable therapeutic option for fatal neuronopathic GD.

MR1-reactive T cells, as pathogenic T cells in
autoimmune diseases
MHC class I-related protein 1 (MR1) is a metabolite-presenting
molecule that restricts MR1-reactive T cells including mucosalassociated invariant T (MAIT) cells. In contrast to MAIT cells, thefunction of other MR1-restricted T cell subsets is largely unknown.
Here, we report that mice in which a T cell-specific transcription
factor, B-cell lymphoma/leukemia 11B (Bcl11b), was ablated inimmature thymocytes (Bcl11bΔiThy mice) develop chronic
inflammation. Bcl11bΔiThy mice lack conventional T cells and MAIT
cells, whereas CD4+IL-18R+ αβ T cells expressing skewed Traj33(Jα33)+ T cell receptors (TCR) accumulate in the periphery, which
are necessary and sufficient for the pathogenesis. The disorders
observed in Bcl11bΔiThy mice are ameliorated by MR1-deficiency,transfer of conventional T cells, or germ-free conditions. We

Figure 2.
Novel molecular mechanisms and therapeutic options for Gaucher disease.

Recent Publications
1. Watanabe M, Motooka D, Yamasaki S. The kinetics of signaling throughthe common Fc receptor γ (FcRγ) chain determine cytokine profiles indendritic cells . Sci Signal. 16:eabn9909 (2023).
2. Shimizu T, Schutt CR, Izumi Y, Tomiyasu N, Omahdi Z, Kano K,
Takamatsu H, Aoki J, Bamba T, Kumanogoh A, Takao M, Yamasaki S.
Direct activation of microglia by β-glucosylceramide causes
phagocytosis of neurons that exacerbates Gaucher disease. Immunity
56:307-319.e8 (2023).

4. Lu X, Hosono Y, Nagae M, Ishizuka S, Ishikawa E, Motooka D, et al.
Identification of conserved SARS-CoV-2 spike epitopes that expand
public cTfh clonotypes in mild COVID-19 patients. J Exp Med.
218:e20211327 (2021).
5. Nagata M, Toyonaga K, Ishikawa E, Haji S, et al. Helicobacter pylori
metabolites exacerbate gastritis through C-type lectin receptors. J
Exp Med. 218:e20200815 (2021).

3. Shibata K, Motozono C, Nagae M, Shimizu T, Ishikawa E, Motooka D,
Okuzaki D, et al. Symbiotic bacteria-dependent expansion of MR1reactive T cells causes autoimmunity in the absence of Bcl11b. Nat
Commun. 13:6948 (2022).

39

Stem Cell Biology and Developmental Immunology

Professor

Takashi Nagasawa

Associate Professor

Yoshiki Omatsu

Research Assistant4

Support Staff

1

Recently, Buechler et al. performed a meta-analysis of singlecell RNA sequencing (scRNA-seq) datasets from fibroblasts across

16 tissues and hypothesized that two clusters of fibroblasts they
designated as universal fibroblasts present in all organs might
give rise to distinct tissue-specific fibroblast subsets they
designated as specialized fibroblasts, including CAR cells, splenic
red pulp reticular fibroblasts, and Foxl1+ telocytes, which havebeen shown to create niches for intestinal stem cells (Buechler etal., Nature 593; 575, 2021). However, there is no direct evidence
that universal fibroblasts have potential to give rise to specialized
fibroblasts. Thus, we are trying to determine whether populationsof universal fibroblasts have potential to give rise to CAR cells andclarify molecular mechanisms that regulate the development,
maturation, and functions of CAR cells during development andhomeostasis and in diseases.

Immunology

Takashi Nagasawa, MD/PhD

CAR cells require Runx1 or Runx2 to prevent their fibrotic
conversion and maintain HSCs and hematopoiesis in adults(Omatsu et al., Nat Commun 2022). Clinically, expression of Runx1and Runx2 was reduced in CAR cells in a mouse model of marrow
fibrosis, which affects up to 20% of myeloproliferative neoplasms(MPN) patients and is associated with a poor prognosis. These
results strengthen the claim that CAR cells are the bone marrowspecific fibroblasts, which express specific and criticaltranscription factors, including Foxc1, Ebf 1/3, and Runx1/2,
providing HSC niches and bone (Omatsu et al., Nat Commun2022).

Figure 1.
The functions of Runx1/2 in CAR cell maintenance.
CAR cells require Runx1 or Runx2 to prevent their fibrotic conversion andmaintain HSCs and lympho-hematopoiesis in adult bone marrow.

Special microenvironments known as niches are essential forthe maintenance of hematopoietic stem cells (HSCs), which giverise to blood cells, and lympho-hematopoiesis within bonemarrow cavities. We isolated a chemokine, CXCL12 (SDF-1/PBSF),
as a molecule that stimulates the growth of B cell precursors(Nagasawa et al. PNAS 1994) and found that CXCL12 and its
receptor CXCR4 are essential for colonization of bone marrow by
HSCs during embryogenesis (Nagasawa et al. Nature 1996; Ara etal. Immunity 2003), maintenance of a pool of HSCs (Sugiyama etal. Immunity 2006), and development of immune cells, including
B cells, plasmacytoid dendritic cells (pDCs) and NK cells in bonemarrow as well as vascular formation and cardiogenesis(Tachibana et al. Nature 1998). Based on a key role of CXCL12 in
HSC maintenance, we identified a population of fibroblastic
reticular cells expressing CXCL12 at high levels, termed CXCL12abundant reticular (CAR) cells, within murine bone marrow(Tokoyoda et al. Immunity 2004; Sugiyama et al. Immunity 2006)
and found that CAR cells are the major producer of CXCL12 andSCF (Omatsu at al. Immunity 2010), and the major cellularcomponents of niches for HSCs and immune cells, including B
cells and plasma cells (Tokoyoda et al. Immunity 2004; Sugiyama
et al. Immunity 2006; Omatsu at al. Immunity 2010). Furthermore,
we showed that numerous HSC niches remain empty and that all
CAR cells create facultative niches for HSCs inconsistent with theclassical concept (Shimoto et al. Blood 2017).
In addition, we showed that CAR cells are mesenchymal stem
cells, which give rise to adipocytes and osteoblasts, and thattranscription factors, Foxc1 and Ebf3 are preferentially expressedin CAR cells and play a critical role in the formation and40

maintenance of niches for HSCs and immune cells, inhibiting
differentiation of CAR cells into adipocytes and osteoblasts,
respectively (Omatsu et al. Nature 2014; Seike et al. Genes Dev.
2018). These studies clarified the nature and functions of CAR
cells in murine bone marrow.
In addition to mouse, we revealed the human counterpart ofCAR cells, which specifically expressed CXCL12, Foxc1, and Ebf3,
were the major component of nonhematopoietic cells in humanbone marrow and enabled the evaluation of their alterations invarious hematological disorders by flow cytometric andhistological analyses (Aoki et al., Br J Haematol 2021).
The results that Runx2, which is essential for generation of
osteoblasts, is highly expressed in CAR cells prompted us to
examine its role in the development and/or maintenance of CAR
cells. We showed that Runx1, which is known to be essential forthe establishment of definitive hematopoiesis in hemogenic
endothelial cells during ontogeny, is predominantly expressed in
CAR cells in adult bone marrow. Although CAR cells and HSC
niches are normally formed and maintained in mice lacking
Runx1 or Runx2 in CAR cells, mice lacking both Runx1 and Runx2
in CAR cells (tamoxifen-treated Ebf3-CreERT2;Runx1f/fRunx2f/f
mice) displayed an increase in fibrosis and bone formation withmarkedly reduced HSCs, hematopoietic progenitor cells, andimmune cells in the bone marrow. Consistent with this, CAR cells
from the mutants displayed markedly increased expression offibrotic genes, including Col1a1, Col3a1, and Col6a3. In vitro,
Runx1 was induced by Foxc1, and enforced expression of Runx1
decreased fibrotic gene expression in cultured CAR cells. Thus,

Figure 2.
The development and functions of CAR cells.
CAR cells are the major cellular component of non-hematopoietic cells in bonemarrow characterized by several salient features in both mouse and human. The
transcription factors, Foxc1, Ebf1/Ebf3, and Runx1/2 and cytokines, CXCL12 andSCF are preferentially expressed in CAR cells and critical for formation andmaintenance of niches for HSCs and immune cells, within the bone marrow.

Figure 3.
Presumptive common fibroblast progenitors for CAR cells.
Universal fibroblasts might have potential to give rise to specialized fibroblasts
creating niches for tissue stem cells, including CAR cells, splenic red pulp reticularfibroblasts, and Foxl1+ telocytes. ISC: intestinal stem cells.

Recent Publications
1. Omatsu Y, Aiba S, Maeta T, Higaki K, Aoki K, Watanabe H, Kondoh G,
Nishimura R, Takeda S, Chung UI, Nagasawa T. Runx1 and Runx2
inhibit fibrotic conversion of cellular niches for hematopoietic stem
cells. Nat Commun. 13:2654 (2022).

4. Omatsu Y, Sugiyama T, Kohara H, Kondoh G, Fujii N, Kohno K, Nagasawa
T. The essential function of adipo-osteogenic progenitors as thehematopoietic stem and progenitor cell niche. Immunity 33:387-399(2010).

2. Seike M, Omatsu Y, Watanabe H, Kondoh G, Nagasawa T. Stem cellniche-specific Ebf3 maintains the bone marrow cavity. Genes Dev.
32:359-372 (2018).

5. Sugiyama T, Kohara H, Noda M, Nagasawa T. Maintenance of thehematopoietic stem cell pool by CXCL12-CXCR4 chemokine signaling
in bone marrow stromal cell niches. Immunity 25:977-988 (2006).

3. Omatsu Y, Seike M, Sugiyama T, Kume T, Nagasawa T. Foxc1 is a criticalregulator of hematopoietic stem/progenitor cell niche formation.
Nature 508:536-540 (2014).

41

Aging Biology
Immunology

Eiji Hara, PhD

Professor

Eiji Hara

Assistant Professor

Shimpei Kawamoto
Tomonori Matsumoto
Masahiro Wakita

Cellular senescence is a state of irreversible cell-cycle arrest
induced by a variety of potentially oncogenic stimuli and istherefore thought to serve as an important tumour suppression
mechanism. On the other hand, however, senescent cells also
cause senescence-associated secretory phenotypes (SASP),
which secrete a variety of pro-inflammatory factors (Fig.1).
Therefore, the accumulation of senescent cells, which is often
seen with aging and obesity, ultimately leads to harmful side
effects, and there is currently a worldwide effort to develop drugs
that selectively kill senescent cells. However, since senescent cells
also play beneficial roles, for example, in promoting woundhealing, maintaining the blood-tissue barrier, and activating theimmune system, blindly removing senescent cells may be
harmful. Therefore, identifying and preventing the causes ofcellular senescence in vivo, rather than killing senescent cells,
may be a safer and more efficient way to address the harmful side
effects of senescent cells. However, to date, the triggers of cellularsenescence in vivo, are poorly understood. Recently, we havediscovered through studies using human clinical samples andmouse model that both butyrate-producing gut bacteria andsevere acute respiratory syndrome corona virus 2 (SARS-CoV-2)
induce cellular senescence in vivo.
In the case of butyrate-producing bacteria, cellular senescenceis induced directly in the affected cells via induction of p16INK4a

Research Assistant

3

Visiting Scientist

2

Support Staff2

and p21Waf1 expression, while in the case of SARS-CoV-2, TNFα
secreted from infected cells causes cellular senescence insurrounding uninfected cells. We also found that mice infectedwith a mouse-adapted strain of SARS-CoV-2 exhibit prolonged
signs of cellular senescence and SASP in the lung at 14 days postinfection when the virus was no longer detectable, but this canbe greatly reduced by administration of senolytic agents thatspecifically kill senescent cells. The sustained infection-induced
senescence described here may be involved in the long-term
inflammation caused by SARS-CoV-2 infection known as longCOVID. These results suggest that senolytic drug may be effective
in alleviating long COVID. However, SASP has not only harmful
but also beneficial effects, and it has recently been reported thatthe removal of accumulated senescent cells in mice results insevere liver dysfunction. In this regard, it is interesting to notethat hamsters infected with SARS-CoV-2 showed resistance tosuperinfection with influenza virus A H1N1 (Fig. 2). Thus, it is also
tempting to speculate that SARS-CoV-2-induced senescent cells
may have some beneficial effects, depending on the biologicalcontext. Accordingly, a more rigorous analysis is needed todetermine whether senolytic drug can serve as a preventive
measure against long COVID. Nevertheless, our findings provide
valuable new insights into the pathogenesis of long COVID andsuggest new possibilities for its control.

Figure 1.
Cellular senescence initially functions as a fail-safe mechanism by inhibiting the proliferation ofdamaged cells in response to various stimuli. In the long term, however, senescent cells eventuallypromote various inflammatory diseases such as tumorigenesis via SASP.

Figure 2.
a-c. Syrian hamsters were intranasally inoculated with SARS-CoV-2 or medium (mock). After 14days post-infection of SARS-CoV-2, mock or SARS-CoV-2 infected hamsters were intranasally
inoculated influenza virus A (H1N1). Hamsters infected with mock followed by H1N1 (mock+H1N1;
n=6) and SARS-CoV-2 followed by H1N1 (CoV2+H1N1; n=6). The timeline of the experiment was
shown (a). The body weight was monitored until day 4 post H1N1 infection (b). These hamsters
were euthanized on day 4 after H1N1 infection, and the expression of H1N1 genomic RNA was
analyzed using RT-qPCR (c).

Recent Publications
1. Tsuji S, Minami S, Hashimoto R, Konishi Y, et al. SARS-CoV-2 infection
triggers paracrine senescence and leads to a sustained senescenceassociated inflammatory response. Nat Aging. 2:115-124 (2022). doi:
10.1038/s43587-022-00170-7.

3. Wakita M, Takahashi A, Sano O, et al. A BET family protein degrader
provokes senolysis by targeting NHEJ and autophagy in senescentcells. Nat Commun. 11:1935 (2020). doi: 10.1038/s41467-020-15719-6.

2. Okumura S, Konishi Y, Narukawa M, et al. Gut bacteria identified incolorectal cancer patients promote tumourigenesis via butyrate
secretion. Nat Commun. 12:5674 (2021). doi: 10.1038/s41467-02125965-x.

4243

Oncogene Research

Immunology(Nakatani et al. Nature Commun. 2021) and that the lysosomal
Ragulator complex activates NLRP3 inflammasome in vivo via
HDAC6 (Tsujimoto et al. EMBO J. 2022). These studies unraveled
unique roles of the p18-Ragulator complex in the immune
system, and provided new insights in the function of the p18Ragulator complex on the lysosome membrane.

Masato Okada, PhD

Professor

Masato Okada

Associate Professor

Shigeyuki Nada

Assistant Professor

Kentaro Kajiwara(S.A.) Tetsuya Kimura(S.A.) Makoto Matsuda

Research Assistant1

Figure 1.
Role of CDCP1-Src signaling in the regulation of tissue regeneration and tumor malignancy.

Role of Src tyrosine kinase in tumor progression
We have investigated the role of Src tyrosine kinase in tumor
progression. Src is the first-identified oncogenic tyrosine kinase,but no significant mutation of the SRC gene occurs in any type ofhuman cancer. Nonetheless, the function of Src is frequently
upregulated in various malignant cancers, and it is appreciatedthat upregulated Src plays a crucial role in tumor progression,
particularly in the acquisition of invasive and metastatic features.
To elucidate the molecular mechanisms underlying upregulationof Src, we investigated the regulatory mechanism of SRC gene
expression and searched for Src-activating factors. We found that
TGF-β treatment directly induced SRC gene expression via the
Smad pathway in coupled with additional transcription factors,
and determined the promoter and enhancer regions located in
the SRC gene. The upregulation of Src contributes to theprogression of cell motility accompanied by TGF-β–induced
epithelial-mesenchymal transition. On the other hand, we
identified CUB-domain containing protein 1 (CDCP1) as a Srcactivating membrane glycoprotein in lipid rafts of epithelial cells.
Upregulation of CDCP1 induces prominent activation of Src and
the STAT3 pathway, which promotes the invasive activity ofepithelial cells. We also showed that ablation of CDCP1 inhibits
HGF-induced morphological changes and cell growth, andattenuates membrane presentation of MET, resulting in inhibitionof invasive activity induced by HGF (Kawase et al. J Biol Chem.
2022). These findings suggest that CDCP1 is a co-receptor of MET
and thereby stabilizes its signaling (Fig. 1). Furthermore, we
revealed that ablation of CDCP1 suppresses the compensatory
renal hypertrophy, indicating that CDCP1 is required for the HGF44

MET signaling even in vivo (Kajiwara et al. Life Sci Alliance. 2021).
Analysis of the CDCP1-Src axis in the epithelial cells also showedthat Src activation in lipid rafts confers epithelial cells withinvasive potential to escape from apical extrusion during cellcompetition (Fig. 2. Kajiwara et al. Curr Biol. 2022). These findings
underscore the crucial role of the CDCP1-Src axis in the tissue
regeneration and the initial phase of tumor progression.

Role of p18 in the regulation of mTORC1 nutrient
signaling
We previously identified a new Src substrate termed p18/
Lamtor1, which exclusively localizes to lipid rafts of lysosomes.
p18 functions by forming a hetero-heptamer complex (Ragulator),
which is required for activation of mTORC1 on lysosomes.
Subsequent in vivo analyses confirmed that p18-Ragulator istightly associated with the regulation of mTORC1 nutrient
signaling. The crystal structure of p18-Ragulator provided
significant insights into the role of p18-mediated regulation ofmTORC1 on lysosomes. Recent in vitro analysis also showed that
p18-Ragulator complex provides a regulatory platform that is
indispensable for amino acid-dependent regulation of mTORC1(Fig. 3). Mathematical modeling of the mTORC1 signaling further
supported our prediction. On the other hand, we found an
additional function of the p18-Ragulator complex as a substratespecific mTORC1 scaffold in regulating the nuclear translocationof transcription factor EB (Kimura et al. J Biol Chem. 2022).
Collaborative studies with a member of IFReC (Prof. Kumanogoh)
further revealed that the lysosomal Ragulator complex plays anessential role in leukocyte trafficking by activating myosin II

Figure 2.
Role of CDCP1-Src in the regulation of the fate of pre-cancerous cells.

Figure 3.
Structural basis for the regulation of mTORC1 signaling via the p18-Ragulator
complex.

Recent Publications
1. Tsujimoto K, Jo T, Nagira D, Konaka H, et al. The lysosomal Ragulator
complex activates NLRP3 inflammasome in vivo via HDAC6. EMBO J.
e111389. doi.org/10.15252/embj.2022111389 (2022).
2. Kajiwara K, Chen PK, Abe Y, et al. Src activation in lipid rafts confers
epithelial cells with invasive potential to escape from apical extrusion
during cell competition. Curr Biol. 32(16):3460-3476 (2022).

4. Kawase N, Sugihara A, Kajiwara K, et al. SRC kinase activator CDCP1
promotes hepatocyte growth factor-induced cell migration/invasionof a subset of breast cancer cells. J Biol Chem. Mar;298(3):101630(2022).
5. Kajiwara K, Yamano S, Aoki K, Okuzaki D, Matsumoto K, Okada M.
CDCP1 promotes compensatory renal growth by integrating Src andMet signaling. Life Sci Alliance. 4(4):e202000832 (2021).

3. Kimura T, Hayama Y, Okuzaki D, Nada S, Okada M. The Ragulator
complex serves as a substrate-specific mTORC1 scaffold in regulating
the nuclear translocation of transcription factor EB. J Biol Chem.
298(3):101744 (2022).

45

Signal Transduction
Immunology

Nobuyuki Takakura, MD/PhD

Professor

Nobuyuki Takakura

Assistant Professor

Fumitaka Muramatsu
Weizhen Jia
Bal Zeynep
Keigo Akuta

Vasculogenesis and angiogenesis are processes in theformation of blood vessels where the formation of a primary
vascular plexus is induced by vascular endothelial growth factor(VEGF), which binds to its cognate receptor VEGFR2 on endothelial
cells (ECs), and the formation process involves the development,
proliferation, migration and tube formation of ECs. Subsequently,
mural cells are recruited near ECs and adhere to them, inducing
the blood vessels to mature. Platelet-derived growth factor
secreted from ECs promotes the recruitment of mural cells nearECs, and angiopoietin-1 (Ang1) secreted from mural cells via its
specific receptor Tie2 on ECs induces the adhesion of mural cells
to ECs.
We analyzed the function of Tie2 activation during thematuration process of blood vessels and discovered the criticalroles of apelin. Apelin is a ligand for APJ, which is a G proteincoupled receptor with 7 transmembrane domains expressed on
ECs. We found that apelin is produced from ECs upon stimulation
with Ang1 and stimulates APJ through an autocrine process to
induce cell-cell aggregation of ECs, thereby resulting in theformation of larger blood vessels. Blood vessels become larger incaliber when a higher number of mural cells adhere to ECs, and
we identified how blood vessels sense caliber size depending on
the number of mural cells through Ang1/Tie2-apelin/APJ axis
(EMBO J 2008). Moreover, we found that activation of APJ on ECs
stabilizes membrane expression of VE-Cadherin in ECs, inducing
tight adhesion of ECs and non-leaky blood vessels (Blood 2010).
We also found that apelin/APJ plays a critical role in the alignment
between arteries and veins. After blood vessels commit toforming into arteries and veins, apelin from arterial ECs

46

Postdoctoral Fellow

2

Research Assistant

6

Support Staff

3

significantly promotes migration of venous ECs expressing APJ.
Furthermore, upon stimulation with apelin, venous ECs start toexpress sFRP1, promoting the production of matrix
metalloproteinases from neutrophils around veins, and thereby
enhancing of movement of veins to arteries (Dev Cell 2015).
We applied the function of vascular maturation by apelin to
regulate tumor angiogenesis. When apelin expression isenhanced in tumor microenvironment, natural killer cells and
CD8 T cells penetrate the tumor parenchyma to create immune
hot spots that inhibit tumor growth (Oncogene 2012, Sci Rep
2021).
On the other hand, we found that APJ is not only expressed on
ECs but also in cancer cells in tumor microenvironment, and its
roles on cancer cells are unclear at the moment. Recently, we
discovered that APJ in cancer cells is involved in vascular mimicry,in which cancer cells themselves form vascular tube like structures(Pathol Oncol Res 2023). In cancer cells, APJ usually negatively
regulates epithelial mesenchymal transition (EMT), although inthe absence of APJ, cancer cells exhibit vascular mimicry tosupply nutrients and support tumor growth. Deficiency of APJ incancer cells induces Zeb1 expression, which is involved in EMT.
However, we found that Zeb1 expression is not regulated by the
TGF/smad pathway. Further analysis is required to understandthe underlying mechanism of this vascular mimicry regulated by
apelin/APJ.

Figure.
Diverse function of apelin/APJ in vascular formation.
APJ is a receptor for apelin and is not only expressed on endothelial cells but also on cancer cells. Apelin/APJ is involved in thematuration process of blood vessels through APJ on ECs, i.e., caliber size regulation, barrier formation between ECs, and juxtapositional alignment between arteries and veins. Therefore, when APJ activation is induced on ECs in the tumor microenvironment,
the blood vessels in tumors maturate, improving cancer drug delivery and immune cell infiltration. Moreover, APJ on cancer cells
inhibits vascular mimicry. Taken together, APJ should be activated in the tumor microenvironment to suppress tumor growth.
However, some controversial opinions suggest APJ suppression benefits tumor growth. Therefore, the function of APJ in tumors
may be diverse depending on tumor cell type, and further analysis is required for the development of effective tumor therapies
associated with apelin/APJ.

Recent Publications
1. Jia W, Kong L, Kidoya H, Naito H, Muramatsu F, Hayashi Y, Hsieh HY,
Yamakawa D, Hsu DK, Liu F-T, and Takakura N. Indispensable role of
Galectin-3 in promoting quiescence of hematopoietic stem cells.
Nature Commun. 12:2118 (2021).

4. Naito H, Iba T, Wakabayashi T, Tai-Nagara I, Suehiro JI, Jia W, Eino D,
Sakimoto S, Muramatsu F, Kidoya H, Sakurai H, Satoh T, Akira S, Kubota
Y, Takakura N. TAK1 prevents endothelial apoptosis and maintains
vascular integrity. Dev Cell 48:151-166 (2019).

2. Naito H, Wakabayashi T, Ishida M, Gil CH, Iba T, Rahmawati FN, Shimizu
S, Yoder MC, Takakura N. Isolation of tissue-resident vascularendothelial stem cells from mouse liver. Nat Protoc. 15:1066-1081(2020).

5. Wakabayashi T, Naito H, Suehiro JI, 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 andregenerative properties. Cell Stem Cell 22:384-397 (2018).

3. Kidoya H, Muramatsu F, Shimamura T, Jia W, Satoh T, Hayashi Y, Naito H,
Kunisaki Y, Arai F, Seki M, Suzuki Y, Osawa T, Akira S, Takakura N.
Regnase-1-mediated post-transcriptional regulation is essential forhematopoietic stem and progenitor cell homeostasis. Nat Commun.
10:1072 (2019).

47

Cutaneous Immunology
Manabu Fujimoto, MD/PhD

Professor

IL-10-Producing Potency from Blood B Cells Correlateswith the Prognosis of Alopecia Areata
We investigated the role of B cells in the pathogenesis ofalopecia areata (AA), an autoimmune disorder that causes hairloss. While cytotoxic T cells have been identified as a major factor,
the involvement of B cells had not been studied. We found that B
cells from patients with AA produced more of the antiinflammatory cytokine IL-10 than B cells from healthy individuals.
When AA patients were divided into good prognosis and poor
prognosis groups based on hair regrowth, B cells from the good
prognosis group produced more IL-10 than those from the poor
prognosis group. CD8 T cells of patients with poor prognosis also
showed reduced responsiveness to B cell-induced upregulationof IFN-g–producing activity.

Possible Plasticity of Cytotoxic Resident Memory T
Cells in Fixed Drug Eruption
We examined the phenotypical characteristics of T cells fromfixed drug eruption (FDE) lesions and analyzed the origin of
CD49a+CCR7+ T cells in FDE lesions. This study showed that theratio of central memory T (TCM) cells was increased in recurrent
FDE lesions, and the ratio of T cells expressing resident memory T(TRM) cell markers was limited. Both CD4 and CD8 T cells fromrecurrent FDE lesions highly expressed CD49a, a marker for
IFN-g–producing cytotoxic TRM (cTRM) cells. The T-cell receptor(TCR) clones were also examined, and the commonality of TCR
clones was the highest between skin cTRM and skin TCM cells,suggesting that TCM cells in recur are not originated from blood
TCM cells.
48

Manabu Fujimoto

Research Assistant4

Support Staff

1

Neurofibromatosis 1 (NF1) is a hereditary neurocutaneous
disorder with different clinical phenotypes, including cutaneous
neurofibroma (cNF) and plexiform neurofibroma (pNF). This
study using single-cell RNA sequencing and immunohistochemical
analysis found that cNF and pNF have distinct transcriptional
profiles and microenvironments. pNF had more Schwann cells,
fibroblasts with cancer-associated fibroblast-like phenotypes,
angiogenic endothelial cells, and M2-like macrophages, whilecNF had more CD8 T cells with tissue residency markers. This
study provides new insights into the different features of cNF andpNF, which could be useful in developing targeted therapies for
NF1 patients.

Collagen homeostasis paradoxically maintains invitiligo lesion
The lesional skin of vitiligo would be more resilient thanuninvolved lesion even in sun-exposed areas. Therefore, wehypothesized that a collagen homeostasis might paradoxicallymaintain in vitiligo lesion irrespective of substantial excessiveoxidative stress condition without melanin protection. Single-cell
RNA sequencing analysis showed that the expressions ofcollagen-related and anti-oxidative enzyme genes were upregulated in the fibroblasts of lesional skin compared to those ofuninvolved skin. Our results suggest that the dermal fibroblasts
in vitiligo may play a protective role against the locally-exposedoxidative stress.

Immunology

Distinct transcriptional profiles in the different
phenotypes of neurofibroma from the sameneurofibromatosis 1 subject

Epidermal clearance of Candida albicans is mediatedby IL-17 but independent of fungal innate immune
receptors
We examined the role of IL-17 in host defense against Candida
albicans in the epidermis. Using a murine model of epicutaneous
candidiasis, we found that group 3 innate lymphoid cells (ILC3s)
and γδT cells were the major IL-17 producers in the epicutaneous
candidiasis model. Analyses of Rag2−/− mice and Rag2−/− Il2rg−/−
mice revealed that production of IL-17A and IL-17F by ILC3s was
sufficient for C. albicans clearance. These findings indicate acritical and redundant function of IL-17A and IL-17F produced by
ILC3s in host defense against C. albicans in the epidermis. The
results suggest that epidermal C. albicans clearance isindependent of innate immune receptors.

Sirolimus relieves seizures and neuropsychiatric
symptoms via changes of microglial polarity intuberous sclerosis complex model mice
Tuberous sclerosis complex (TSC) is a genetic disorderassociated with epilepsy and serious neuropsychiatric symptoms,
collectively known as TSC-associated neuropsychiatric disorders(TAND). The overactivation of mTORC1 by mutations in TSC1 or
TSC2 is thought to cause TSC, and mTORC1 inhibitors such as
sirolimus are effective against various tumor types of TSC. We
showed TSC2 conditional knockout mice exhibited phenotypesof TAND as well as epileptic seizures. Gene expression analysis
revealed that changes to M1 in microglial polarity were involvedin the onset of TSC epilepsy and neuropsychiatric symptoms andsirolimus treated epilepsy by shifting microglial polarity to M2.

Figure.
Representative H&E and immunofluorescence results showing CD4/CD8 and CD8/CD20 from subjects with good prognosis (GP)and poor prognosis (PP). White arrows indicate B cells. In subjects with GP, a representative immunofluorescence result of CD19/
IL-10 is also shown. Bars = 50 mm.

Recent Publications
1. Matsumura Y, Watanabe R, Koguchi-Yoshioka H, Kume M, Nakai S,
Furuta J, Azukizawa H, Ishitsuka Y, Tanemura A, Taminato M, Tashima
H, Otani N, Tomita K, Kubo T, Fujimoto M. Possible Plasticity ofCytotoxic Resident Memory T Cells in Fixed Drug Eruption. J Invest
Dermatol. S0022-202X(22)02895-0 (2022).
2. Matsumura Y, Watanabe R, Koguchi-Yoshioka H, Nakamura Y, Saito A,
Kume M, Nakai S, Ishitsuka Y, Furuta J, Fujimoto M. IL-10-Producing
Potency from Blood B Cells Correlates with the Prognosis of Alopecia
Areata. J Invest Dermatol. 143(5):871-874.e5 (2023).

4. Koike-Kumagai M, Fujimoto M, Wataya-Kaneda M. Sirolimus relieves
seizures and neuropsychiatric symptoms via changes of microglial
polarity in tuberous sclerosis complex model mice. Neuropharmacology.
218:109203 (2022).
5. Iwasawa MT, Miyachi H, Wakabayashi S, et al. Epidermal clearance ofCandida albicans is mediated by IL-17 but independent of fungal
innate immune receptors. Int Immunol. 34(8):409-420 (2022).

3. Matsumura Y, Watanabe R, Fujimoto M. Suppressive mechanisms ofregulatory B cells in mice and humans. Int Immunol. 35(2):55-65(2023).

49

Innate Immune Systems

Professor

Kazuyo Moro

Associate Professor

Yasutaka Motomura

Assistant Professor

Takuya Yashiro

The most significant finding of this study was the identification of
APX-induced hyperplasia of tuft cells in the colon. To understandthe role of IL-25 in UC, we performed APX in IL-25 knockout miceand found that suppression of DSS-induced colitis was abolishedin these mice. In contrast, IL-25 administration produced the
opposite result. Many studies on IBD have focused on factors thatcause colitis; however, by focusing on factors that inhibit thedevelopment of colitis, as in this project, we hope that new
methods of preventing IBD can be established.

Immunology

Kazuyo Moro, DDS/PhD

intestinal atrophy, and weight loss induced by DSS were reducedin APX mice compared to those in sham-operated mice. To
understand the immunological changes in the colon after APX,
we examined the immune cell profiles and found that ILC2s weresignificantly increased after APX. Consistent with this result, wefound that type 2 cytokines, such as IL-5 and IL-13, increased after
APX. In addition, measurements of IL-25 and IL-33, known
activators of ILC2s, showed that IL-25 was elevated in the colonicepithelial fraction, whereas IL-33 was not altered. IL-25 is known
to be produced by chemosensory epithelial cells called tuft cells.

Satoshi Koga

1. Innate IgE exacerbates human allergic disease via
amplification of ILC2 activation
ILC2s induce allergies by interacting with various immune andnon-immune cells; however, their relationship with B cells is
unclear. In this study, we found that IL-33 markedly promoted B1cell proliferation via ILC2s and induced the production of “innate
IgE,” which recognizes autoantigens but not foreign antigens. B1
cells are innate type B cells that contribute to the clearance of
microorganisms and apoptotic cells by producing low-affinity
IgM that recognizes T cell-independent antigens, such as lipids
and polysaccharides. Most research on B1 cells has been
conducted using B1 cells in the peritoneal cavity of mice, andsome researchers still believe that B1 cells do not exist in humans.
Our results demonstrated that the class switch of IgE in B1 cells
occurs in peripheral tissues by IRF4+ILC2-derived IL-4 in a CysLTdependent manner. Experiments using IRF4-deficient mice
showed that IRF4 was essential for IL-4 production from ILC2s,
and innate IgE was virtually undetected in ILC2-deficient mice.
Innate IgE did not induce granulocyte degranulation but directly
promoted the survival and lipid production of FcεR+ mast cells
and basophils, resulting in amplification of ILC2/eosinophildependent allergic inflammation.
We focused on eosinophilic chronic rhinosinusitis (ECRS) to
confirm the importance of innate IgE in humans. We found that
ILC2s accumulate in the nasal polyps of ECRS patients and are
predominantly correlated with IgE-bearing mast cells as well as
eosinophils. The significant correlation between ILC2s and IgEproduction in nasal polyps suggests that ILC2s induce innate IgE
50

Postdoctoral Fellow

1

Research Assistant2

Support Staff

1

production in B1 cells, leading to eosinophilic inflammation.
Single-cell RNA-sequencing analysis demonstrated that B1 cells
are also present in the nasal polyps of patients with ECRS and that
ILC2s are major IL-4 producing cells. A comparison of B1 and B2
cells isolated from nasal polyps revealed that most IgE wasproduced by B1 cells. Taken together, our results indicate that
innate IgE contributes to the pathogenesis of ECRS by forming acircuit that amplifies ILC2 function by promoting mast cell andbasophil survival, and CysLT production.

2. Identification of appendectomy-related factors that
inhibit development of ulcerative colitis
Ulcerative colitis (UC) is an inflammatory bowel disease (IBD)
that affects a growing number of people worldwide. In recent
years, the advent of biologics, such as anti-TNF-α antibodies, has
expanded the treatment options for UC, but no curative therapy
has yet to be established. One cohort study reported that patients
who underwent appendectomy by the age of 20 had a lower
lifetime risk of developing UC. Subsequently, similar results havebeen obtained in cohort studies conducted in various countries.
Although this phenomenon is well known to clinicians, no basic
studies have examined this mechanism over the past 20 years.
Therefore, we initiated this project with the aim of developing a
new therapeutic approach by elucidating the mechanism bywhich appendectomy reduces the risk of colitis.
We first generated an appendectomy (APX) mouse modeland
induced colitis by dextran sulfate sodium (DSS). Similar to thecohort study, pathologies such as IL-1β and IL-6 production,

Figure.
IL-4 produced from T cells promotes antigen-specific IgE production from B2 cells in lymph nodes and induces mast cell
degranulation. On the other hand, IL-4 produced from ILC2s induces the production of Innate IgE from B1 cells and supports
survival, proliferation and lipid production of basophils and mast cells.

Recent Publications
1. Kobayashi T, Moro K. A hairy situation for ILC2s. Immunity 55:17561758 (2022).Kabata H, Motomura Y, Kiniwa T, Kobayashi T, Moro K. ILCs
and Allergy. Advances in experimental medicine and biology 1365:7595 (2022).

3. Momiuchi Y, Motomura Y, Suga E, et al. Group 2 innate lymphoid cells
in bone marrow regulate osteoclastogenesis in a reciprocal manner
via RANKL, GM-CSF and IL-13. International immunology 33:573-585(2021).

2. Kobayashi T, Moro K. Tissue-Specific Diversity of Group 2 Innate
Lymphoid Cells in the Skin. Frontiers in immunology 13:885642(2022).

4. Hikichi Y, Motomura Y, Takeuchi O, Moro K. Posttranscriptional
regulation of ILC2 homeostatic function via tristetraprolin. The Journalof experimental medicine 218 (2021).

51

Human Single Cell Immunology
Immunology

James Badger Wing, PhD

The antibody response to COVID-19 is a key part of our defense
against infection. Broadly speaking there are two main routes ofantibody production; the follicular route, typified by theinteraction between T-follicular helper (Tfh) T cells and germinal
center B-cells, and the extrafollicular route typified by theinteraction between T-peripheral helper (Tph) cells andextrafollicular B-cells. A further complication is that antibody
production is controlled by a population of regulatory T-cells
named T-follicular regulatory cells (Tfr). However, since thecomplex interaction of these rare cell types are difficult to resolveby common techniques our understanding of these processes isincomplete.
We used single cell analysis of proteomics by mass cytometry(CyTOF) to examine the status of rare cells of immune system inhigh detail in a cohort of COVID-19 patients with severe disease.
Using this approach; we were able to find that there was a sex
biased loss of circulating Tfr cells (cTfr) in all patients. In addition,

Associate Professor

James Badger Wing

Assistant Professor

Jonas N. Søndergaard

Postdoctoral Fellow

3

Research Assistant

1

Visiting Scientist

1

Support Staff

1

we found that SARS-CoV2 neutralizing antibody concentrations
were strongly associated with a network of extrafollicular cells
related to antibody production. T-peripheral helper cells (Tph),proliferating memory B-cells and atypical/extrafollicular B-cells,
while cTfr were negatively correlated with this network. This
trend is stronger in male patients who also show increased
numbers of antibody producing T and B-cells and fewer Tfr incomparison to female patients (Fig. 1, Søndergaard et al. PNAS,
2023). These results suggest that sex specific differences to thebalance of cTfr and a network of extrafollicular antibodyproduction associated cell types may be a key factor in the alteredhumoral immune responses between male and female COVID-19
patients. A better understanding of the cellular interactions
controlling antibody production in COVID-19 may allow thedevelopment of new treatments to control the disease.
Additionally, the finding that male patients have strong, butdysregulated, antibody production may give us information that
we must treat male and female COVID-19 patients differently.

Figure 1.
Sex biased imbalance of cells that inhibit or boost antibody production during COVID-19 infection.
T-follicular regulatory cells (Tfr) inhibit antibody production. T-peripheral helper cells (Tph)stimulate atypical B-cells to form antibody producing plasma cells.

Recent Publications
1. Søndergaard JN, Tulyeu J, et al. A sex-biased imbalance between Tfr,
Tph and atypical B cells, determines antibody responses in COVID-19
patients. Proc Natl Acad Sci USA. 120(4) e2217902120 (2023).

4. Yamaguchi Y, Kato Y, Edahiro R, Søndergaard JN, et al. Consecutive
BNT162b2 mRNA vaccination induces short-term epigenetic memory
in innate immune cells. JCI Insight. (2022) 10.1172/jci.insight.163347.

2. Yokoi T, et al. Identification of a unique subset of tissue-resident
memory CD4+ T cells in Crohn’s disease. Proc Natl Acad Sci USA. 120(1)e2204269120 (2023).

5. Namkoong H, Edahiro R, et al. DOCK2 is involved in the host genetics
and biology of severe COVID-19. Nature. 609:754-760 (2022).

3. Shibata K, et al. Symbiotic bacteria-dependent expansion of MR1reactive T cells causes autoimmunity in the absence of Bcl11b. Nat
Commun. 13(1):1-15 (2022).

52

53

Human Immunology (Single Cell Genomics)

54

Associate Professor

Daisuke Okuzaki

Postdoctoral Fellow

3

Visiting Scientist

2

Support Staff

1

The Human Immunology Laboratory was established in
November 2019 with the aim of accelerating the application of
single-cell sequencing technology and advancing clinicalresearch. As part of the largest single-cell RNA analysis initiativein Japan, our laboratory collaborated with the "Team Osaka
University COVID-19 Research Group" to conduct whole blood
single-cell RNA analysis of samples obtained from patients
admitted to Osaka University Hospital. This effort was led byProfessors Yukinori Okada and Kumanogoh from the School of
Medicine, who oversaw the storage and management ofspecimens until the sixth wave of the pandemic. Our laboratory
played a vital role in this project, contributing to the analysis of
more than 200 specimens. The data was later utilized by the"Corona Control Task Force," a collaborative project involving
Osaka University (led by Professor Okada), as well as over 100
hospitals and major universities in Japan. The project's findings,
including single-cell RNA analysis, were published in Nature inAugust 2022. The study identified a correlation between genetic
polymorphisms in the DOCK2 gene region and COVID-19
aggravation, representing the most extensive genome-wide
association analysis of COVID-19 patients in Asia. Furthermore,combined with single-cell analysis, a COVID-19-associated risk
variant at the IFNAR2 locus (rs13050728) had context-specificand monocyte-specific expression quantitative trait locus effects.
This discovery was published in Nature Genetics.

CoV1804 clonotype underwent robust clonal expansion in a
subset of COVID-19 patients. PA-N-CoV1804 was expressed
exclusively in plasmablasts from COVID-19 patients. PA-NCoV1804 harbors numerous somatic mutations like the antiviral
antibodies derived from pre-existing memory for seasonal
human coronaviruses. However, these clonotypes were strongly
reactive to the N protein of SARS-CoV-2 but not to that of seasonalcoronaviruses. Therefore, these clones seem to be originatedfrom naive B cells and developed through de novo clonal
expansion after SARS-CoV-2 infection (Figure 1).

We discovered a novel public antibody clonotype, PA-NCoV1804, within the data that reacts with both the SARS-CoV-2 N
protein and several self-antigens. We found that the PA-N-

In terms of proteomics research, blood protein analysis of
COVID-19 patients was conducted both in the US and at Osaka
University in Japan, and the analysis identified five proteinsOn the other hand, in a joint research project conducted with
Critical Care Medicine at Osaka University, a platform serving as a
guide for determining whether mechanical ventilation would beneeded and for how long was established for severe COVID-19
patients who are transported to the ICU in Osaka University
Hospital . In a latent class analysis of whole blood RNA collected
and sequenced from 40 patients, 45 genes were identified as
effective markers for classifying the patients into three classes.
Interactions between microRNA and mRNAs were also studied
through simultaneous measurements of the mRNAs andmicroRNAs in the whole blood of severe COVID-19 patients. The
integrated analysis revealed that, compared to interferon
signaling in healthy subjects, interferon signaling was more
activated in the COVID-19 patients.

mechanisms of COVID-19 and has the potential to inform future
approaches to managing the pandemic.
Our laboratory has been able to build a single-cell platform at
IFReC while concurrently serving as an NGS core facility. It is now
the leading single-cell analysis facility in Japan. Three years ofcollaborative research on COVID-19 with multiple institutions
have also steadily produced results. Original studies such as thedevelopment of a method for simultaneous detection of bacteria
and eukaryotic cells at the single-cell level, and the developmentof a method for detecting circRNA using long-read sequencers
will advance research in many fields.

Immunology

Daisuke Okuzaki, PhD

related to COVID-19 aggravation. Some COVID-19 patients
became severely ill and required treatments, such as mechanicalventilation. We used a technology called Explore 1536 from Olink
to identify the proteins in serum. To further identify effective
diagnostic biomarkers, ROC analysis of four plasma proteins was
conducted. Based on an analysis of each marker alone, we founda combination of three to four proteins that had higher prognostic
accuracy than other predictors, such as CRP and D-dimer.
Ultimately, we found that the four proteins related to aggravation
were elevated in the blood of deceased patients. The utilizationof single-cell data in collaborative efforts such as the "Corona
Control Task Force" has led to important insights into the

Figure 1.
Clonal landscape of viral infection-induced autoantibody production.

Recent Publications
1. Edahiro R, Shirai Y, Takeshima Y, et al. Single-cell analyses and hostgenetics highlight the role of innate immune cells in COVID-19
severity. Nat Genet. 55(5):753-767 (2023).

4. Ito H, Ishikawa M, Matsumoto H, Sugihara F, Okuzaki D, Hirata H,
Ogura H. Transcriptional differences between coronavirus disease2019 and bacterial sepsis. Virol J. 19(1):198 (2022).

2. Namkoong H, Edahiro R, Takano T, et al. DOCK2 is involved in the hostgenetics and biology of severe COVID-19. Nature. 609(7928):754-760(2022).

5. Yamaguchi Y, Kato Y, Edahiro R,et al. Consecutive BNT162b2 mRNA
vaccination induces short-term epigenetic memory in innate immune
cells. JCI Insight. Nov 22;7(22):e163347 (2022).

3. Ishikawa M, Shimada Y, Ozono T, et al. Single-cell RNA-seq analysis
identifies distinct myeloid cells in a case with encephalitis temporally
associated with COVID-19 vaccination. Front Immunol. 14:998233(2023).

55

Immune Homeostasis
Immunology

Yasutaka Okabe, PhD

Associate Professor

Yasutaka Okabe

Postdoctoral Fellow

1

Research Assistant2

Support Staff

1

Figure.

Peritoneal cavity, the largest fluid-filled abdominal cavity in
mammals, contains visceral organs such as stomach, spleen, liver,and intestine. Although peritoneal cavity is normally sterile, theinfection, which can occur by a pathological or traumatic loss ofintestinal wall integrity, cirrhosis, pancreatitis, abdominal surgery,or peritoneal dialysis, can cause life-threatening sepsis since theperitoneal cavity serves as a conduit to other vital organs forpathogen spreads.
Omental milky spots in the peritoneal cavity are lymphoidtissues exhibiting hybrid nature between secondary lymphorgans and ectopic lymphoid tissues, although the mechanism of
their development and maturation is poorly understood. We
previously reported that retinoic acid, which controls thefunctional specialization of peritoneal macrophages, isabundantly present in omentum (Okabe & Medzhitov, 157, 832844, Cell). Whereas retinoic acid is important for the developmentof secondary lymphoid organs such as lymph nodes and Peyer’s
patches, its role in milky spot formation remains under-explored.
We identified a subset of omental fibroblastic reticular cells(FRCs) that are characterized by the expression of retinoic acidconverting enzyme. We found these FRCs are uniquely present inmilky spots but not in lymph nodes. Furthermore, these FRCs are
essential for the recruitment of circulating lymphocytes to milky
spots, which is mediated by the induction of chemokine CXCL12
in a manner dependent on retinoic acid. Thus, our study
demonstrates the stromal-immune cell interaction in theformation of nonclassical lymphoid tissues.

Recent Publications
1. Yoshihara T & Okabe Y. Aldh1a2+ fibroblastic reticular cells regulate
lymphocyte recruitment in omental milky spots. J Exp Med. 220(5),e20221813 (2023).
2. Okabe Y. Immune Niche Within the Peritoneal Cavity. Curr Top
Microbiol Immunol. 434:123-134 (2021).

4. Okabe Y & Medzhitov R. Tissue Biology Perspective on Macrophages.
Nat Immunol. 17:9-17 (2016).
5. Okabe Y & Medzhitov R. Tissue-specific signals control reversible
program of localization and functional polarization of macrophages.
Cell. 157:832-844 (2014).

3. Okabe Y. Molecular Control of the Identity of Tissue-Resident
Macrophages. Int Immunol. 30:485-491 (2018).

56

57

Cellular Immunotherapy
Immunology

Naoki Hosen, MD/PhD

Professor

Naoki Hosen

Associate Professor

Hisashi Kato
Kentaro Fukushima
Jiro Fujita

Assistant Professor

Michiko Ichii
Yasutaka Ueda
Tomoaki Ueda

We are focusing on cellular immunotherapy, especiallychimeric antigen receptor (CAR)-T cell therapy for cancers. CAR-T
cells specifically recognize cancer cells using the cancer-specificmAb-derived antigen-recognition domain, and are activated.
Activated CAR-T cells kill tumor cells and also proliferate
extensively. CD19 CAR-T cells showed surprisingly higheffectiveness against acute lymphocytic leukemia and malignant
lymphoma. We discovered that the active conformer of an
integrin could serve as a specific therapeutic target for multiple
myeloma (MM), which is an incurable hematological cancer
characterized by the accumulation of neoplastic plasma cells inthe bone marrow (BM). Clinical trial of the CAR T-cell targeting theactive conformation of integrin β7 for MM is now on-going.

Identification of a novel target antigen for multiple
myeloma and development of CAR-T cell therapy
targeting themCancer-specific cell surface antigens are ideal therapeutictargets for monoclonal antibody (mAb)-based therapy. However,most transcripts or proteins highly specific for cancer cells havealready been identified after extensive efforts using transcriptome
or proteome analyses. We screened more than 10,000 mAb
clones raised against MM cells, and identified R8H283 as a mAb
that bound to MM cells but not to normal hematopoietic or nonhematopoietic cells. R8H283 specifically recognized CD98hc.
R8H283 did not react with CD98hc monomer, but bound to
CD98hc forming heterodimers with the light chains, which areamino-acid transporters. MM cells abundantly expressed CD98

58

Visiting Scientist

1

Support Staff

3

heterodimers to intake amino acids for constitutive production of
immunoglobulin. Although CD98 heterodimers were also
expressed in normal leukocytes, R8H283 did not react with them.
Normal leukocytes expressed CD98hc glycoforms different fromthose expressed in MM cells, which may be a cause for lack of
R8H283 reactivity in normal leukocytes. R8H283 exerted
significant anti-MM effects without damaging normal
hematopoietic cells. These findings not only suggest that R8H283
is a new source for mAb-based therapies such as CAR-T celltherapy against MM, but also that a cancer-specific conformational
epitope in a ubiquitous protein, which cannot be identified bytranscriptome or proteome analyses, can be found by extensive
screening with primary human tumor samples. We are now
developing R8H283-derived CAR T-cells.

Figure 1.
The strategy for identifying novel cancer-specific cell surface targets for CAR-T cell therapy.

Figure 2.
Novel target antigen structures that we have identified for CAR-T cell therapy against multiple
myeloma.

Development of CAR-T cell therapy targeting antigen
structures formed as results of post-translational
events in various cancers
We applied the same strategy to various types of cancers. For
hematological cancers such as acute myeloid leukemia (AML),
the only hurdle for developing CAR-T cell therapy is lack of an
appropriate cancer-specific cell surface antigen. We have alreadyestablished huge numbers of mAbs reacting with AML cells andfound ones recognizing antigen structures highly specific for
AML cells. We also applied the same strategy to several types ofsolid tumors in collaboration with several departments treating
cancers in Osaka University Hospital. We have recently showedthat our screening method also works in glioblastoma.

Recent Publications
1. Nakagawa T, Kijima N, Hasegawa K, et al. Identification of glioblastomaspecific antigens expressed in patient-derived tumor cells ascandidate targets for chimeric antigen receptor T cell therapy.
Neurooncol Adv. 5:vdac177 (2023).
2. Uchihara Y, Permata TBM, Sato H, et al. DNA damage promotes HLAclass I presentation by stimulating a pioneer round of translationassociated antigen production. Mol Cell. 82:2557-2570 e2557 (2022).

3. Hino A, Fukushima K, Kusakabe S, et al. Prolonged gut microbial
alterations in post-transplant survivors of allogeneic haematopoietic
stem cell transplantation. Br J Haematol. (2022).
4. Hasegawa K, Ikeda S, Yaga M, et al. Selective targeting of multiple
myeloma cells with a monoclonal antibody recognizing the ubiquitous
protein CD98 heavy chain. Sci Transl Med. 14:eaax7706 (2022).

59

Microbiology and Immunology
Immunology

Nobuhiko Kamada, PhD

Professor

Nobuhiko Kamada

Associate Professor

Sho Kitamoto
Hiroko Kitamoto

Our team has been studying the role of microbiota in thepathogenesis of gastrointestinal diseases, such as inflammatory
bowel disease (IBD) and colorectal cancer (CRC). It has beenreported that certain pathogenic members of commensal
bacteria (namely ‘pathobionts’) are enriched under disease
conditions and contribute to disease pathogenesis. However, theprecise mechanisms by which such pathobionts thrive in disease
conditions and trigger and/or exacerbate disease remain
incompletely understood.
We recently demonstrated that L-serine metabolism plays avital role in the survival of some pathobionts, including adherent–
invasive Escherichia coli, a pathobiont associated with IBD. AIEC
utilizes L-serine supplied by dietary protein intake in the gut
lumen. Therefore, deprivation of dietary L-serine can suppress
the expansion of AIEC in the gut. However, certain commensal
bacteria can help AIEC overcome the dietary nutrient limitation.
The presence of mucolytic bacteria allows AIEC to grow evenunder the restriction of dietary L-serine. Mucolytic bacteria, suchas Akkermansia muciniphila, degrade the mucus layer andfacilitate the encroachment of AIEC to the epithelial niche. In theepithelial niche, AIEC acquires L-serine from the amino acid poolof the colonic epithelium, allowing them to grow even under
diet-derived L-serine restriction. Thus, the interaction between

60

Research Assistant1

Support Staff

1

pathobionts and mucolytic commensal bacteria helps
pathobionts switch their source of essential nutrients from thediet to host cells. In addition to AIEC for IBD, we are identifying
pathobionts associated with various gastrointestinal diseases,
such as CRC and intestinal fibrosis. We aim to elucidate themechanisms by which these pathobionts adapt to diseasespecific environments. Moreover, we are identifying partner
bacteria that cooperate with pathobionts to promote diseaseprogression and suppressors that inhibit the expansion ofpathobionts. Also, we focus on the microbial and immune
connections between the oral and gut mucosae in thepathogenesis of gastrointestinal diseases. We have discoveredthat inflammation in the oral mucosa results in the outgrowth of
inflammatory oral pathobionts. Amassed oral pathobionts thennaturally translocate to the gut and contribute to thepathogenesis of gut diseases. In addition, inflammatory immune
cells arising during oral inflammation can also migrate to the gut.
Gut-migrated inflammation T cells of oral origin are activated byectopically colonized oral pathobionts and contribute toinflammation in the gut mucosa.
Note: The PI is cross-appointed at IFReC and the University ofMichigan (USA). These research projects were conducted ateither IFReC or the University of Michigan.

Figure.
Pathobionts promote various gastrointestinal diseases, including IBD, CRC, and intestinal fibrosis. Some pathobionts
are oral origins. Certain symbiotic bacteria, such as mucolytic bacteria, act as ‘cooperator’ and help pathobionts
acquire required nutrients. Some symbiotic bacteria may serve as ‘suppressors.’ These suppressors may directly andindirectly inhibit the expansion of pathobionts and subsequent disease progression.

Recent Publications
1. Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, et al.
Mucolytic bacteria license pathobionts to acquire host-derived
nutrients during dietary nutrient restriction. Cell Reports. 40(3):111093(2022). doi: 10.1016/j.celrep.2022.111093.
2. Imai J, Ichikawa H, Kitamoto S, Golob JL, Kaneko M, Nagata J, Takahashi
M, Gillilland MG, Tanaka R, Nagao-Kitamoto H, Hayashi A, Sugihara K,
Bishu S, Tsuda S, Ito H, Kojima S, Karakida K, Matsushima M, Suzuki T,
Hozumi K, Watanabe N, Giannobile WV, Shirai T, Suzuki H, Kamada N. A
potential pathogenic association between periodontal disease andCrohn's disease. JCI Insight. e148543 (2021). doi: 10.1172/jci.
insight.148543.

3. Kitamoto S, Nagao-Kitamoto H, et al. The intermucosal connection
between the mouth and gut in commensal pathobiont-driven colitis.
Cell. 182(2):447-462 (2020).
4. Nagao-Kitamoto H, Leslie JL, Kitamoto S, et al. Interleukin-22mediated host glycosylation prevents Clostridioides difficile infection
by modulating the metabolic activity of the gut microbiota. Nat Med.
26(4):608-617 (2020).
5. Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, et al. Dietary
L-serine confers a competitive fitness advantage to Enterobacteriaceae
in the inflamed gut. Nat Microbiol. 5(1):116-125 (2020).

61

during an infection outbreak in a neonatal intensive care unit
(NICU) in a hospital in Japan.

Immunology

Cutaneous Allergy and Host Defense
Yumi Matsuoka-Nakamura, MD/PhD

Professor

Our laboratory team was established in November 2023. We
are interested in understanding the pathogenesis of inflammatory
skin diseases, such as atopic dermatitis (AD) and acne vulgaris.
We also aim to unravel the mechanism by which Methicillinresistant Staphylococcus aureus (MRSA) develops multi-drugresistance and instigates intractable infections in hospitals. In
particular, our research projects are focused on the interaction
between the S. aureus accessory gene regulator (Agr) quorum
sensing (QS) and host innate immune responses. QS refers to theability of bacteria to sense their population density. As bacterial
populations grow, they risk nutrient scarcity. Consequently, theyalter their behavior by regulating the production of various genes
and substances, aiming to acquire more nutrients from the hostor eliminate bacteria with similar nutritional requirements.
The expression of Staphylococcus Agr is crucial for epidermalcolonization and is associated with the development of AD,
which often correlates with colonization by S. aureus on theaffected skin. AD is the most prevalent allergic skin disease,affecting 15-20% of children and 2-10% of adults worldwide.
Both intrinsic genetic factors, such as susceptibility to type 2
inflammation or skin barrier dysfunction, and extrinsic
environmental factors, like air pollen and skin microbiota,
contribute to AD. S. aureus, which does not typically colonize theskin of healthy individuals, is often found in the lesional skin ofpatients with AD, correlating with disease flares. However, therole of S. aureus in the pathogenesis of AD has not been fully
elucidated. We previously discovered that Th2-type dermatitis
can be induced through mast cell degranulation triggered by

62

Yumi Matsuoka-Nakamura

δ-toxin under Agr-QS expression. We also found that PSMα under
Agr-QS expression induces skin barrier disruption and IL-17dependent dermatitis. In our study using whole-genome
sequencing of S. aureus strains isolated from the skin of Japanese
infants, we observed that infants who developed AD early in life
were more likely to have cheek skin colonized by S. aureus.
Interestingly, infants harboring S. aureus with spontaneous
mutations in agr were more likely to remain healthy, despite thepresence of this bacterium on their skin. This work suggests that
S. aureus and functional QS may play a role in the onset of AD inchildren.
In a separate infant cohort study in collaboration withpediatricians at Chiba University, we monitored patients who
received skincare interventions, and obtained longitudinal skinmicrobiome samples from the presymptomatic stage of infantile
AD and food allergies (FA). We are currently analyzing theassociation between presymptomatic changes in the infant skinmicrobiome and the onset of AD and FA.
In our ongoing project, we are investigating how Agr-QS in S.
aureus contributes to MRSA's adaptation in hospital environments
and its acquisition of multidrug resistance. MRSA is a significant
health problem worldwide, not only due to its high pathogenicity
but also its propensity to cause infection outbreaks. The
mechanisms by which bacteria adapt to hospital environments
to cause recurrent disease remain unknown. To understand thebacterial factors that enable S. aureus to survive and persist in thehospital environment, we are analyzing MRSA strains isolated

Figure.
The role of the Staphylococcus aureus accessory gene regulator quorum sensing system in the development of atopic dermatitis.

Recent Publications
1. Iwasawa MT, Miyachi H, Wakabayashi S, et al. Epidermal clearance ofCandida albicans is mediated by IL-17 but independent of fungal
innate immune receptors . Int Immunol. 34(8):409-420 (2022).

4. Miyachi H, Wakabayashi S, Sugihira T, et al. Keratinocyte IL-36
Receptor/MyD88 Signaling Mediates Malassezia-Induced IL-17Dependent Skin Inflammation . J Infect Dis. 223(10):1753-1765 (2021).

2. Matsumoto M, Nakagawa S, Zhang L, Nakamura Y, Villaruz AE, Otto M,
Wolz C, Inohara N, Núñez G. Interaction between Staphylococcus Agrvirulence and neutrophils regulates pathogen expansion in the skin .
Cell Host Microbe. 29(6):930-940 (2021).

5. Nakagawa S, Matsumoto M, Katayama Y, Oguma R, Wakabayashi S,
Nygaard T, Saijo S, Inohara N, Otto M, Matsue H, Núñez G, Nakamura Y.
Staphylococcus aureus Virulent PSMα Peptides Induce Keratinocyte
Alarmin Release to Orchestrate IL-17-Dependent Skin Inflammation
Cell Host Microbe. 22(5):667-677 (2017).

3. Nakamura Y, Takahashi H, Takaya A, et al. Staphylococcus Agr virulenceis critical for epidermal colonization and associates with atopic
dermatitis development . Sci Transl Med. 12(551): eaay4068 (2020).

63

Single Molecule Imaging

Imaging

Overall, this suggests that optimal treatment of immune
disease may require targeting both immune process peripherally,and brain processes centrally. This highlights the potential
application of our currently research developing novel
interventional technologies that could achieve this.

Toshio Yanagida, PhD
Ben Seymour, MD/PhD
Professor

Toshio Yanagida
Ben Seymour

Illness, infection and injury are an inevitable consequence oflife in a hazardous and competitive world, and animals’ ubiquitous
capability for tissue healing provides a passage to recovery thathas been an essential feature of life across species throughout
evolution. Alongside immune mechanisms, illness is associatedwith a pattern of recuperative behaviour that allows safe andeffective recovery, typically including pain, fatigue, and changes
in sleep, appetite, and mood. These behaviours are consideredadaptive in an evolutionary context, as they help promote
optimal recovery and maximise survival chance. But they remain
poorly understood and frequently appear in clinical contexts tobe exaggerated. Thus they reflect a major component ofsymptomatic states and quality of life in many patients, spanning
immune disease to musculoskeletal injury, and often do notrespond to treatment of the tissue event itself. A major goal of
our lab is to try and understand the central, brain process thatreflect the highest level of control of illness and injury states,
directing physiological, immune, and behavioural changes.
At the heart of our approach is conceptualising illness/injury
homeostasis as control-theoretic problem, and building modelsof brain information processing that optimize some quantitative
function of recovery. We have proposed that this process
approximates a hierarchical Bayesian control process, which thebrain uses multimodal sensory information to infer injury andillness states, represented in cortical-subcortical networks,
spanning insula and hypothalamic hubs in particular. These thencontrol multiple effector processing, including modulation ofautonomic, immune and endocrinological processes, alongside64

behavioural control processes (Seymour et al, 2023).
We have explored several aspects of this homeostatic control
model. On the sensor arm of the process, one key question is how
the brain monitors the temporal evolution of injury through theconstant stream of nociceptive (pain) information. We haverecently shown, using fMRI, how this feeds into a statistical modelof the pain-causing process, and relies on a pathway throughsomatosensory cortices in the brain (Mancini et al, 2022).
Critically, and consistent with the Bayesian model, higher (topdown) cortical processing modulate the incoming sensory signals
according to their uncertainty (Mulders et al, 2023).
On the effector side, another question is how behaviour iscontrolled: in particular, whether opiidergic or dopaminergic
signalling pathways modulate the perception of pain in thiscontrol loop. We have recently shown that dopaminergic
pathways appear most important, and discovered a highly
specific modulation of pain perception according to informationspecific components of control (Dersch et al, 2023).
This ultimately leads to the question as to whether theseputative insula-centric neural control hubs are relevant to ourunderstanding of symptom generation – pain, fatigue, and moodchanges – in immunological disease. Our ongoing clinicalresearch in rheumatoid arthritis suggests that it is, and using
brain network modelling we’ve been able to show that insula
centrality (a graph-theoretic measure of brain networks) appears
central to symptom states.

Figure.
Information flows and afferent (left) and efferent (right) pathways for insula-centered injury-state inference and effector control. At the heart of this is an insulacentered hierarchy with successively higher latent abstractions of the injury state. Afferent pathways feed various inputs to the hub, from subcortical and corticocortical projections; and efferent routes can implement different types of responses. This includes the multiple afferent pathways that ascend the spinal cord tovarious brainstem nuclei, such as the parabrachial, periaqueductal gray (PAG), dorsal respiratory group (DRG), locus coeruleus (LC) and others, forming the bidirectional
brainstem-subcortical network. Below this is a schematic illustration of an insula-hub perspective for injury state representations in more details, including thedifferent types of sensory information important for inference. The anterior, mid, and posterior segments of the insula have distinct and complementary functionalroles. Note that the injury state inference may be shared with broader cortical areas, including the ACC and VMPFC, which are omitted here.

Recent Publications
1. Seymour B, Crook RJ & Chen ZS. Post-injury pain and behaviour: acontrol theory perspective. Nat Rev Neurosci. 1-15 (2023).

4. Desch S, Schweinhardt P, Seymour B, Flor H, & Becker S. Evidence for
dopaminergic involvement in endogenous modulation of pain relief.
Elife. 12:e81436 (2023).

2. Mancini F, Zhang S, & Seymour B. Computational and neuralmechanisms of statistical pain learning. Nat Commun. 13(1):6613(2022).
3. Mulders D, Seymour B, Mouraux A, & Mancini F. Confidence of
probabilistic predictions modulates the cortical response to pain. Proc
Natl Aca Sci USA. 120(4):e2212252120 (2023).

65

Immunology and Cell Biology
Imaging

Masaru Ishii, MD/PhD
Professor

Masaru Ishii

Associate Professor

Junichi Kikuta
Yasuhito Yahara

Assistant Professor

Yutaka Uchida
Kentaro Fujii
Maki Uenaka

Crowds of people crossing streets, cars streaming along
roadways, and trains that come and go carrying passengers:
These are examples of ubiquitous, tightly organized humandynamics that support and vitalize societies. Similarly, in thehuman body, a variety of cells with different roles move andfunction according to their features and locations; collectively
they comprise complex biological systems. A typical example isthe immune system. Lymphocytes and macrophages migrate to
every region of the body and gather in specific environments to
exchange information and maintain normal immune responses.
Thus, organisms are shaped by organizational dynamics. These
dynamics are natural in life and do not occur following death.
Understanding the dynamic cellular society by elucidating how
cells move, or are moved, to maintain life is a fundamental themein the life sciences. However, researchers have only recently
succeeded in analyzing cellular movement. Recent advances in invivo fluorescence imaging technologies have enabled researchers
to look inside the bodies of live animals and analyze cellular andmolecular dynamics. In our laboratory, we have developed anovel multiphoton excitation microscopy technique for studying
the movement of immune cells in vivo using minimally invasive
observational and analytical methods that maintained
spatiotemporal information intact. Since we successfully
observed the interior of live bone tissue, we have energeticallypursued the analysis of cellular dynamics for various types of cells(Figure 1).

Postdoctoral Fellow

5

Research Assistant

2

Visiting Scientist

2

Support Staff

2

The ability to observe live, moving cells has led to theidentification of cell populations with novel functions that would
not have been discovered using conventional methods. For
example, macrophages are chameleon-like cells that change
their properties according to their specific location in tissue.
Using conventional analytical methods to isolate macrophages
from tissue or organs of interest would result in changes to theirphenotypes; thus, cell populations specifically inhabiting local
tissue would not be recognized with these methods. To date, wehave successfully identified novel cell fractions that can only befound in live tissue by using unique imaging technologies undera variety of pathological conditions. For example, osteoclasts aremacrophage lineage cells that digest old bone and facilitate theturnover of bone tissue; it is believed that overactivation of
osteoclasts in rheumatoid arthritis and bone metastasis cancause pathological bone destruction. We captured images
showing the process of inflammation-induced bone/joint
destruction and discovered a novel type of “bad” osteoclast in
the diseased bone tissue, in contrast to the “good” osteoclasts
observed in normal tissue (Figure 2). Similarly, we utilized
intravital imaging techniques to identify the specific pathogenic
macrophage that induces fibrogenesis in chronic and refractoryinterstitial pneumonia. These achievements in discovering novel
cell fractions were based on the observation of live, moving cells
in tissue. Imaging analysis of the dynamic cellular society has
proven effective for identifying a variety of new members.

Figure 1.
A dynamic cellular system inside the living body.

Figure 2.
Schematic illustration of ‘bad’ osteoclast differentiation axis in arthritic inflammation.

Recent Publications
1. Taniguchi S, Matsui T, Kimura K, Funaki S, Miyamoto Y, Uchida Y, Sudo
T, Kikuta J, Hara T, Motooka D, Liu Y-C, Okuzaki D, Morii E, Emoto N,
Shintani Y, Ishii M. In vivo induction of activin A-producing alveolar
macrophages supports the progression of lung cell carcinoma. Nat
Commun. 14(1):143 (2023).

4. Morimoto A, Kikuta J, Nishikawa K, et al. SLPI is a critical mediator that
controls PTH-induced bone formation. Nat Commun. 2(1):2136 (2021).
5. Hasegawa T, Kikuta J, Sudo T, et al. Identification of a novel arthritisassociated osteoclast precursor macrophage regulated by FoxM1. Nat
Immunol, 20(12):1631-1643 (2019).

2. Uenaka M, Yamashita E, Kikuta J, et al. Osteoblast-derived vesicles
induce a switch from bone-formation to bone-resorption in vivo. Nat
Commun. 13:1066 (2022).
3. Sudo T, Motomura Y, Okuzaki D, Hasegawa T, et al. Group 2 innate
lymphoid cells support hematopoietic recovery under stressconditions. J Exp Med., 218(5):e20200817 (2021).

66

67

Chemical Imaging Techniques‘OFF–ON–OFF’ fluorescence protein-labeling probe forreal-time visualization of the degradation of shortlived proteins in cellular systems
Short-lived proteins play critical roles in various cellular
processes, but their rapid turnover poses a challenge forresearchers studying their functions and dynamics. Traditional
methods for monitoring protein degradation, such as pulsechase experiments or Western blotting, provide only static
snapshots of protein levels, making it difficult to capture thedynamic changes in protein levels that occur in real time. Several
covalent self-labeling fluorescent tags for imaging protein
constructs in cell systems have been developed. However, theselabeling systems are not well-suited to imaging cellular protein
degradation, because the fluorophore remains fluorescent after
the protein-probe conjugate has been degraded.
We here present a new approach for tracking the degradationof short-lived proteins in living cells through use of new
trifunctional PYP-tag labeling ‘OFF–ON–OFF’ probes that contain
distinct xanthene fluorophore, coumarin ligand binding anddinitroaryl quenching units. Xanthene-based fluorophore
fluoresce in the green to near-infrared (NIR) region with highquantum yields and good molar absorptions that are well suitedfor cellular imaging studies. The fluorophore of the unboundprobe is turned‘OFF’ via intramolecular association between thexanthene fluorophore and the dinitroaryl quenching unit.
Covalent binding of the probe's coumarin ligand to thehydrophobic pocket of a PYP-tag protein results in a transthioesterification reaction with the thiol unit of Cys69, whichcleaves the probe's quenching unit to produce a PYP-tag–probe
68

Professor

Kazuya Kikuchi

Associate Professor

Masafumi Minoshima

Assistant Professor

Tomoya Yamamoto

Postdoctoral Fellow

2

Research Assistant1

Support Staff

1

conjugate whose fluorescence is turned ‘ON’. Subsequent
proteolytic degradation of the fluorescent PYP-tag–probe
conjugate then generates probe-labeled fragments whose
fluorescence are turned ‘OFF’ through intramolecular quenchinginteractions between the probe's xanthene fluorophore and its
coumarin ligand unit (Fig. 1, top). Therefore, the fluorescencesignal emitted by the probe is an "OFF–ON–OFF" pattern, withthe signal initially off, turning on upon degradation of the target
protein, and then turning off again as the fluorescence protein isdegraded.
In vitro treatment of PYP-tag with F5-DNB2 resulted in rapid
formation of fluorescent PYP-tag–probe conjugates that gave
maximal fluorescence intensities after 60 min. These fluorescentconjugates were then treated with trypsin to induce proteolytic
digestion, with the fluorescence intensities of both PYP-tag–probe conjugates decreasing gradually over time, reachingstable fluorescence minima after 130 min. These results
demonstrate that proteolysis of the fluorescent PYP-tag–probe
conjugates produces the desired ‘ON–OFF’ switch in fluorescencein probe cleavage products. Next, real-time imaging of theproteolytic degradation of short-lived proteins in cellular systems
using an OFF–ON–OFF fluorescence switch was performed.
Mouse ornithine decarboxylase (MODC) was chosen as a potential
short-lived protein to explore degradation studies because its
C-terminal domain is rich in Pro, Glu, Ser and Thr (PEST sequence)residues that are known to induce rapid proteasomal degradation.
F5-DNB2 probe was then used to visualize the expression(fluorescence ‘ON’) and proteolytic degradation (fluorescence‘OFF’) of a PYP-tag-MODC422-461 in cell nuclei in real time. Time-cells. The probe can be adapted to target other short-lived
proteins of interest and can be combined with other imaging
techniques, such as confocal microscopy, to provide moredetailed insights into protein degradation pathways.The probe
has broad applications in drug discovery, basic research, andbiomedical imaging, and has the potential to open up new
avenues of investigation into the mechanisms that regulate
protein turnover in living cells.

ImagingKazuya Kikuchi, PhD

lapse imaging of the transfected cells using confocal microscopy
revealed that the green fluorescence intensity of the cell nuclei
decreased steadily over time (Fig. 1, bottom).
The "OFF–ON–OFF" fluorescence protein-labeling probe
represents a significant improvement over traditional methods
for monitoring protein degradation. It provides a real-time,
dynamic readout of protein degradation that can be used to
study the functions and dynamics of short-lived proteins in living

Figure 1.
Schematic illustration of OFF-ON-OFF imaging for protein degradation using fluorogenic probes (top), Livecell imaging of degradation of short-lived protein using F5-DNB2 (bottom).

Recent Publications
1. Minoshima M, Umeno T, Kadooka K, Roux M, Yamada N, Kikuchi K.
Development of a Versatile Protein Labeling Tool for Live-Cell Imaging
Using Fluorescent β-Lactamase Inhibitors. Angew Chem Int. Ed. 2023,
in press. doi: 10.1002/anie.202301704.
2. Yari S, Kikuta J, et al. JAK Inhibition Ameliorates Bone Destruction by
Simultaneously Targeting Mature Osteoclasts and Their Precursors.
Inflamm Regen., 43:1-12 (2023).

4. Hashimoto R, Minoshima M, et al. Efficient Visible/NIR Light-Driven
Uncaging of Hydroxylated Thiazole Orange-Based Caged Compounds
in Aqueous Media. Chem Sci. 13:7462-7467 (2022).
5. Reja SI, Hori Y, et al. An "OFF-ON-OFF" fluorescence protein-labelingprobe for real-time visualization of the degradation of short-lived
proteins in cellular systems. Chem Sci. 13:1419-1427 (2022).

3. Salaam J, Minoshima M, Kikuchi K. Recent Advances in Activatable 19F
Magnetic Resonance Imaging Nano-Probes for the Detection of
Biomarkers. Anal Sens. 2023, in press. doi: 10.1002/anse.202200081.

69

Immune Response Dynamics

Our research focus has been to discover novel mechanismsthat control lymphocyte migration and elucidate their
physiological and pathological significance. Our previous studies
showed that inputs from adrenergic neurons to the β2-adrenergic
receptor expressed on lymphocytes enhance the responsivenessof a specific set of chemokine receptors and inhibit lymphocyte
exit from lymph nodes (Nakai et al., J. Exp. Med. 2014). Thismechanism was found to generate diurnal variations inlymphocyte numbers in lymph nodes and consequently themagnitude of adaptive immune responses in phase with thecircadian oscillation of adrenergic neuron activity (Suzuki et al., J.
Exp. Med. 2016). These studies provided insights into themolecular basis of the interaction between the nervous andimmune systems.
In our efforts to elucidate the mechanism of the crosstalk
between the β2-adrenergic receptor and chemokine receptors,
we identified a protein complex consisting of copper metabolism
MURR1 domain-containing (COMMD) 3 and COMMD8(COMMD3/8 complex) as a positive regulator of chemokine
receptor signaling. Our study demonstrated that the COMMD3/8
complex plays important roles in the control of B cell migrationand the induction of humoral immune responses (Nakai et al., J.
Exp. Med. 2019). However, the contribution of the COMMD3/8
complex to the pathogenesis of immunological disorders was
unclear.
Based on the important role of the COMMD3/8 complex inhumoral immune responses, we tested its involvement in

70

Professor

Kazuhiro Suzuki

Assistant Professor

Akiko Nakai

Postdoctoral Fellow

1

Research Assistant2

Support Staff

3

Since alanine substitution of C170 (C170A) on COMMD3
rendered the COMMD3/8 complex resistant to celastrol while
preserving the function of the protein complex, we generated amouse strain expressing COMMD3C170A from the endogenous
Commd3 locus and examined whether the effects of celastrol are

abolished in these mice. B cells isolated from COMMD3C170A mice
showed complete resistance to celastrol in chemotactic
migration. Humoral immune responses and collagen-induced
arthritis in the mutant mice were not suppressed by celastrol
treatment. These findings indicated that the COMMD3/8 complex
is a major target of celastrol (Shirai et al., Sci. Immunol. 2023).

Imaging

Kazuhiro Suzuki, MD/PhD

We then asked whether celastrol reproduces the functional
consequences caused by COMMD3/8 complex deficiency.
Celastrol inhibited chemotactic migration of B cells in vitro and invivo. Celastrol treatment suppressed antibody responses with
reduced production of germinal center B cells and plasma cells.
The progression of collagen-induced arthritis was blocked bycelastrol treatment started at the disease onset. Thus, celastrol
treatment phenocopied COMMD3/8 complex deficiency,
suggesting that celastrol may target the COMMD3/8 complex in
the context of humoral immune responses and autoimmunity.

Having established the involvement of the COMMD3/8
complex in a mouse model of rheumatoid arthritis, wedemonstrated that celastrol exerts anti-inflammatory activity bytargeting the COMMD3/8 complex. These findings provide a
proof of concept that disrupting the interaction between
COMMD3 and COMMD8 may be a useful strategy for thetreatment of autoimmune diseases and supports theconsideration of celastrol as a lead candidate in that endeavor.

collagen-induced arthritis, a B cell-dependent mouse model ofrheumatoid arthritis. COMMD3/8 complex deficiency induced at
the onset of arthritis inhibited disease progression. This was
accompanied by a reduced humoral immune response tocollagen. These findings suggested that the COMMD3/8 complex
may contribute to the pathogenesis of rheumatoid arthritis(Shirai et al., Sci. Immunol. 2023).
Prompted by this finding, we performed a chemical screen to
identify inhibitors of the COMMD3/8 complex that could be used
for the treatment of autoimmune diseases. Since the function of
the COMMD3/8 complex depends on the association between
COMMD3 and COMMD8, we sought for compounds that disrupt
the physical interaction between the two COMMD proteins. Afterscreening of a chemical library that was relatively enriched innatural products, we identified celastrol as the most potent
compound. Celastrol is a bioactive molecule extracted from a
medicinal herb, Tripterygium wilfordii, and exhibits antiinflammatory properties. However, its mechanism of action had
been poorly understood. Celastrol disrupted the COMMD3/8
complex in living cells or in the purified form, indicating direct
action of celastrol on the COMMD3/8 complex. Using sitedirected mutagenesis, molecular dynamics simulations (Figure)and liquid chromatography-tandem mass spectrometry, we
revealed that celastrol covalently binds to cysteine 170 (C170) on
COMMD3 to dissociate the COMMD3/8 complex (Shirai et al., Sci.
Immunol. 2023).

Figure.
A model of the celastrol-bound COMMD3/8 complex.

Recent Publications
1. Shirai T, Nakai A, Ando E, Fujimoto J, Leach S, Arimori T, Higo D, vanEerden FJ, Tulyeu J, Liu Y-C, Okuzaki D, Murayama MA, Miyata H,
Nunomura K, Lin B, Tani A, Kumanogoh A, Ikawa M, Wing JB, Standley
DM, Takagi J, Suzuki K. Celastrol suppresses humoral immune
responses and autoimmunity by targeting the COMMD3/8 complex.
Sci Immunol. 8: eadc9324 (2023).

3. Suzuki K, Hayano Y, Nakai A, Furuta F and Noda M. Adrenergic controlof the adaptive immune response by diurnal lymphocyte recirculation
through lymph nodes. J Exp Med 213:2567-2574 (2016).
4. Nakai A, Hayano Y, Furuta F, Noda M and Suzuki K. Control oflymphocyte egress from lymph nodes through β2-adrenergic
receptors. J Exp Med. 211:2583-2598 (2014).

2. Nakai A, Fujimoto J, Miyata H, Stumm R, Narazaki M, Schulz S, Baba Y,
Kumanogoh A and Suzuki K. The COMMD3/8 complex is a determinantof GRK6 specificity for chemoattractant receptors. J Exp Med.
216:1630-1647 (2019).

71

Biophotonics

Imaging

the Raman analysis could successfully determine the presence ofNETs, could discriminate clearly between NETs and other types ofcell debris (such as occurs in necrosis) and could even determine
which pathway had been used to activate the NET response.

Nicholas Isaac Smith, PhD

Nicholas Isaac Smith

Assistant Professor

Alison Hobro

Postdoctoral Fellow

1

Support Staff

1

The Biophotonics laboratory develops tools for label-free
analysis of single cells. Single-cell analysis is a popular target for alarge number of researchers, usually pursued by labeling surface
markers, by introducing fluorescent dyes into the cell, or byinvasive, yet comprehensive, techniques such as single cell RNA
sequencing. In contrast, our tools are based on label-free opticalmethods, which aim to produce some of the same discriminatory
capability as the more invasive methods. Additionally, label-freemethods are based on endogenous contrasts of the cell, and canalso find novel features that can be used to discriminate between
cell phenotypes or cell states.

undergo activation and then differentiate into effector cells when
co-cultured with artificial antigen-presenting cells (aAPCs), andRaman spectra were collected from groups of between 20002500 cells per group, per day. Statistical models were developed
to assess the degree of changes occurring on a single-cell level,
and these label-free metrics were further validated by additionallyusing gold-standard T-cell analytic methods such as CD25/CD69
and CD62L/CD44 surface marker measurements. The use ofmachine learning methods can also be used to assist in thevisualization of the transitory single-cell states across the wholeexperiment. See Pavillon et al 2023, and figure 1 for details.

In the last year, we made several important advances.
Extending our previous project focused on macrophage uptakeof fatty acids, we looked at metabolic and spatiotemporalchanges in macrophages in a fatty acid-specific manner. Of highimportance for artherosclerosis and lifestyle diseases, HDL and
LDL cholesterol uptake in macrophages plays a critical role inplaque formation. Therefore we imaged HDL and LDL uptake inmacrophages and found evidence that the form of cholesterol
may be changing (i.e. in terms of degree of crystallization) after
the uptake occurs, and found a specific Raman biomarker thatcan be used to identify crystallized cholesterol within the cell.

We completed several works with collaborating groups
including in microscopy techniques with the Fujita group in
Applied Physics, where we share a common interest in higher
throughput label-free imaging. Dr Lelliot also completed a study
with collaborators in the Kumanogoh group, where we evaluateda long-standing goal in the lab to determine whether label-free
Raman analysis could be implemented to reliably identify thepresence of the neutrophil extracellular trap (NET) response in a
non-invasive manner. Neutrophils produce extracellular debris,which is a loosely aggregated gel-like structure that contains
various biomolecules, forming in response to a wide variety of
disease conditions, including COVID-19. While it is known that
NETs are implicated in many diseases, there is still considerable
debate on how they should be defined, and whether apparent
subtypes should be considered as separate processes. We used
Raman analysis on NETs from human donors, and even though
the NETs themselves are less dense than our typical cell targets,

Methods for rapid and non-invasive detection of cell
phenotype continue to be one of our primary interests, especiallyat higher throughputs than typically used in Raman analysis.
Accordingly, we completed a Raman-based study to monitor
T-cell activation/differentiation states. Murine naïve T-cells

72

Associate Professor

Figure.
Early T cell differentiation monitored with Raman spectroscopy. (A) Experimental protocol, where murine T cells are stimulatedwith artificial APCs and measured every day during 5 days. (B) Average single-cell Raman spectra (approximately 2000 cells per
day and per type), showing that only small changes can be observed during the onset of activation. (C) Median fluorescenceintensity signal derived from the expression of surface markers of CD4 cells over time, representative of T cell activation anddifferentiation. (D) UMAP decomposition of Raman data, where the gradual evolution of the signal upon activation can bereadily observed. Differences between phenotypes (CD4/CD8) are also clearly visible. All results are representative of at least 3
experiments. (E) Quantification of the daily signal changes with the Mahalanobis-like distance. Curves are the average of 3
experiments, error bars indicate standard deviation. See Pavillon et al 2023 for details.

Recent Publications
1. Pavillon N, and Smith NI. Non-invasive monitoring of T celldifferentiation through Raman spectroscopy. Scientific Reports
13(1):3129 (2023).
2. Lelliott PM, et al. Cellular Adhesion Is a Controlling Factor in Neutrophil
Extracellular Trap Formation Induced by Anti-Neutrophil Cytoplasmic
Antibodies. ImmunoHorizons 6(2):170-183 (2022).

4. Sugiyama T, Hobro AJ, Pavillon N, Umakoshi T, Verma P, and Smith N.
Label-free Raman mapping of saturated and unsaturated fatty aciduptake, storage, and return toward baseline levels in macrophages.
Analyst 146(4): 1268-1280 (2020).
5. Pavillon N, Hobro AJ, Akira S and Smith NI. Noninvasive detection ofmacrophage activation with single-cell resolution through machinelearning. Proc Natl Acad Sci. USA 115(12):E2676-E2685 (2018).

3. Pavillon N, and Smith NI. Deriving accurate molecular indicators ofprotein synthesis through Raman-based sparse classification. Analyst
146:3633-3641 (2021).

73

Bioinformatics

Systems Immunology
Daron M. Standley, PhD

Professor

Daron M. Standley

Associate Professor

Kazutaka Kato
Li Songling
Soyoung Park

Assistant Professor

Shuhei Sakakibara
Chao-Yuan Tsai

Postdoctoral Fellow

Classification of health/disease from Adaptive Immune
Receptors (AIRs)
We are developing methods to predict health/disease statusfrom AIRs. In particular, we are interested in identifying signaturesof past or present antigen engagement that are accessible inblood. One of our goals is to represent such signatures as machinelearnable features that generalize well to new donors (i.e. ,notseen by the classifier). We have found that the most widely used
AIR features (clonotype clusters) do not generalize well to new
donors, but that our proposed paratope network features do
generalize well. Our preliminary data for COVID-19, autoimmune
hepatitis (AIH), and breast cancer suggests that these features arerobust and have the potential to be novel disease biomarkers(Fig.1).

Drawbridge model for T cell receptor triggering
T cell receptors (TCRs) play a critical role in adaptive immunity.
Despite decades of research, the mechanism that transmits
peptide-MHC (pMHC) binding to intracellular signaling – TCR
triggering – remains enigmatic. TCR-CD3 complexes both withand without a bound peptide-MHC (pMHC) exhibit little variation
by single-particle cryo-EM microscopy, which makes it difficult tounderstand how changes in TCR structure trigger signalingacross the plasma membrane. To visualize TCR dynamics, weFigure 1.
Classification of health/disease from Adaptive Immune Receptors (AIRs). A, AIRs can be easilyacquired from a routine blood sample, sequenced and transformed into feature vectors for use
in machine-learning based classifiers.
B, We have tested the performance of classifiers trained using the popular clonotype cluster
features and on our newly proposed paratope network features. In a wide range of diseases,
including COVID-19, autoimmune hepatitis, and breast cancer, the paratope network features
were more robust than clonotype cluster features.

Figure 2.
Drawbridge model for T cell receptor triggering. At rest, the Tcell receptor adopts a bent conformation in which it retains theCD3 proteins (left). Binding to a pMHC involves the elongationof the T cell receptor. This breaks the interactions between the Tcell receptor and the CD3 proteins, and the CD3 proteins aresubsequently free to diffuse around the T cell receptor (right).

3

Research Assistant2

Support Staff

1

performed molecular dynamics simulations of TCR-CD3 and TCRCD3-pMHC complexes in which the TCR-CD3 and pMHC
components were embedded in separate membranes. CD3protein dynamics were qualitatively different in the two systems,
and we found that conformational changes in the TCR directly
regulated CD3 dynamics. Specifically, in the TCR-CD3-pMHC
system, the TCR acted as a "drawbridge" that allowed the CD3proteins to move freely, thus transmitting the signal from outside
to inside the T cell (Fig. 2).

Structure/function analysis and development of RNA
inhibitors of Regnase-1
Regnase-1 is an important RNA binding protein that controls
inflammatory and immune responses. Regnase-1-deficient CD8+
T cells markedly improve therapeutic outcomes in mouse modelsof melanoma (J. Wei et al. Nature, 2019). We are investigating
RNA-bound structures of Regnase-1 and developing nucleic acidtherapeutics to inhibit Regnase-1 using chemically modified
oligonucleotides. We have designed amino acid-conjugatedoligonucleotides based on structural analysis of Regnase-1 andare investigating their binding efficacy and inhibitory activity
using biophysical techniques such as electrophoretic mobility
shift assays and microscale thermophoresis (Fig. 3).

Figure 3.
Structure/function analysis and development of RNA inhibitors of Regnase-1. A, A model of the Regnase-1 tetramer
showing critical residues at the dimer-dimer interface (inset). B, Design of modified RNA inhibitors based criticalresidues involved in RNA binding and cleavage. C, Microscale thermophoresis showing the spectral shift of Cy5labeled RNAs binding to recombinant Regnase-1 protein.

Recent Publications
1. Tanaka A, Maeda S, Nomura T.et al. Construction of a T cell receptor
signaling range for spontaneous development of autoimmune
disease. J Exp Med. 220 (2023) 10.1084/jem.20220386.

4. Xu Z, Davila A, Wilamowski J, Teraguchi S. & Standley DM. Improved
Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.
Chembiochem 23:e202200303 (2022) 10.1002/cbic.202200303.

2. Jiravejchakul N, Abe GL, Loza M, Park S, Matangkasombut P, Sasaki JI,
Imazato S, Diez D & Standley DM. Intercellular crosstalk in adult dental
pulp is mediated by heparin-binding growth factors Pleiotrophin andMidkine. BMC Genomics 24:184 (2023) 10.1186/s12864-023-09265-w.

5. Shirai T, Nakai A, et al. Celastrol suppresses humoral immune
responses and autoimmunity by targeting the COMMD3/8 complex.
Sci Immunol. 8 (2023), eadc932410.1126/sciimmunol.adc9324.

3. Eerden FJv, Sherif AA, et al. TCR-pMHC complex formation triggers
CD3 dynamics. eLife 2023 in press.

74

75

Statistical Immunology

catalog of candidate compounds and target genes for drug
repositioning (Namba S et al. Cell Genom 2022). We applied thesedrug discovery methods to the cross-population GWAS results ofstroke and reported multiple promising targets (Mishra A et al.
Nature 2022).

Bioinformatics

directional dosage effect on drug targets, which facilitatesefficient high-throughput screening of chemical compounds
library. We introduced a practical guideline for genomics-driven
drug discovery as lessons from the Global Biobank Meta-analysis
Initiative (GBMI). Integration of the three methods (GREP, TransPhar, endophenotype Mendelian randomization) provided a

Yukinori Okada, MD/PhD

Professor

Yukinori Okada

Associate Professor

Qingbo S Wang

Assistant Professor

Kenichi Yamamoto

Research Assistant

6

Support Staff

2

Figure 1.
JMAG (Japanese Metagenome Assembled Genomes Platform) and JVD (Japanese Virus Database) databasefor Japanese gut microbiome catalogue.

Goal of our laboratory
Genetic backgrounds of individuals have substantial impacts
on risk of a wide range of immune-related diseases. Statisticalimmunology is a research field that evaluates causality of human
genetic variations on immune-related diseases, using statisticaland bioinformatics approaches. The goal of our laboratory is todevelop such methods and apply to the latest large-scale disease
genome and multi-layer omics data.

Metagenome-wide association study of gut microbiome
and virome revealed disease-specific features
Microbiomes play substantial roles in homeostasis and biology
of a variety of human diseases through interaction with host.
Metagenome-wide association studies (MWAS) utilizing wholegenome shotgun sequencing is a promising tool to elucidate
microbiome etiology. To construct gut microbiome catalogue ofJapanese, we assembled 19,084 prokaryotic and 31,395 viralgenomes from 787 Japanese gut metagenome shotgun
sequencing data; JMAG and JVD (Figure 1). Traditional Japanesefood-related features were observed in Japanese microbial
genome, such as natto (fermented soybeans) and nori (laver).
Dietary-related Enterococcus_B lactis and Streptococcus
thermophilus were nominally associated with the East Asianspecific missense variant rs671:G>A in ALDH2, which was
associated with dairy consumption. We annotated subtypes of
crAss-like phages and identified their associations with diseasestatus and microbiome diversity. In particular, crAss-like phage
dosages were decreased in autoimmune diseases including
rheumatoid arthritis (RA), systemic lupus erythematosus, and76

inflammatory blow diseases (Tomofuji Y et al. Cell Genom 2022).

A cross-population atlas of human genotype-phenotype
associations.
Construction of human genotype-phenotype catalog isessentially important to elucidate genetic backgrounds andunderlying biology of diseases. Through leading international
collaboration partnerships, we reported the cross-population
GWAS meta-analysis integrating diverse human ancestry of RA(RACI consortium; Ishigaki K et al. Nat Genet 2022) and adultheight (GIANT consortium; Yengo L et al. Nature 2022). These
results highlighted the value of cross-population GWAS to
improve disease risk prediction model and showed saturated
map of common variant impacts on phenotype heritability. As forour current challenges in the COVID-19 pandemic, we conducted
the COVID-19 GWAS of Japanese, which identified a risk variant
close to the dedicator of cytokinesis 2 gene (DOCK2). Single-cell RNAseq (scRNA-seq) identified cell-type-specific DOCK2downregulation
and a COVID-19-specific decreasing effect of the risk allele in nonclassical monocytes (Figure 2). DOCK2 inhibition increased theseverity of pneumonia in a Syrian hamster model of SARS-CoV-2
infection. DOCK2 has an important role in severe COVID-19, andcould be further explored as a potential biomarker and/or
therapeutic target (NamKoong H et al. Nature 2022).

In silico drug repositioning based on human disease
genomics
Utilization of human disease genetics for novel drug discovery
is essential. Biological dynamics in disease status provides

Figure 2.
Non-classical monocyte-specific and COVID-19 specific eQTL effect of the DOCK2 variant.

Recent Publications
1. Namkoong H, et al. DOCK2 is involved in the host genetics and biologyof severe COVID-19. Nature 609:754-760 (2022).
2. Yengo L, et al. A saturated map of common genetic variants associatedwith human height. Nature 610:704-712 (2022).
3. Namba S, et al. A practical guideline of genomics-driven drug
discovery in the era of global biobank meta-analysis. Cell Genom
2:100190 (2022).

4. Tomofuji Y, et al. Prokaryotic and viral genomes recovered from 787
Japanese gut metagenomes revealed microbial features linked todiets, populations, and diseases. Cell Genom 2:100219 (2022).
5. Ishigaki K, et al. Multi-ancestry genome-wide association analyses
identify novel genetic mechanisms in rheumatoid arthritis. Nat Gen.
54:1640-1651 (2022).

77Quantitative Immunology
Units

Our group applies computational and single cell genomics
techniques to understand the immune system. We develop
computational methods to analyze single cell data. We integrate
experimental data (including transcriptome, chromatin
accessibility, protein expression, immune repertoire and spatialtranscriptomics) with publicly available information into networkmodels of immune regulation. We apply this framework to study
gene regulatory networks controlling immune cell development
and function.

Development of computational methods
An important problem in single cell genomics is how to
combine different datasets while correcting for batch effects. A
key focus is on preserving the original cell population structure
while not introducing bias. We have developed Canek, a methodthat leverages a fuzzy logic framework that enables efficientbatch correction without bias. Another problem is theidentification of marker genes. In collaboration with Alexis
Vandenbon at Kyoto University, we have developed
singleCellHaystack, a method to identify differentially expressed
genes from multi-dimensional representations of single cell
genomics data.

Mathematical modeling
The large number of cells obtained in single cell genomics
experiments opens the door to approaches that study the
immune system using mathematical modeling and machinelearning. Transcriptional regulatory networks are critical
determinants of cell identity and function. We use machine

78

Associate Professor

Diego Diez

Postdoctoral Fellow

1learning to model immune transcriptional regulatory networks.
Using the expression level of the regulators as a proxy for theiractivities we apply these methods to study how transcriptional
networks change during immune cell differentiation and disease.

Applications to immunology
SKG mice have a mutation in ZAP70 that weakens TCR
signaling, resulting in a bias towards development of NKT1
compared to NKT2 in the wild type (BALB/c). Using single celltranscriptomics, protein expression, immune repertoire, andchromatin accessibility we study the differentiation of NKT cells
in the thymus and spleen of SKG and WT mice. This approachenables us to understand how changes in regulatory networks
during development effect NKT specification. In a clinical setting,
we apply single cell genomics to get insight into IgA nephritis
onset and therapies. We study the transcriptome, protein
expression and immune repertoire of immune cells in PBMCs andtonsils from IgAN patients before and after tonsillectomy andsteroid immunosuppression.
We collaborate with other groups at IFReC to study diverse
aspects of immune responses in a basic and clinical setting. With
the Experimental Immunology laboratory and the Systems
Immunology laboratories, we study how TCR signaling impacts T
cell repertoire in SKG mice. With the Immune Regulationlaboratory, we study the role of CD4 T cells in human Eosinophilic
Chronic Rhinosinusitis. With the Host Defense laboratory, we
study the role of the RNase Reg-1 in immune cell development.

Figure.
Single cell genomics identifies RNA and TCR features of differentiating NKT cells.

Recent Publications
1. Loza M, Teraguchi S, Standley DM & Diez D. Unbiased integration of
single cell transcriptome replicates. NAR Genom Bioinform 4, lqac022,
doi:10.1093/nargab/lqac022 (2022).
2. Diez D, Morte B & Bernal J. Single-Cell Transcriptome Profiling of
Thyroid Hormone Effectors in the Human Fetal Neocortex: Expressionof SLCO1C1, DIO2, and THRB in Specific Cell Types. Thyroid 31. 15771588 (2021).

4. Teraguchi S, Saputri DS, Llamas-Covarrubias MA, Davila A, Diez D, et al.
Methods for sequence and structural analysis of B and T cell receptor
repertoires. Comput Struct Biotechnol J 18, 2000-2011, doi:10.1016/j.
csbj.2020.07.008 (2020).
5. Diez D, Agusti A & Wheelock CE. Network analysis in the investigationof chronic respiratory diseases. From basics to application. American
journal of respiratory and critical care medicine 190:981-988,
doi:10.1164/rccm.201403-0421PP (2014).

3. Vandenbon A and Diez D. A clustering-independent method forfinding differentially expressed genes in single-cell transcriptome
data. Nat Commun 11(1):4318, doi:10.1038/s41467-020-17900-3(2020).

79

Events & Outreach Activities

The 12 th International Symposium of IFReC
This symposium was co-organized with the Center for Infectious Disease
Education and Research (CiDER) at Osaka University, the project for "Selfreferential immune perception" (Grant-in-Aid for Transformative Research
Areas, JSPS), and Osaka International Conference Center. Centering on basic
research achievements relating to microbiology and immunology, this
symposium consists of 11 lectures by world-leading scientists. This symposium
was a significant opportunity for the participants to share ideas and expertisefor further development of microbiology, immunology, and life science.
◆ Date :Events & Outreach Activities

International Symposium on Microbiology and Immunology

February 3, 2023

◆ Venue : Osaka International Convention Center (Grand Cube Osaka)

Speaker82

Title

Keiji Itaka(CiDER, Osaka University/Tokyo Medical and
Dental University, Japan)"mRNA as a new drug modality"

Anna C. Aschenbrenner(DZNE, Bonn, Germany)"From acute infection to chronification: What can transcriptomics
teach us about a new disease?"

Yumi Matsuoka-Nakamura(IFReC, Osaka University, Japan)"Impact of Staphylococcal Agr quorum-sensing system on atopic
dermatitis and systemic infection"

Ron Geller(University of Valencia, Spain)"Comprehensive profiling of polyclonal sera targeting a nonenveloped viral capsid"

Sidonia Eckle(University of Melbourne, Australia)“Probing the universe of MAIT cell antigens and associated immune
functions by MAIT cells"

Nobuhiko Kamada(IFReC, Osaka University, Japan)"Intermucosal innate and adaptive immune networks in inflammatory
disease"

Alison Simmons(University of Oxford, UK.)

"Human intestinal cellular anatomy through development, in healthand inflammatory bowel disease"

Koji Yasutomo(Tokushima University, Japan)"AFF genes as regulators for B and T cells"

Pavel Tolar(University College London, UK)"Regulation of antigen persistence in germinal centres"

Hisashi Arase(IFReC, Osaka University, Japan)“Autoimmunity by aberrant MHC class II self-antigen presentation
associated with viral infection"

Alexander Rudensky(Memorial Sloan Kettering Cancer Center, USA)

"Regulatory T cells as purveyors of immune tolerance"

83

IFReC - Doherty Institute &Partners Immunology Symposium◆ Date :◆ Date :May 13, 2022

◆ Venue : Conference room at the University College of London

Speakers (order of talk)March 20-21, 2023

◆ Venue : Melbourne Connect, Forum 3 & University House, Matthaei Room

Speakers (order of talk)

1. Shimon Sakaguchi (IFReC)

1. Kiyoshi Takeda (IFReC)

2. Anne Pesenacker (UCL)

2. Andrew Brooks (UoM/Doherty Institute)

3. James Badger Wing (IFReC)

3. Tomohiro Kurosaki (IFReC)

4. Dave Sansom (UCL)

4. Sammy Bedoui (UoM/Doherty Institute)

5. Kiyoshi Takeda (IFReC)

5. Sho Yamasaki (IFReC)

6. Benedict Seddon (UCL)

6. Katherine Kedzierska (UoM/Doherty Institute)

7. Kazuyo Moro (IFReC)

7. Hisashi Arase (IFReC)

8. Masaru Ishii (IFReC)

8. Alexandra Corbett (UoM/Doherty Institute)

9. Lucy Walker (UCL)

9. Masaru Ishii (IFReC)

10. Tomohiro Kurosaki (IFReC)

10. Michelle Boyle (Burnet Institute)

11. Claudia Mauri (UCL)

11. Kazuyo Moro (IFReC)

12. Emma Morris (UCL)

12. Stephen Nutt (WEHI)

13. Steve Ley (UCL)

13. Yumi Matsuoka (IFReC)

14. Maddi Noursadeghi (UCL)

14. Amy Chung (UoM/Doherty Institute)

Events & Outreach Activities

UCL - IFReC Osaka University
Immunology Symposium

15. James Badger Wing (IFReC)
16. Axel Kallies (UoM/Doherty Institute)84

85

The International School on Advanced Immunology started in 2022 and is jointly organized by IFReC and ImmunoSensation2,
Germany. The purpose of the school is to foster young immunologists into leaders of the next generation to lead to breakthroughsin the field of immunology. In the four-day intensive course, the school provided an opportunity for 49 international PhD students
and young postdocs to meet with a faculty of 15 world-class experts to push the frontiers of immunology and network with peers of
the same generation.

Events & Outreach Activities

The 1st ImmunoSensation 2 - IFReC International
School on Advanced Immunology◆ Date :November 7-10, 2022
◆ Venue : Awaji Yumebutai International Conference Center, Awaji-city, Hyogo, Japan

Lecturers
Shizuo Akira (IFReC, Osaka University)
Ido Amit (Weizmann Institute of Science)
Eva Bartok (University Hospital Bonn, ImmunoSensation 2 )Keishi Fujio (The University of Tokyo)
Florent Ginhoux (Singapore Immunology Network)
Koji Hase (Keio University)
Axel Kallies (The University of Melbourne)
Eicke Latz (University Hospital Bonn, ImmunoSensation 2 )Elvira Mass (University of Bonn, ImmunoSensation 2 )Gabriel Núñez (University of Michigan)
Marion Pepper (University of Washington)
Marco Prinz (University of Freiburg)
Michel Sadelain (Memorial Sloan Kettering Cancer Center)
Shimon Sakaguchi (IFReC, Osaka University)
Ziv Shulman (Weizmann Institute of Science)

86

87

The "NGS Expo" is a new academic event for users and potential users of next
generation sequencer, and organized by IFReC and RIMD, Osaka University.
About 500 people participated in this symposium, both on-site and online. We
experimentally incorporated "online salon", a communication tool between
participants, and nearly 40,000 page views were obtained.
◆ Date :October 18-19, 2022
◆ Venue : Osaka International Convention Center (Grand Cube Osaka)

Colloquia and Seminars◆IFReC Colloquia : Important events allowing IFReC researchers to gather together, and held every two months.

Date
May 26, 2022

July 21, 2022

Speakers
Yukinori Okada (PI, Statistical Immunology Lab)
Kazuhiro Suzuki (PI, Immune Response Dynamics Lab)
Sho Yamasaki (PI, Molecular Immunology Lab)Events & Outreach ActivitiesNGS Expo 2022

Masahiro Yamamoto (PI, Immunoparasitology Lab)

September 15, 2022

Yasuharu Nagahama (Host Defense Lab)Bo Li (Mucosal Immunology Lab)

November 17, 2022

Shunsuke Mori (Immunochemistry Lab)
Motonao Osaki (Experimental Immunology Lab)

March 16, 2023

Takashi Saito (PI, Cell signaling Lab)
Michelle Lee (Malaria Immunology Lab)

◆IFReC ImmunoSeminar : Inviting world-class immunologists mainly online.

Date

Speakers

April 28, 2022

Henrique Veiga-Fernandes (Champalimaud Center for the Unknown, Lisboa, Portugal)

June 24, 2022

James McCluskey (The University of Melbourne, Australia)

January 23, 2023

Laurent Rénia (Lee Kong Chian School of Medicine/ A*STAR Infectious Diseases Labs, Singapore)◆Other Seminars : Inviting wide variety of scientists as speakers.

Date
November 4, 2022

December 15, 2022

January 31, 2023

February 14, 2023

88

Speakers
Noboru Mizushima (Graduate School of Medicine, University of Tokyo, Japan)
Ryo Morimoto (Thomas Boehm Lab, Max Planck Institute of Immunobiology and Epigenetics,
Freiburg, Germany)

Anna C. Aschenbrenner (Systems Medicine, DZNE, Bonn, Germany)
Samuel Liegeois (Host-Pathogen Interactions and Resilience, Insect Models of Innate Immunity,
Strasbourg University, France)89

In 2022, face-to-face outreach events were revived while implementing COVID-19 preventive measures.

Osaka University Co-Creation Day at EXPOCITY◆ Date :June 13, 2022

◆ Venue : LaLaport EXPOCTY

The 11th WPI Science Symposium◆ Date :November 23, 2022
Ito Memorial Hall, The University of Tokyo◆ Venue :◆ Speakers : Kazuyo Moro (IFReC), et al.

Events & Outreach Activities

Outreach Activities

Life Science Seminar for High School Students◆ Date :August 8, 2022
Taniguchi Memorial Hall, RIMD and IFReC◆ Speakers : Yumi Matsuoka (IFReC), et al.
◆ Venue :Kagaku Zam-mai in Aichi◆ Date :December 27, 2022
Okazaki Conference Hall
◆ Speakers : Students from Super Science High Schools◆ Venue :Science Café at the Nakanoshima Festival◆ Date :December 4, 2022
Lecture Hall A, Osaka University School of Medicine◆ Speaker : Yoko Fukushima (Department of Ophthalmology,
Osaka University School of Medicine)◆ Venue :SpringX Super School - Online Lecture series for protecting our lives from
infectious diseases ◆ Speakers :・Yumi Matsuoka : “Staphylococcus aureus, an old but new bacteria” (Jun. 24, 2022)

・Daisuke Okuzaki : “Data analysis for COVID-19” (Aug. 26, 2022)
・Sho Yamasaki : “ Immune system for eliminating pathogens” (Nov. 25, 2022)
・Masahiro Yamamoto : “Science of Toxoplasma” (Feb. 24, 2023)

90

91

Japanese Language Class

Message from Ms. Tomomi Tomomune, class instructor for 2023.
“I would like to support you by providing effective lessons to make your life moreenjoyable. As we learn, we use Japanese to communicate and learn about eachother. Through interaction with others, you can gain insight into unique, fascinating
cultures and broaden your perspective. I am looking forward to meeting you all at
IFReC.”

Information

Message from the students of the Japanese class“It has been essential in my Japanese language development. I am very thankful to have this course and I
appreciate all of the effort put in to make this happen.”“Tajima-sensei has been an absolutely fantastic instructor. She has done a wonderful job engaging the students
and creating a fun/educational environment.”92

93Advanced Postdoc Program at IFReC● Clarivate Highly Cited Researchers (HCR) 2022

IFReC has been recruiting post-doctoral researchers for its Advanced
Postdoc Program. This program offers three-year employment andfunding (3 million JPY per year) for original research to promising young
researchers. Selected applicants have access to continually upgradedstate-of-the-art facilities at IFReC for their research, including equipment
for single-cell analysis.

Shizuo Akira
Nobuhiko Kamada
Shimon Sakaguchi● Commended by the Minister ofInternal Affairs and Communications
Toshio Yanagida

Information

Major Awards● The Takeda Prize for Medical Science 2022

Kiyoshi Takeda

Grant for Next Generation Principal Investigators
This program aims to foster the next generation of principal investigators at IFReC. In particular, challenging research that has thepotential to create a new field of study in immunology is selected. The grant helped to generate excellent research achievements
in 2022.

● The Osaka Science Prize 2022
Yukinori Okada● The Hideyo Noguchi Memorial Prize 2022
Sho Yamasaki

Original Support Programs for Young Researchers● The Order of the Sacred Treasure,Gold and Silver Star
Shigekazu Nagata● The Japanese Society for Immunology
Prize 2022

To strengthen our international research network and our basis for international collaborative research, IFReC has established
two kinds of financial support programs for researchers. 1) “IFReC Kishimoto Foundation Fellowship,” which has been used to inviteinternational researchers to Osaka. 2) “Program for International Circulation of Young Talented Researchers” for those who wish toparticipate in overseas research activities. Since 2009, over 140 researchers have received these grants.

Masaru Ishii

Support for Paper Submission● The Toyoichi Ohtawara Award 2022

Hisashi Arase● The 13th Ikushi Prize by Japan Society
for the Promotion of Science

Due to the influence of COVID-19, it has been difficult for researchers
to find opportunities to present their research results at overseas
conferences. This program aims to support the dissemination of research
results by the researchers of IFReC.

Yoshihiko Tomofuji
Yoshiaki Yasumizu

94

95

Common Facilities (IFReC, RIMD, Animal Resource Center)

Information

IFReC and its parent institution, the Research Institute for Microbial Diseases (RIMD) are located on the same
site, constituting a large research complex. The complex contains the Core Instrumentation Facility, the Animal
Resource Center and the Network Administration Office, all of which are jointly operated by IFReC and RIMD. The
Core Instrumentation Facility is equipped with various highly advanced instruments and skilled technicians provide
in-house services to IFReC and RIMD researchers. The Animal Resource Center consists of three buildings for specificpathogen-free (SPF) animals and the live immuno-imaging facility. With a largecapacity animal-breeding facility in
IFReC, researchers are able to choose animal rooms suitable for their experiment purpose. Using these common
facilities, IFReC researchers are able to effectively and smoothly carry out their experiments to promote their worldleading research at IFReC.

Composition & Finance● Composition
Number of IFReC Staff

As of Feb 1

350
Researchers (JPN)

Researchers (Overseas)

Administrative and Support Staff

300
97

250

117

102

106

105

92

102

89

90

70

200

103

90
86
55

52

150

6
3

38

100

48

55

54

54

117

119

128

138

137

50

4

5

2

1

2011

2012

2013

2014

2015

50

51

47

43

44

130

124

124

117

2016

2017

2018

2019

43

42

24
16
8

42

53

129

142

162

151

2020

2021

2022

2023

93
65

44

0
2008

2009

2010

Year

❶ IFReC Research Building❷ Integrated Life Science Building❸ Main Building, Research Institute for Microbial Diseases, RIMD

● Finance❹ South Building, Research Institute for Microbial Diseases, RIMD

Sources❺ Cutting-Edge Research Building for Infectious Diseases

Expenditure❻ Animal Resource Center for Infectious Diseases
From the
University
12.6%

Animal Resource Center for Infectious Diseases

Network Administration Office■ Specific pathogen-free (SPF) animal facility■ Provision and maintenance of network infrastructure:■ Sperm/ embryo freezing and preservation

LAN system and servers (web, mail, mailing lists, etc.)

Main Grant
32.1%

JPY
4,153,437,291r■ In vitro fertilization and embryo transplantation

Management
Expenses Grant
14.2 %

Personnel
26.8 %
Individual
Research
Projects
35.9 %

JPY
4,153,437,291

Donation
7.3 %■ Intracytoplasmic sperm injection■ Transgenic and knock-out animals■ Genome editing in experimental animals

Core Instrumentation Facility■ Basic and advanced instruments

Live immuno-imaging facility■ SPF animal experiment facility with 11.7T MRI, in vivo imager& two-photon microscope.

96■ In-house service■ DNA sequencing, cell sorting, electron microscopy, mass

Grant-in-Aid
for Scientific
Research
6.0 %Contract Research
27.8 %

Equipment
11.5 %

Project
Activities
25.8 %

Travel 0.1%

spectrometry and next-generation sequencing analysis■ Radio isotope facility

97

Selected Articles
Multi-trait and cross-population genome-wide association studies across autoimmune andallergic diseases identify shared and distinct genetic component.

Otake-Kasamoto Y, Kayama H, et al.

Shirai Y, Nakanishi Y, et al.

J Exp Med. 219(7): e20211291 (2022).

Ann Rheum Dis. 81(9):1301-1312 (2022).

Microbiota alteration and IFN-γ–producing CD4+ T
cell overactivation are implicated in Crohn’s disease (CD)pathogenesis. However, it remains unclear how dysbiosis
enhances Th1 responses, leading to intestinal inflammation.
The research group of Yuriko Otake-Kasamoto, Hisako
Kayama, and Kiyoshi Takeda identified key metabolites
derived from dysbiotic microbiota that induce enhanced
Th1 responses and exaggerate colitis in mouse models. Theirfindings elaborate on the mechanism by which metabolites
elevated in patients with CD harboring dysbiotic microbiota
promote Th1-mediated intestinal pathology.

Autoimmune and allergic diseases are outcomes ofthe dysregulation of the immune system. Yukinori Okada
and his research group analyzed the human genome
information of 840,000 individuals, and identified their
genetic characteristics common to autoimmune and allergic
diseases. Their multi-trait and cross-population study should
elucidate complex pathogenesis shared components acrossautoimmune and allergic diseases.

Runx1 and Runx2 inhibit fibrotic conversion of cellular niches for hematopoietic stem cells.

How myasthenia gravis develops in thymoma patients?

Omatsu Y, Aiba S, et al.

Yasumizu Y, Ohkura N, et al.

Nat Commun. 13:2654 (2022).

Nat Commun. 13:4230 (2022).

In bone marrow, special microenvironments, known as
niches, are essential for the maintenance of hematopoietic
stem cells (HSCs). Yoshiki Omatsu, Takashi Nagasawa, and theresearch group showed HSC cellular niches require Runx1
or Runx2 to prevent their fibrotic conversion and maintain
HSCs and hematopoiesis in adults.

Although Myasthenia gravis (MG) frequently develops
in thymoma patients, the etiologic factors for MG are notwell understood. By constructing a comprehensive atlas ofthymoma using bulk and single-cell RNA-sequencing. The
group of Yoshiaki Yasumizu, Naganari Ohkura, and Shimon
Sakaguchi identified ectopic expression of neuromuscularmolecules in MG-type thymoma. These molecules arefound within a distinct subpopulation of medullary thymic
epithelial cells (mTECs), and named as "neuromuscular
mTECs (nmTECs)" by the authors. This study suggests that
nmTECs have a significant function in MG pathogenesis via
ectopic expression of neuromuscular molecules.

Information

Lysophosphatidylserines derived from microbiota in Crohn,s disease elicit pathologicalTh1 response.

Figure : CAR cells are specialized mesenchymal stem cells, which express the
specific transcription factors, including Runx1/2 as well as Foxc1 and Ebf1/3.
Runx1/2 prevents fibrotic conversion of CAR cells to maintain HSC niches.

98

99

Progressive differentiation towards the long-lived plasma cell compartment in the bonemarrow.

Ochiai Y, Suzuki C, et al.

Koike T, Fujii K, et al.

Proc Natl Acad Sci USA. 119(18): e2200582119 (2022).

J Exp Med. 220 (2): e20221717 (2023).

Yuki Ochiai, Katsumori Segawa ( Tokyo Medical and
Dental University), Shigekazu Nagata and the researchgroup showed that a flippase Atp11a at the plasma
membrane plays an important role in the formation ofsyncytiotrophoblasts in placental development.

Many plasma cells die shortly after participating in an
immune response, but a small population of plasma cells
called long-lived plasma cells (LLPCs) can survive in the bodyfor months or even years. The research group led by Wataru
Ise and Tomohiro Kurosaki generated a time-stamping
method to trace the development and survival of plasma
cells in the bone marrow and spleen. They found that plasma
cells were continuously replenished by new cells, a small
portion of which differentiated into LLPCs. Their findings
may aid in the development of new vaccines that efficiently
induce LLPCs.

Figure : Embryonic lethality of Atp11a-/- mice. Atp11a-/- mouse embryos diedat E14.5 with thin-walled heart ventricles. However, the cardiomyocyte- or
epiblast-specific Atp11a deletion did not affect mouse development,suggesting the inability of Atp11a-/- placentas to support the embryos.

100

Construction of a T-cell receptor signaling range for spontaneous development of
autoimmune disease.

Antibody feedback contributes to the development of Omicron-reactive memory B cells.

Tanaka A, Maeda S, et al.

Takeshi Inoue T, Shinnakasu R, et al.

J Exp Med. 220 (2): e20220386 (2023).

J Exp Med. 220 (2): e20221786 (2023).

“How an anomaly in a TCR signaling molecule leads tospontaneous autoimmunity over immunodeficiency?”
is unclear. Atsushi Tanaka and Shimon Sakaguchi groupexpressed in normal mice mutated ZAP-70 molecules withdifferent affinities for the CD3 chains, or wild-type ZAP-70
at graded expression levels under tetracycline-inducible
control. Both manipulations reduced TCR signaling intensity
to various extents and thereby rendered those normallydeleted self-reactive thymocytes to become positively
selected and form a highly autoimmune TCR repertoire. The
results provide a general model of how altered TCR signaling
evokes autoimmune disease.

In contrast to a second dose of the SARS-CoV-2 vaccine,a third dose elicits potent neutralizing activity against
the Omicron variant. Takeshi Inoue, Tomohiro Kurosaki,
and the research group examined spike receptor binding
domain-specific memory B cells in vaccinated individuals.
They showed that pre-generated antibodies modulate
the selection of GC and subsequent memory B cells after
the second vaccine dose, accumulating more Omicronreactive memory B cells over time, which contributes to thegeneration of Omicron-neutralizing antibodies elicited by
the third vaccine dose.

Information

Inefficient development of syncytiotrophoblasts in the Atp11a-deficient mouse placenta.

101

A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody
responses in COVID-19 patients.

Taniguchi S, Matsui T, et al.

Søndergaard JN, Tulyeu J, et al.

Nat Commun. 14:143 (2023).

Proc Natl Acad Sci USA. 120 (4): e2217902120 (2023).

Alveolar macrophages (AMs) are crucial for maintaining
normal lung function. They are abundant in lung cancer
tissues, but their pathophysiological significance remains
unknown. Using an orthotopic murine lung cancer modeland human carcinoma samples, Masaru Ishii and his
research group revealed that AMs support cancer cellproliferation and thus contribute to unfavorable outcome.

Sex-biased humoral immune responses to COVID-19
patients have been observed. The identification of thecellular basis for the known sex-specific differences will
be key in protecting everyone, especially those most at
risk from COVID-19 infection. The research group of Jonas
Søndergaard and James Wing uncovered the sex-specificdifferences in a type of regulatory T cells (Treg), and in the
production of antibodies.

Information

Activin A-producing alveolar macrophage supports the progression of lung cell carcinoma.

Figure : The findings demonstrate the critical pathological role of activin
A-producing AMs in tumorigenesis, and provides means to clearly distinguishthem from their healthy counterparts.
Figure : Sex skewed disruption between T-follicular regulatory cells(Tfr), T-peripheral helper cells (Tph) and antibody producing B-cells
and plasmablasts during acute COVID-19.

Direct activation of microglia by b-glucosylceramide causes phagocytosis of neurons thatexacerbates Gaucher disease.

Aldh1a2+ fibroblastic reticular cells regulate lymphocyte recruitment in omental milky
spots.

Shimizu T, Schutt CR, et al.

Yoshihara T, and Okabe Y.

Immunity 56:307-319 (2023).

J Exp Med. 220 (5): e20221813 (2023).

Gaucher's disease is a disease that develops due to thesystemic accumulation of glucosylceramide. Although thedisorders of central nervous system are particularly severe,
the detailed molecular mechanisms are unknown and there
are no effective treatments. The research group led by Sho
Yamasaki revealed the direct activation of microglia by
β-glucosylceramide causes phagocytosis of neurons thatexacerbates Gaucher disease. The blockade of this pathway
with FDA-approved drugs improves symptoms and survival.

Lymphoid clusters in visceral adipose tissue omentum,
k nown as milk y spots, play a central role in the
immunological defense in the abdomen. However, theirdevelopment and maturation mechanisms are poorly
understood. Tomomi Yoshihara and Yasutaka Okabe
identified a subset of fibroblastic reticular cells (FRCs) thatare uniquely present in omental milky spots.

Figure : The proposed model for the recruitment of circulating lymphocytes
into milky spots. Aldh1a2+ fibroblastic reticular cell (FRC)-derived retinoic
acid induces CXCL12 expression in the endothelium, which regulates theconstitutive recruitment of circulating lymphocytes to the milky spots.

102

103

Publications

Ishikawa M, Shimada Y, et al.

Front Immunol. 14: 998233 (2023).
Recently accumulating evidence has highlighted
the rare occurrence of COVID-19 vaccination-induced
inflammation in the central nervous system. However,the precise information on immune dysregulation related
to the COVID-19 vaccination-associated autoimmunity
remains elusive. Using scRNA-seq analysis, Daisuke Okuzaki
and his group identified a distinct myeloid cell population
during the acute phase of encephalitis. This specific myeloid
population was detected neither in the remission phase of
the disease nor in the healthy cohort.

Celastrol suppresses humoral immune responses and autoimmunity by targeting the
COMMD3/8 complex
Shirai T, Nakai A, et al.

19

Harapan H, Ophinni Y, Megawati D, Frediansyah A, Mamada SS,
Salampe M, Bin Emran T, Winardi W, Fathima R, Sirinam S, Sittikul P,
Stoian AM, Nainu F, Sallam M. Monkeypox: A Comprehensive Review.
Viruses-Basel 14, 2155 (2022).

20

Hasebe R, Murakami K, Harada M, Halaka N, Nakagawa H, Kawano F,
Ohira Y, Kawamoto T, Yull FE, Blackwell TS, Nio-Kobayashi J, Iwanaga T,
Watanabe M, Watanabe N, Hotta H, Yamashita T, Kamimura D, TanakaY, Murakami M. ATP spreads inflammation to other limbs throughcrosstalk between sensory neurons and interneurons. Journal of
Experimental Medicine 219, e20212019 (2022).

21

Hasegawa T, Ishii M. Pathological Osteoclasts and Precursor
Macrophages in Inflammatory Arthritis. Frontiers in Immunology 13,
867368 (2022).

22

An SB, Yang BG, et al. Combined IgE neutralization and Bifidobacterium
longum supplementation reduces the allergic response in models offood allergy. Nature Communications 13, 5669 (2022).

Hashimoto R, Minoshima M, Sakata S, Ono F, Ishii H, Watakabe Y,
Nemoto T, Yanaka S, Kato K, Kikuchi K. Efficient visible/NIR light-driven
uncaging of hydroxylated thiazole orange-based caged compounds
in aqueous media. Chemical Science 13, 7462-7467 (2022).

23

Hashimoto S, Kishimoto T. Roles of RNA-binding proteins in immune
diseases and cancer. Seminars in Cancer Biology 86, 310-324 (2022).

6

Asano K, et al. Diversities of allergic pathologies and their modifiers:
Report from the second DGAKI-JSA meeting. Allergology
International 71, 310-317 (2022).

24

7

Bando K, Yabuuchi S, Li ML, Kubo T, Oketani R, Smith NI, Fujita K.
Bessel-beam illumination Raman microscopy. Biomedical Optics
Express 13, 3161-3170456138 (2022).

Hashizaki E, Sasai M, Okuzaki D, Nishi T, Kobayashi T, Iwanaga S,
Yamamoto M. Toxoplasma IWS1 Determines Fitness in Interferongamma-Activated Host Cells and Mice by Indirectly Regulating ROP18
mRNA Expression. mBio 14, (2023).

8

Bernal J, Morte B, Diez D. Thyroid hormone regulators in humancerebral cortex development. Journal of Endocrinology 255, R27-R36(2022).

25

Hatazawa J. The Clinical Value of Breast Specific Gamma Imaging andPositron Imaging: An Update. Seminars in Nuclear Medicine 52, 619627 (2022).

9

Butler-Laporte G, et al. Exome-wide association study to identify
rare variants influencing COVID-19 outcomes: Results from the Host
Genetics Initiative. PLOS Genetics 18, e1010367 (2022).

26

Hayashi H, et al. Modified DNA vaccine confers improved humoral
immune response and effective virus protection against SARS-CoV-2
delta variant. Scientific Reports 12, 20923 (2022).

27

10

Choi HS, Yum JH, Jeong Y, Lim S, Kumagai T, Cha HJ, Park S.
Fluorogenic bisazide cyanine probe as a highly efficient acrolein
detection tool for diagnosing triple negative breast cancer. Sensors
and Actuators B-Chemical 380, 133404 (2023).

Hayashi H, et al. Preclinical study of a DNA vaccine targeting SARSCoV-2. Current Research in Translational Medicine 70, 103348 (2022).

28

Hayashi Y, et al. MDS cells impair osteolineage differentiation of
MSCs via extracellular vesicles to suppress normal hematopoiesis.
Cell Reports 39, 110805 (2022).

11

Dofuku S, et al. Genome-Wide Association Study of Intracranial
Artery Stenosis Followed by Phenome-Wide Association Study.
Translational Stroke Research 14, 322-333 (2023).

29

12

Ebihara T, Matsubara T, Togami Y, Matsumoto H, Tachino J, Matsuura
H, Kojima T, Sugihara F, Seno S, Okuzaki D, Hirata H, Ogura H.
Combination of WFDC2, CHI3L1, and KRT19 in Plasma Defines a
Clinically Useful Molecular Phenotype Associated with Prognosis in
Critically III COVID-19 Patients. Journal of Clinical Immunology 43,
286-298 (2023).

Hino A, Fukushima K, Kusakabe S, Ueda T, Sudo T, Fujita J, Motooka
D, Takeda AK, Shinozaki NO, Watanabe S, Yokota T, Shibayama
H, Nakamura S, Hosen N. Prolonged gut microbial alterations in
post-transplant survivors of allogeneic haematopoietic stem celltransplantation. British Journal of Haematology 201, 725-737 (2023).

30

Hioki K, Hayashi T, Natsume-Kitatani Y, Kobiyama K, Temizoz B, Negishi
H, Kawakami H, Fuchino H, Kuroda E, Coban C, Kawahara N, Ishii KJ.
Machine Learning-Assisted Screening of Herbal Medicine Extracts as
Vaccine Adjuvants. Frontiers in Immunology 13, 847616 (2022).

13

Ebihara T, Matsumoto H, Matsubara T, Togami Y, Nakao S, Matsuura
H, Onishi S, Kojima T, Sugihara F, Okuzaki D, Hirata H, Yamamura H,
Ogura H. Resistin Associated With Cytokines and Endothelial Cell
Adhesion Molecules Is Related to Worse Outcome in COVID-19.
Frontiers in Immunology 13, 830061 (2022).

31

Hiramatsu Y, Suzuki K, Nishida T, Onoda N, Satoh T, Akira S, Ikawa
M, Ikeda H, Kamei J, Derouiche S, Tominaga M, Horiguchi Y. The
Mechanism of Pertussis Cough Revealed by the Mouse-Coughing
Model. mBio 13, e03197-21 (2022).

32

Hirashima S, Park S, Sugiyama H. Evaluation by Experimentationand Simulation of a FRET Pair Comprising Fluorescent Nucleobase
Analogs in Nucleosomes. Chemistry-A European Journal (2023).

14

Feng SY, Tuipulotu DE, Pandey A, Jing WD, Shen C, Ngo C, Tessema
MB, Li FJ, Fox D, Mathur A, Zhao AY, Wang RL, Pfeffer K, Degrandi D,
Yamamoto M, Reading PC, Burgio G, Man SM. Pathogen-selective
killing by guanylate-binding proteins as a molecular mechanism
leading to inflammasome signaling. Nature Communications 13,
4395 (2022).

33

Hirashima S, Sugiyama H, Park S. Characterization of 2-Fluoro-2'deoxyadenosine in Duplex, G-Quadruplex and i-Motif. ChemBioChem
23, e202200222 (2022).

15

Fujiki F, Morimoto S, Katsuhara A, Okuda A, Ogawa S, Ueda E,
Miyazaki M, Isotani A, Ikawa M, Nishida S, Nakajima H, Tsuboi A, Oka
Y, Nakata J, Hosen N, Kumanogoh A, Oji Y, Sugiyama H. T Cell-Intrinsic
Vitamin A Metabolism and Its Signaling Are Targets for Memory T
Cell-Based Cancer Immunotherapy. Frontiers in Immunology 13,
935465 (2022).

34

Hirata T, Itokazu T, Sasaki A, Sugihara F, Yamashita T. Humanized AntiRGMa Antibody Treatment Promotes Repair of Blood-Spinal Cord
Barrier Under Autoimmune Encephalomyelitis in Mice. Frontiers in
Immunology 13, 870126 (2022).

35

Hirata T, Yang J, Tomida S, Tokoro Y, Kinoshita T, Fujita M, Kizuka Y.
ER entry pathway and glycosylation of GPI-anchored proteins are
determined by N-terminal signal sequence and C-terminal GPIattachment sequence. Journal of Biological Chemistry 298, 102444(2022).

36

Hirayama T, Morita T, Funakoshi K, Yoshimine Y, Minoda S, Murakami
T, Okita Y, Narazaki M, Kumanogoh A. A case of Takayasu arteritis
complicated with pulmonary infarction. Oxford Medical Case Reports
2022, omac140 (2022).

37

Hyodo T, Ito Y, Hosono K, Uematsu S, Akira S, Majima M, Takeda A,
Amano H. The Role of mPGES-1 in Promoting Granulation Tissue
Angiogenesis Through Regulatory T-cell Accumulation. In Vivo 36,
2061-2073 (2022).

38

Ikeda-Yorifuji I, Tsujioka H, Sakata Y, Yamashita T. Single-nucleus
RNA sequencing identified cells with ependymal cell-like featuresenriched in neonatal mice after spinal cord injury. Neuroscience
Research 181, 22-38 (2022).

1

Abe Y, Miyake K, Shiroyama T, Hirata H, Nagatomo I, Takeda Y,
Kumanogoh A. Virtual fluoroscopic preprocedural planning using
Ziostation2 for transbronchial biopsy: A prospective self-controlled
study. Respiratory Investigation 61, 157-163 (2023).

2

Agemura T, Hasegawa T, Yari S, Kikuta J, Ishii M. Arthritis-associatedosteoclastogenic macrophage, AtoM, as a key player in pathologicalbone erosion. Inflammation and Regeneration 42, 17 (2022).

3

Ahmed AKMA, Nakagawa H, Isaksen TJ, Yamashita T. The effects ofBone Morphogenetic Protein 4 on adult neural stem cell proliferation,differentiation and survival in an in vitro model of ischemic stroke.
Neuroscience Research 183, 17-29 (2022).

4

Amano H, Eshima K, Ito Y, Nakamura M, Kitasato H, Ogawa F,
Hosono K, Iwabuchi K, Uematsu S, Akira S, Narumiya S, Majima M.
The microsomal prostaglandin E synthase-1/prostaglandin E-2 axis
induces recovery from ischaemia via recruitment of regulatory T cells.
Cardiovascular Research (2022).

5

Sci Immunol. 8(81): eadc9324 (2023).
Celastrol, a bioactive molecule extracted from the
Tripterygium wilfordii plant, has been shown to exhibit
anti- inflammatory properties. However, its mechanismof action has not been fully elucidated. Taiichro Shirai,
Kazuhiro Suzuki, and the research group showed celastrol
suppresses humoral immune responses and autoimmunity
by targeting the COM MD3/8 complex.

16

Figure : In silico modeling of the celastrol-bound COMMD3/8 complex
Celastrol, an herbal medicinal ingredient, improves the pathology of
autoimmune diseases by suppressing the COMMD3/8 complex.

104

Fukushima K, Matsumoto Y, Matsuki T, Saito H, Motooka D, Komukai
S, Fukui E, Yamuchi J, Nitta T, Niitsu T, Abe Y, Nabeshima H, Nagahama
Y, Nii T, Tsujino K, Miki K, Kitada S, Kumanogoh A, Akira S, Nakamura
S, Kida H. MGIT-seq for the Identification of Nontuberculous
Mycobacteria and Drug Resistance: a Prospective Study. Journal of
Clinical Microbiology 61, (2023).

17

Goda N, Sasada S, Shigematsu H, Masumoto N, Arihiro K, Nishikawa
H, Sakaguchi S, Okada M, Kadoya T. The ratio of CD8+lymphocytes
to tumor-infiltrating suppressive FOXP3+effector regulatory T cells
is associated with treatment response in invasive breast cancer.
Discover Oncology 13, 27 (2022).

18

Haji S, Ito T, Guenther C, Nakano M, Shimizu T, Mori D, Chiba Y, Tanaka
M, Mishra SK, Willment JA, Brown GD, Nagae M, Yamasaki S. Human
Dectin-1 is O-glycosylated and serves as a ligand for C-type lectin
receptor CLEC-2. eLife 11, e83037 (2022).

Information

Single-cell RNA-seq analysis identifies distinct myeloid cells temporally associated with
COVID-19 vaccination.

105

40

41

Inoue K, Yasuda T, Baba Y, Yamamoto T, Kurosaki T, Shinohara
H. Regulation mechanisms of CARMA1-Bcl10-MALT1 complex
assembly inferred from the analysis of TRAF6-deficient cells. Genes
To Cells (2023).

42

Inoue T, Shinnakasu R, Kawai C, Yamamoto H, Sakakibara S, Ono C,
Itoh Y, Terooatea T, Yamashita K, Okamoto T, Hashii N, Ishii-Watabe A,
Butler NS, Matsuura Y, Matsumoto H, Otsuka S, Hiraoka K, TeshimaT, Murakami M, Kurosaki T. Antibody feedback contributes tofacilitating the development of Omicron-reactive memory B cells in
SARS-CoV-2 mRNA vaccinees. Journal of Experimental Medicine 220,e20221786 (2022).

43

Inui H, et al. XCR1+conventional dendritic cell-induced CD4+T helper
1 cell activation exacerbates cardiac remodeling after ischemic
myocardial injury. Journal of Molecular and Cellular Cardiology 176,
68-83 (2023).

44
45

Inukai K, Kise K, Hayashi Y, Jia WZ, Muramatsu F, Okamoto N, Konishi
H, Akuta K, Kidoya H, Takakura N. Cancer apelin receptor suppresses
vascular mimicry in malignant melanoma. Pathology & Oncology
Research 29, 1610867 (2023).
Ishida M, Maki Y, Ninomiya A, Takada Y, Campeau P, Kinoshita T,
Murakami Y. Ethanolamine-phosphate on the second mannose is apreferential bridge for some GPI-anchored proteins. EMBO Reports
23, e54352 (2022).

Kato Y, Morita T, Kumanogoh A. Efficacy and risk of mRNA vaccinationin patients with autoimmune inflammatory rheumatic diseases.
Inflammation and Regeneration 43, 1 (2023).

57

Kawasaki T, et al. Next-generation proteomics of serum extracellular
vesicles combined with single-cell RNA sequencing identifies
MACROH2A1 associated with refractory COVID-19. Inflammation andRegeneration 42, 53 (2022).

58

Kido K, Nojima S, Motooka D, Nomura Y, Kohara M, Sato K, Ohshima
K, Tahara S, Kurashige M, Umeda D, Takashima T, Kiyokawa H, Ukon
K, Matsui T, Okuzaki D, Morii E. Ovarian high-grade serous carcinoma
cells with low SMARCA4 expression and high SMARCA2 expression
contribute to platinum resistance. Journal of Pathology 260, 56-70(2023).

59

Kim Y, Kamada N. The role of the microbiota in myelopoiesis duringhomeostasis and inflammation. International Immunology (2023).

60

Kitamoto S, Kamada N. Untangling the oral-gut axis in thepathogenesis of intestinal inflammation. International Immunology
34, 485-490 (2022).

61

Kobayashi A, Hirata T, Shimazaki T, Munesue Y, Aoshima K, Kimura T,
Nio-Kobayashi J, Hasebe R, Takeuchi A, Matsuura Y, Kusumi S, Koga
D, Iwasaki Y, Kinoshita T, Mohri S, Kitamoto T. A point mutation in GPIattachment signal peptide accelerates the development of priondisease. Acta Neuropathologica 145, 637-650s00401-023-02553-5(2023).

98

Motozono C, Toyoda M, Tan TS, Hamana H, Goto Y, Aritsu Y, Miyashita Y,
Oshiumi H, Nakamura K, Okada S, Udaka K, Kitamatsu M, Kishi H, Ueno
T. The SARS-CoV-2 Omicron BA.1 spike G446S mutation potentiates
antiviral T-cell recognition. Nature Communications 13, 5440 (2022).

80

Manabe Y, Ishibashi T, Asano R, Tonomura S, Maeda Y, Motooka D,
Ueda J, Yanagawa M, Edamoto-Taira Y, Chikaishi-Kirino T, Masaki
T, Inagaki T, Nakamura S, Katada Y, Okazawa M, Narazaki M, Ogo T,
Kumanogoh A, Nakaoka Y. Gut dysbiosis is associated with aortic
aneurysm formation and progression in Takayasu arteritis. Arthritis
Research & Therapy 25, 46 (2023).

99

Mule RD, Kumar A, Sancheti SP, Senthilkumar B, Kumar H, Patil NT.
BQ-AurIPr: a redox-active anticancer Au(i) complex that induces
immunogenic cell death. Chemical Science 13, 10779-10785 (2022).

100

Murata H, Kinoshita M, Yasumizu Y, Motooka D, Beppu S, Shiraishi
N, Sugiyama Y, Kihara K, Tada S, Koda T, Konaka H, Takamatsu H,
Kumanogoh A, Okuno T, Mochizuki H. Cell-Free DNA Derived From
Neutrophils Triggers Type 1 Interferon Signature in Neuromyelitis
Optica Spectrum Disorder. Neurology-Neuroimmunology &Neuroinflammation 9, e1149 (2022).

101

Nagae M, Hirata T, Tateno H, Mishra SK, Manabe N, Osada N,
Tokoro Y, Yamaguchi Y, Doerksen RJ, Shimizu T, Kizuka Y. Discovery
of a lectin domain that regulates enzyme activity in mouseN-acetylglucosaminyltransferase-IVa (MGAT4A). Communications
Biology 5, 695 (2022).

81

Manthrirathna MATP, Kodar K, Ishizuka S, Dangerfield EM, Xiuyuan
L, Yamasaki S, Stocker BL, Timmer MSM. 6-C-Linked trehalose
glycolipids signal through Mincle and exhibit potent. Bioorganic
Chemistry 133, 106345 (2023).

82

Manthrirathna MATP, Dangerfield EM, Ishizuka S, Woods A, Luong
BS, Yamasaki S, Timmer MSM, Stocker BL. Water-soluble trehalose
glycolipids show superior Mincle binding and signaling but impaired
phagocytosis and IL-1 beta production. Frontiers in Molecular
Biosciences 9, 1015210 (2022).

83

Masuhiro K, et al. Bronchoalveolar lavage fluid reveals factors
contributing to the efficacy of PD-1 blockade in lung cancer. JCIInsight 7, e157915 (2022).

102

Nagao-Kitamoto H, Kitamoto S, Kamada N. Inflammatory bowel
disease and carcinogenesis. Cancer and Metastasis Reviews 41, 301316 (2022).

84

Masyeni S, Iqhrammullah M, Frediansyah A, Nainu F, Tallei T, Emran
TB, Ophinni Y, Dhama K, Harapan H. Molnupiravir: A lethal mutagenic
drug against rapidly mutating severe acute respiratory syndrome
coronavirus 2-A narrative review. Journal of Medical Virology 94,
3006-3016 (2022).

103

Naito M, Kumanogoh A. Group 2 innate lymphoid cells and theirsurrounding environment. Inflammation and Regeneration 43, 21(2023).

85

Matsui T, Iwasa A, Mimura M, Taniguchi S, Sudo T, Uchida Y, Kikuta J,
Morizono H, Horii R, Motoyama Y, Morii E, Ohno S, Kiyota Y, Ishii M.
Label-free multiphoton excitation imaging as a promising diagnostic
tool for breast cancer. Cancer Science 113, 2916-2925 (2022).

104

Nakagawa N, Hashii Y, Kayama H, Okumura R, Nakajima H, Minagawa
H, Morimoto S, Fujiki F, Nakata J, Shirakawa T, Katayama T, Takeda K,
Tsuboi A, Ozono K. An oral WT1 protein vaccine composed of WT1anchored, genetically engineered Bifidobacterium longum allows
for intestinal immunity in mice with acute myeloid leukemia. Cancer
Immunology Immunotherapy 72, 39-53 (2023).

105

Nakagawa T, Kijima N, Hasegawa K, Ikeda S, Yaga M, Wibowo T, Tachi
T, Kuroda H, Hirayama R, Okita Y, Kinoshita M, Kagawa N, Kanemura Y,
Hosen N, Kishima H. Identification of glioblastoma-specific antigens
expressed in patient-derived tumor cells as candidate targets forchimeric antigen receptor T cell therapy. Neuro-Oncology Advances
5, vdac177 (2023).

106

Nakagawara K, et al. Impact of upper and lower respiratory
symptoms on COVID-19 outcomes: a multicenter retrospective
cohort study. Respiratory Research 23, 315 (2022).

107

Nakajima H, Fujita S, Kakae M, Nagayasu K, Oh-Hora M, Shirakawa H,
Kaneko S. Orai2 channel regulates prostaglandin E-2 production in
TNF alpha/IL1 alpha-stimulated astrocytes. Glia 70, 1666-1680 (2022).

108

Nakano S, Mikami N, Miyawaki M, Yamasaki S, Miyamoto S, Yamada M,
Temma T, Nishi Y, Nagaike A, Sakae S, Furusawa T, Kawakami R, Tsuji T,
Kohno T, Yoshida Y. Therapeutic Strategy for Rheumatoid Arthritis by
Induction of Myeloid-Derived Suppressor Cells with High Suppressive
Potential. Biological & Pharmaceutical Bulletin 45, 1053-1060 (2022).

109

Nakayama A, Kumamoto Y, Minoshima M, Kikuchi K, Taguchi A, Fujita
K. Photoinitiator-Free Two-Photon Polymerization of Biocompatible
Materials for 3D Micro/Nanofabrication. Advanced Optical Materials
10, 2200474 (2022).

110

Namkoong H, et al. DOCK2 is involved in the host genetics andbiology of severe COVID-19. Nature 609, 754 (2022).

111

Narazaki M, Kishimoto T. Current status and prospects of IL-6-targetingtherapy. Expert Review Of Clinical Pharmacology 15, 575-592 (2022).

112

Ng KW, Faulkner N, Finsterbusch K, Wu M, Harvey R, Hussain S, Greco M,
Liu YF, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, Cherepanov P,
McCauley J, Daniels R, Howell M, Arase H, Wack A, Bauer DLV, Kassiotis
G. SARS-CoV-2 S2-targeted vaccination elicits broadly neutralizing
antibodies. Science Translational Medicine 14, eabn3715 (2022).

113

Nii T, et al. Takeda K. Genomic repertoires linked with pathogenic
potency of arthritogenic Prevotella copri isolated from the gut ofpatients with rheumatoid arthritis. Annals Of The Rheumatic Diseases(2023).

114

Ninomiya T, Nakagawa H, Inoue KI, Nishimura Y, Oishi T, Yamashita T,
Takada M. Origin of Multisynaptic Corticospinal Pathway to Forelimb
Segments in Macaques and Its Reorganization After Spinal Cord
Injury. Frontiers in Neural Circuits 16, 847100 (2022).

115

Nishikawa T, Chang CY, Tai JA, Hayashi H, Sun J, Torii S, Ono C,
Matsuura Y, Ide R, Mineno J, Sasai M, Yamamoto M, Nakagami
H, Yamashita K. Immune response induced in rodents by antiCoVid19 plasmid DNA vaccine via pyro-drive jet injector inoculation.
Immunological Medicine 45, 251-264 (2022).

65
66

Kohyama M, Suzuki T, Nakai W, Ono C, Matsuoka S, Iwatani K, Liu
YF, Sakai Y, Nakagawa A, Tomii K, Ohmura K, Okada M, Matsuura Y,
Ohshima S, Maeda Y, Okamoto T, Arase H. SARS-CoV-2 ORF8 is a viralcytokine regulating immune responses. International Immunology 35,
43-52 (2023).

86

Matsumaru T, Sueyoshi K, Okubo K, Fujii S, Sakuratani K, Saito R,
Ueki K, Yamasaki S, Fujimoto Y. Trehalose diesters containing a polarfunctional group-modified lipid moiety: Synthesis and evaluationof Mincle-mediated signaling activity. Bioorganic & Medicinal
Chemistry 75, 117045 (2022).

67

Koike T, Fujii K, Kometani K, Butler NS, Funakoshi K, Yari S, Kikuta J, Ishii
M, Kurosaki T, Ise W. Progressive differentiation toward the long-lived
plasma cell compartment in the bone marrow. Journal of Experimental
Medicine 220, e20221717 (2022).

87

Matsumaru T, Sakuratani K, Yanaka S, Kato K, Yamasaki S, Fujimoto Y.
Fungal beta-Mannosyloxymannitol Glycolipids and Their Analogues:
Synthesis and Mincle-Mediated Signaling Activity. European Journalof Organic Chemistry 2022, e202200109 (2022).

88

Matsushita M, Fujita K, Hatano K, Hayashi T, Kayama H, Motooka D,
Hase H, Yamamoto A, Uemura T, Yamamichi G, Tomiyama E, Koh Y,
Kato T, Kawashima A, Uemura M, Nojima S, Imamura R, Mubeen A,
Netto GJ, Tsujikawa K, Nakamura S, Takeda K, Morii E, Nonomura N.
High-fat diet promotes prostate cancer growth through histamine
signaling. International Journal of Cancer 151, 623-636 (2022).

89

Matsuzaki T, Terutsuki D, Sato S, Ikarashi K, Sato K, Mitsuno H,
Okumura R, Yoshimura Y, Usami S, Mori Y, Fujii M, Takemi S,
Nakabayashi S, Yoshikawa HY, Kanzaki R. Low Surface Potential
with Glycoconjugates Determines Insect Cell Adhesion at Room
Temperature. Journal of Physical Chemistry Letters 13, 9494-9500(2022).

90

Minohara K, Imai M, Matoba T, Wing JB, Shime H, Odanaka M, Uraki
R, Kawakita D, Toyama T, Takahashi S, Morita A, Murakami S, Ohkura
N, Sakaguchi S, Iwasaki S, Yamazaki S. Mature dendritic cells enrichedin regulatory molecules may control regulatory T cells and theprognosis of head and neck cancer. Cancer Science 114, 1256-1269(2023).

49

68

50

Itotagawa E, Tomofuji Y, Kato Y, Konaka H, Tsujimoto K, Park J, Nagira
D, Hirayama T, Jo T, Hirano T, Morita T, Nishide M, Nishida S, Shima Y,
Narazaki M, Okada Y, Takamatsu H, Kumanogoh A. SLE stratification
based on BAFF and IFN-I bioactivity for biologics and implications of
BAFF produced by glomeruli in lupus nephritis. Rheumatology (2022).

Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S.
Thiopheneextended Fluorescent Nucleosides as Molecular RotorType Fluorogenic Sensors for Biomolecular Interactions. ACS Sensors 8,
923-932 (2023).

69

Kusumoto S, Ikeda JI, Kurashige M, Maeno-Fujinami E, Tahara S, Matsui
T, Nojima S, Okuzaki D, Morii E. Tumor cell plasticity in endometrioid
carcinoma is regulated by neuronal membrane glycoprotein M6-b.
Oncology Letters 25, 45 (2023).

51

Iwahori K, Uenami T, Yano Y, Ueda T, Tone M, Naito Y, Suga Y, Fukushima
K, Shiroyama T, Miyake K, Koyama S, Hirata H, Nagatomo I, Kida H,
Mori M, Takeda Y, Kumanogoh A, Wada H. Peripheral T cell cytotoxicity
predicts the efficacy of anti-PD-1 therapy for advanced non-small celllung cancer patients. Scientific Reports 12, 17461 (2022).

70

Kuwayama R, Suzuki K, Nakamura J, Aizawa E, Yoshioka Y, Ikawa M,
Nabatame S, Inoue KI, Shimmyo Y, Ozono K, Kinoshita T, Murakami
Y. Establishment of mouse model of inherited PIGO deficiency
and therapeutic potential of AAV-based gene therapy. Nature
Communications 13, 3107 (2022).

55

79

Mahajan A, et al. Multi-ancestry genetic study of type 2 diabetes
highlights the power of diverse populations for discovery andtranslation. Nature Genetics 54, 560 (2022).

Kohl L, et al. Macrophages inhibit Coxiella burnetii by the ACOD1itaconate pathway for containment of Q fever. EMBO Molecular
Medicine 15, (2023).

Ito H, Ishikawa M, Matsumoto H, Sugihara F, Okuzaki D, Hirata H,
Ogura H. Transcriptional differences between coronavirus disease2019 and bacterial sepsis. Virology Journal 19, 198 (2022).

Kajiwara K, Chen PK, Abe Y, Okuda S, Kon S, Adachi J, Tomonaga T,
Fujita Y, Okada M. Src activation in lipid rafts confers epithelial cellswith invasive potential to escape from apical extrusion during cellcompetition. Current Biology 32, 3460 (2022).

Monhemi H, Hoang HN, Standley DM, Matsuda T, Housaindokht MR.
The protein-stabilizing effects of TMAO in aqueous and non-aqueousconditions. Physical Chemistry Chemical Physics 24, 21178-21187(2022).

64

48

54

97

Kobayashi T, Moro K. Tissue-Specific Diversity of Group 2 Innate
Lymphoid Cells in the Skin. Frontiers in Immunology 13, 885642 (2022).

Itahashi K, Irie T, Yuda J, Kumagai S, Tanegashima T, Lin YT, Watanabe
S, Goto Y, Suzuki J, Aokage K, Tsuboi M, Minami Y, Ishii G, Ohe Y, Ise W,
Kurosaki T, Suzuki Y, Koyama S, Nishikawa H. BATF epigenetically andtranscriptionally controls the activation program of regulatory T cells
in human tumors. Science Immunology 7, eabk0957 (2022).

Kajihara A, Morita T, Kato Y, Konaka H, Murakami T, Yamaguchi Y,
Koyama S, Takamatsu H, Nishide M, Maeda Y, Watanabe A, Nishida
S, Hirano T, Shima Y, Narazaki M, Kumanogoh A. The proliferative
activity levels of each immune cell population evaluated by mass
cytometry are linked to the clinical phenotypes of systemic lupus
erythematosus. International Immunology 35, 27-41 (2023).

78

63

47

53

96

Maeda Y, Motooka D, Kawasaki T, Oki H, Noda Y, Adachi Y, Niitsu T,
Okamoto S, Tanaka K, Fukushima K, Amiya S, Hara R, Oguro-IgashiraE, Matsuki T, Hirata H, Takeda Y, Kida H, Kumanogoh A, Nakamura
S, Takeda K. Longitudinal alterations of the gut mycobiota andmicrobiota on COVID-19 severity. BMC infectious Diseases 22, 572(2022).

Mochizuki K, Kumamoto Y, Maeda S, Tanuma M, Kasai A, Takemura
M, Harada Y, Hashimoto H, Tanaka H, Smith NI, Fujita K. Highthroughput line-illumination Raman microscopy with multislit
detection. Biomedical Optics Express 14, 1015-1026 (2023).

Kobayashi S, Kita S, Okuzaki D, Fujishima Y, Otsuki M, Kato H, Nishizawa
Y, Miyashita K, Yokoyama C, Fukuhara A, Morii E, Shimomura I.
Favine/CCDC3 deficiency accelerated atherosclerosis and thrombus
formation is associated with decreased MEF2C-KLF2 pathway. iScience25, 105252 (2022).

Ishikawa M, Shimada Y, Ozono T, Matsumoto H, Ogura H, Kihara K,
Mochizuki H, Okuno T, Sakakibara S, Kinoshita M, Okuzaki D. Singlecell RNA-seq analysis identifies distinct myeloid cells in a case withencephalitis temporally associated with COVID-19 vaccination.
Frontiers in Immunology 14, 998233 (2023).

Kaimori JY, Kikkawa Y, Motooka D, Namba-Hamano T, Takuwa A,
Okazaki A, Kobayashi K, Tanigawa A, Kotani Y, Uno Y, Yoshimi K,
Hattori K, Asahina Y, Kajimoto S, Doi Y, Oka T, Sakaguchi Y, Mashimo
T, Sekiguchi K, Nakaya A, Nomizu M, Isaka Y. A heterozygous LAMA5
variant may contribute to slowly progressive, vinculinenhanced
familial FSGS and pulmonary defects. JCI Insight 7, e158378 (2022).

Lu YG, Ikawa M. Eukaryotic fertilization and gamete fusion at a
glance. Journal of Cell Science 135, jcs260296 (2022).

Kobayashi D, Umemoto E, Miyasaka M. The role of extracellular ATP in
homeostatic immune cell migration. Current Opinion in Pharmacology
68, 102331 (2023).

Ishigaki K,et al. Multi-ancestry genome-wide association analyses
identify novel genetic mechanisms in rheumatoid arthritis. Nature
Genetics 54, 1640 (2022).

Iwasawa MT, Miyachi H, Wakabayashi S, Sugihira T, Aoyama R,
Nakagawa S, Katayama Y, Yoneyama M, Hara H, Iwakura Y, Matsumoto
M, Inohara N, Koguchi-Yoshioka H, Fujimoto M, Nunez G, Matsue
H, Nakamura Y, Saijo S. Epidermal clearance of Candida albicans
is mediated by IL-17 but independent of fungal innate immune
receptors. International Immunology 34, 409-420 (2022).

77

62

46

52

106

Imianowski CJ, Whiteside SK, Lozano T, Evans AC, Benson JD,
Courreges CJF, Sadiyah F, Lau CM, Zandhuis ND, Grant FM, Schuijs MJ,
Vardaka P, Kuo P, Soilleux EJ, Yang J, Sun JC, Kurosaki T, Okkenhaug
K, Halim TYF, Roychoudhuri R. BACH2 restricts NK cell maturationand function, limiting immunity to cancer metastasis. Journal of
Experimental Medicine 219, e20211476 (2022).

56

71

Li SS, Bern MD, Miao BP, Fan CX, Xing XY, Inoue T, Piersma SJ, Wang T,
Colonna M, Kurosaki T, Yokoyama WM. The transcription factor Bach2
negatively regulates murine natural killer cell maturation and function.
eLife 11, e77294 (2022).

72

Liu YF, Arase H. Neutralizing and enhancing antibodies against SARSCoV-2. Inflammation and Regeneration 42, 58 (2022).

91

73

Liu YS, Wang YC, Zhou XM, Zhang LP, Yang GL, Gao XD, Murakami Y,
Fujita M, Kinoshita T. Accumulated precursors of specific GPI-anchoredproteins upregulate GPI biosynthesis with ARV1. Journal of Cell
Biology 222, e202208159 (2023).

Minoshima M, Umeno T, Kadooka K, Roux M, Yamada N, Kikuchi
K. Development of a Versatile Protein Labeling Tool for Live-Cell
Imaging Using Fluorescent beta-Lactamase Inhibitors. Angewandte
Chemie-International Edition, SICI e202301704 (2023).

92

Mise-Omata S, et al. Memory B Cells and Memory T Cells Induced
by SARS-CoV-2 Booster Vaccination or Infection Show Different
Dynamics and Responsiveness to the Omicron Variant. Journal of
Immunology 209, 2104-2113 (2022).

93

Mishra A, et al. Stroke genetics informs drug discovery and risk
prediction across ancestries. Nature 611, 115 (2022).

94

Miyasaka M. The lymphatic system and COVID-19 vaccines. Frontiersin Immunology 13, 1041025 (2022).

95

Miyata Y, Yamada K, Nagata S, Segawa K. Two types of type IV P-type
ATPases independently reestablish the asymmetrical distributionof phosphatidylserine in plasma membranes. Journal of Biological
Chemistry 298, (2022).

74

Loong L, et al. Biallelic variants in PIGN cause Fryns syndrome, multiple
congenital anomalies-hypotonia-seizures syndrome, and neurologic
phenotypes: A genotype-phenotype correlation study. Genetics in
Medicine 25, 37-48 (2022).

75

Lu XY, Yamasaki S. Current understanding of T cell immunity against
SARS-CoV-2. Inflammation and Regeneration 42, 51 (2022).

76

Lu YG, Nagamori I, Kobayashi H, Kojima-Kita K, Shirane K, Chang HY,
Nishimura T, Koyano T, Yu ZF, Castaneda JM, Matsuyama M, KuramochiMiyagawa S, Matzuk MM, Ikawa M. ADAD2 functions in spermiogenesis
and piRNA biogenesis in mice. Andrology 11, 698-709 (2023).

Information

39

Ikemura N, Taminishi S, Inaba T, Arimori T, Motooka D, Katoh K, Kirita
Y, Higuchi Y, Li SL, Suzuki T, Itoh Y, Ozaki Y, Nakamura S, Matoba S,
Standley DM, Okamoto T, Takagi J, Hoshino A. An engineered ACE2
decoy neutralizes the SARS-CoV-2 Omicron variant and confers
protection against infection in vivo. Science Translational Medicine
14, eabn7737 (2022).

107

117

Noguchi Y, Yamamoto Y, Iwahori K, Matsumoto M, Hirata M, Okuyama
H, Shintani Y, Kumanogoh A, Wada H. Tetracyclines Enhance Antitumor T-Cell Responses Induced by a Bispecific T-Cell Engager.
Biological & Pharmaceutical Bulletin 45, 429-437 (2022).

118

Nojima S. Class IV semaphorins in disease pathogenesis. Pathology
International 72, 471-487 (2022).

119

Ochiai Y, Suzuki C, Segawa K, Uchiyama Y, Nagata S. Inefficientdevelopment of syncytiotrophoblasts in the Atp11a-deficient mouseplacenta. Proceedings of the National Academy of Sciences USA 119,e2200582119 (2022).

120

Ogino T, Takeda K. Immunoregulation by antigen-presenting cells
in human intestinal lamina propria. Frontiers in Immunology 14,1138971 (2023).

121

Ogura H, Gohda J, Lu XY, Yamamoto M, Takesue Y, Son A, Doi S,
Matsushita K, Isobe F, Fukuda Y, Huang TP, Ueno T, Mambo N,
Murakami H, Kawaguchi Y, Inoue JI, Shirai K, Yamasaki S, Hirata JI,
Ishido S. Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T
lymphocytes in patients recovering from severe COVID-19. Nature
Communications 13, 7063 (2022).

122

Oji Y, et al. WT1 Trio Peptide-Based Cancer Vaccine for Rare Cancers
Expressing Shared Target WT1. Cancers 15, 393 (2023).

123

Omatsu Y, Aiba S, Maeta T, Higaki K, Aoki K, Watanabe H, Kondoh
G, Nishimura R, Takeda S, Chung UI, Nagasawa T. Runx1 and Runx2
inhibit fibrotic conversion of cellular niches for hematopoietic stem
cells. Nature Communications 13, 2654 (2022).

124

Osada N, Nagae M, Nakano M, Hirata T, Kizuka Y. Examination ofdifferential glycoprotein preferences of N-acetylglucosaminyltransferase-IV isozymes a and b. Journal of Biological Chemistry298, 102400 (2022).

137

Sano E, Suzuki T, Hashimoto R, Itoh Y, Sakamoto A, Sakai Y, Saito A,
Okuzaki D, Motooka D, Muramoto Y, Noda T, Takasaki T, Sakuragi
JI, Minami S, Kobayashi T, Yamamoto T, Matsumura Y, Nagao M,
Okamoto T, Takayama K. Cell response analysis in SARS-CoV-2
infected bronchial organoids. Communications Biology 5, 516(2022).

138

Sasai M, Yamamoto M. Anti-Toxoplasma host defense systems andthe parasitic counterdefense mechanisms. Parasitology International
89, 102593 (2022).

139

Sato T, Ogawa Y, Yokoi K, Nagasaka Y, Ishikawa A, Shiokawa I,
Kinoshita M, Watanabe R, Shimada S, Tanaka A, Momosawa A,
Kawamura T. Characterization of human epithelial resident memory
regulatory T cells. Frontiers in Immunology 13, 962167 (2022).

140

Saunders GRB, et al. Genetic diversity fuels gene discovery for
tobacco and alcohol use. Nature 612, 720 (2022).

141

Scheele CLGJ, Herrmann D, Yamashita E, Lo Celso C, Jenne CN, Oktay
MH, Entenberg D, Friedl P, Weigert R, Meijboom FLB, Ishii M, Timpson
P, van Rheenen J. Multiphoton intravital microscopy of rodents.
Nature Reviews Methods Primers 2, 89 (2022).

142

155

Tachino J, Matsumoto H, Sugihara F, Seno S, Okuzaki D, Kitamura
T, Komukai S, Kido Y, Kojima T, Togami Y, Katayama Y, Nakagawa Y,
Ogura H. Development of clinical phenotypes and biological profiles
via proteomic analysis of trauma patients. Critical Care 26, 241 (2022).

156

Takata S, Miyake K, Maeda D, Hatake K, Nagatomo I, Shiroyama
T, Masuhiro K, Yaga M, Shirai Y, Mitsui Y, Yachida S, Kumanogoh A.
Proposal of a novel pipeline involving precise bronchoscopy of distal
peripheral pulmonary lesions for genetic testing. Scientific Reports
12, 19774 (2022).

157

Takata S, Takeda Y, Hirata H, Shirai Y, Morita T, Futami Y, Naito Y,
Masuhiro K, Shiroyama T, Miyake K, Naka T, Kumanogoh A. Leucinerich a-2 glycoprotein as a potential biomarker of idiopathic
multicentric Castleman disease with pulmonary involvement: asingle-center case-control study from Japan. Journal of Thoracic
Disease 14, 1332 (2022).

174

Watanabe A, Nishida S, Burcu T, Shibahara T, Kusakabe T, Kuroda E,
Ishii KJ, Kumanogoh A. Safety and immunogenicity of a quadrivalentseasonal influenza vaccine adjuvanted with hydroxypropyl-betacyclodextrin: A phase 1 clinical trial. Vaccine 40, 4150-4159 (2022).

175

Watase M, et al. Impact of accumulative smoking exposure andchronic obstructive pulmonary disease on COVID-19 outcomes:
report based on findings from the Japan COVID-19 task force.
International Journal of Infectious Diseases 128, 121-127 (2023).

176

Xie ZQ, Kawasaki T, Zhou HY, Okuzaki D, Okada N, Tachibana M.
Targeting GGT1 Eliminates the Tumor-Promoting Effect andEnhanced Immunosuppressive Function of Myeloid-Derived
Suppressor Cells Caused by G-CSF. Frontiers in Pharmacology 13,873792 (2022).

158

Takata Y, Yamanaka H, Nakagawa H, Takada M. Morphologicalchanges of large layer V pyramidal neurons in cortical motor-relatedareas after spinal cord injury in macaque monkeys. Scientific Reports
13, (2023).

177

Yamada S, Kitai Y, Tadokoro T, Takahashi R, Shoji H, Maemoto T,
Ishiura M, Muromoto R, Kashiwakura J, Ishii KJ, Maenaka K, Kawai T,
Matsuda T. Identification of RPL15 60S Ribosomal Protein as a Novel
Topotecan Target Protein That Correlates with DAMP Secretion andAntitumor Immune Activation. Journal of Immunology 209, 171-179(2022).

Shibata K, Motozono C, Nagae M, Shimizu T, Ishikawa E, Motooka D,
Okuzaki D, Izumi Y, Takahashi M, Fujimori N, Wing JB, Hayano T, Asai Y,
Bamba T, Ogawa Y, Furutani-Seiki M, Shirai M, Yamasaki S. SymBiotic
bacteria-dependent expansion of MR1-reactive T cells causes
autoimmunity in the absence of Bcl11b. Nature Communications 13,
6948 (2022).

159

Tanaka A, Maeda S, Nomura T, Llamas-Covarrubias MA, Tanaka S, Jin
L, Lim EL, Morikawa H, Kitagawa Y, Akizuki S, Ito Y, Fujimori C, Hirota
K, Murase T, Hashimoto M, Higo J, Zamoyska R, Ueda R, Standley DM,
Sakaguchi N, Sakaguchi S. Construction of a T cell receptor signaling
range for spontaneous development of autoimmune disease.
Journal of Experimental Medicine 220, e20220386 (2022).

178

Yamagishi R, et al. Gasdermin D-mediated release of IL-33 fromsenescent hepatic stellate cells promotes obesity-associatedhepatocellular carcinoma. Science Immunology 7, eabl7209 (2022).

179

143

Shibata K, Shimizu T, Nakahara M, Ito E, Legoux F, Fujii S, Yamada
Y, Furutani-Seiki M, Lantz O, Yamasaki S, Watarai M, Shirai M. The
intracellular pathogen Francisella tularensis escapes from adaptive
immunity by metabolic adaptation. Life Science Alliance 5,e202201441 (2022).

160

Tanaka R, Imai J, Tsugawa H, Eap KB, Yazawa M, Kaneko M,
Ohno M, Sugihara K, Kitamoto S, Nagao-Kitamoto H, Barnich N,
Matsushima M, Suzuki T, Kagawa T, Nishizaki Y, Suzuki H, KamadaN, Hozumi K. Adherent-invasive E. coli - induced specific IgA limits
pathobiont localization to the epithelial niche in the gut. Frontiers in
Microbiology 14, 1031997 (2023).

Yamaguchi Y, Kato Y, Edahiro R, Sondergaard JN, Murakami T, Amiya
S, Nameki S, Yoshimine Y, Morita T, Takeshima Y, Sakakibara S, Naito
Y, Motooka D, Liu YC, Shirai Y, Okita Y, Fujimoto J, Hirata H, Takeda Y,
Wing JB, Okuzaki D, Okada Y, Kumanogoh A. Consecutive BNT162b2
mRNA vaccination induces short-term epigenetic memory in innate
immune cells. JCI Insight 7, e163347 (2022).

180

144

Shibuya N, Itokazu T, Ueda T, Yamashita T. Intravital Imaging Reveals
the Ameliorating Effect of Colchicine in a Photothrombotic Stroke
Model via Inhibition of Neutrophil Recruitment. Translational Stroke
Research 14, 100-110 (2023).

161

Tang S, Luc Y, Skinnere WM, Sanyala M, Lishko PV, Ikawa M, Kim
PS. Human sperm TMEM95 binds eggs and facilitates membranefusion. Proceedings of the National Academy of Sciences USA 119,e2207805119 (2022).

Yamamoto K, Sonehara K, Namba S, Konuma T, Masuko H, Miyawaki S,
Kamatani Y, Hizawa N, Ozono K, Yengo L, Okada Y. Genetic footprints
of assortative mating in the Japanese population. Nature Human
Behaviour 7, 65 (2023).

181

162

Tay C, Tanaka A, Sakaguchi S. Tumor-infiltrating regulatory T cells astargets of cancer immunotherapy. Cancer Cell 41, 450-465 (2023).

Yamamoto Y, Shiroyama T, Hirata H, Matsumoto K, Kuge T, Yoneda
M, Yamamoto M, Uchiyama A, Takeda Y, Kumanogoh A. Secondary
subcutaneous abscess due to mixed infections by Peptoniphilus
olsenii and Gleimia europaea after COVID-19. Clinical Case Reports
11, e06844 (2023).

163

Temizoz B, Hioki K, Kobari S, Jounai N, Kusakabe T, Lee MSJ, Coban
C, Kuroda E, Ishii KJ. Anti-tumor immunity by transcriptional synergy
between TLR9 and STING activation. International Immunology 34,
353-364 (2022).

182

Yari S, Kikuta J, Shigyo H, Miyamoto Y, Okuzaki D, Furusawa Y,
Minoshima M, Kikuchi K, Ishii M. JAK inhibition ameliorates bone
destruction by simultaneously targeting mature osteoclasts andtheir precursors. Inflammation and Regeneration 43, 18 (2023).

164

Temma K, Oketani R, Lachmann R, Kubo T, Smith NI, Heintzmann
R, Fujita K. Saturatedexcitation image scanning microscopy. Optics
Express 30, 13825-13838 (2022).

183

Yasumizu Y, et al. Myasthenia gravis-specific aberrant neuromusculargene expression by medullary thymic epithelial cells in thymoma.
Nature Communications 13, 4230 (2022).

184

165

Thumkeo D, Punyawatthananukool S, Prasongtanakij S, Matsuura
R, Arima K, Nie H, Yamamoto R, Aoyama N, Hamaguchi H, Sugahara
S, Takeda S, Charoensawan V, Tanaka A, Sakaguchi S, Narumiya S.
PGE(2)eP2/EP4 signaling elicits immunosuppression by driving the
mregDC-Treg axis in inflammatory tumor microenvironment. Cell
Reports 39, 110914 (2022).

Yokoi K, Watanabe R, Kume M, Yamane S, Tanaka A, Fujimoto M,
Tanemura A. Melanocyte-specific CD49a(+)CD8(+) T cells in vitiligo
lesion potentiate to maintain activity during systemic steroid
therapy. Journal of Dermatology 50, 710-714 (2023).

185

Yoshihara T, Okabe Y. Aldh1a2 (+) fibroblastic reticular cells regulate
lymphocyte recruitment in omental milky spots. Journal of
Experimental Medicine 220, e20221813 (2023).

186

Yoshioka Y, Kobiyama K, Hayashi T, Onishi M, Yanagida Y, Nakagawa
T, Hashimoto M, Nishinaka A, Hirose J, Asaoka Y, Tajiri M, Hayata A,
Ishida S, Omoto S, Nagira M, Ishii KJ. A-910823, a squalene-based
emulsion adjuvant, induces T follicular helper cells and humoral
immune responses via alpha-tocopherol component. Frontiers in
Immunology 14, 1116238 (2023).

187

Yukawa-Muto Y, Kamiya T, Fujii H, Mori H, Toyoda A, Sato I, Konishi
Y, Hirayama A, Hara E, Fukuda S, Kawada N, Ohtani N. Distinct
responsiveness to rifaximin in patients with hepatic encephalopathy
depends on functional gut microbial species. Hepatology
Communications 6, 2090-2104 (2022).

188

Zalewski M, Janasik D, Kapala A, Minoshima M, Sugihara F, Raj W,
Pietrasik J, Kikuchi K, Krawczyk T. pH-Sensitive Polymethacrylates as
Potential Contrast Agents in F-19 MRI. Macromolecular Chemistry
and Physics 223, 2200027 (2022).

189

Zhang SS, Tsuji H, Jin H, Kitagori K, Akizuki S, Nakashima R, Yoshifuji
H, Tanaka M, Arase H, Ohmura K, Morinobu A. Rheumatoid factor
recognizes specific domains of the IgG heavy chain complexed with
HLA class II molecules. Rheumatology (2023).

190

Zhang Y, et al. Recycling of memory B cells between germinal centerand lymph node subcapsular sinus supports affinity maturation to
antigenic drift. Nature Communications 13, 2460 (2022).
Zhou HY, Xie ZQ, Morikawa N, Sakurai F, Mizuguchi H, Okuzaki
D, Okada N, Tachibana M. Modified method for differentiationof myeloid- derived suppressor cells in vitro enhances
immunosuppressive ability via glutathione metabolism.
Biochemistry and Biophysics Reports 33, 101416 (2023).

Shichinohe N, Kobayashi D, Izumi A, Hatanaka K, Fujita R, Kinoshita
T, Inoue N, Hamaue N, Wada K, Murakami Y. Sequential hydrolysisof FAD by ecto-5' nucleotidase CD73 and alkaline phosphatase isrequired for uptake of vitamin B2 into cells. Journal of Biological
Chemistry 298, 102640 (2022).

125

Otake-Kasamoto Y, Kayama H, Kishikawa T, Shinzaki S, Tashiro T,
Amano T, Tani M, Yoshihara T, Li B, Tani H, Liu L, Hayashi A, Okuzaki
D, Motooka D, Nakamura S, Okada Y, Iijima H, Takeda K, Takehara T.
Lysophosphatidylserines derived from microbiota in Crohn's diseaseelicit pathological Th1 response. Journal of Experimental Medicine
219, e20211291 (2022).

146

126

Otsuka T, Nishida S, Shibahara T, Temizoz B, Hamaguchi M, Shiroyama
T, Kimura K, Miyake K, Hirata H, Mizuno Y, Yagita M, Manabe Y,
Kuroda E, Takeda Y, Kida H, Ishii KJ, Kumanogoh A. CpG ODN (K3)toll-like receptor 9 agonist-induces Th1-type immune response andenhances cytotoxic activity in advanced lung cancer patients: aphase I study. BMC Cancer 22, 744 (2022).

127

Oura S, Hino T, Satoh TS, Noda TE, Koyano TS, Isotani AE, Matsuyama
MS, Akira SE, Ishiguro KIS, Ikawa ME. Trim41 is required to regulate
chromosome axis protein dynamics and meiosis in male mice. PLOS
Genetics 18, e1010241 (2022).

147

Shirai T, Nakai A, Ando E, Fujimoto J, Leach S, Arimori T, Higo D,
van Eerden FJ, Tulyeu J, Liu YC, Okuzaki D, Murayama MA, Miyata
H, Nunomura K, Lin BZ, Tani A, Kumanogoh A, Ikawa M, Wing JB,
Standley DM, Takagi J, Suzuki K. Celastrol suppresses humoral
immune responses and autoimmunity by targeting the COMMD3/8
complex. Science Immunology 8, eadc9324 (2023).

128

Ozawa T, Fujii K, Sudo T, Doi Y, Nakai R, Shingai Y, Ueda T, Baba Y,
Hosen N, Yokota T. Special AT-Rich Sequence-Binding Protein 1
Supports Survival and Maturation of Naive B Cells Stimulated by B
Cell Receptors. Journal of Immunology 208, 1937-1946 (2022).

148

Shirai Y, et al. Multi-trait and cross-population genome-wide
association studies across autoimmune and allergic diseases identify
shared and distinct genetic component. Annals Of The Rheumatic
Diseases 81, 1301-1312 (2022).

166

129

Ozono T, Kimura Y, Suenaga T, Beck G, Jinno J, Aguirre C, Ikenaka
K, Krainc D, Mochizuki H, Arase H. Extracellular transportation of
a-synuclein by HLA class II molecules. Biochemical and BiophysicalResearch Communications 644, 25-33 (2023).

149

167

130

Pavillon N, Smith NI. Non-invasive monitoring of T cell differentiation
through Raman spectroscopy. Scientific Reports 13, (2023).

Singh S, Murillo-Leon M, Endres NS, Soto AFA, Gomez-Marin JE,
Melbert F, Kanneganti TD, Yamamoto M, Campos C, Howard JC,
Taylor GA, Steinfeldt T. ROP39 is an Irgb10-specific parasite effector
that modulates acute Toxoplasma gondii virulence. PLOS Pathogens
19, e1011003 (2023).

Togami Y, Matsumoto H, Yoshimura J, Matsubara T, Ebihara T,
Matsuura H, Mitsuyama Y, Kojima T, Ishikawa M, Sugihara F, Hirata
H, Okuzaki D, Ogura H. Significance of interferon signaling basedon mRNA-microRNA integration and plasma protein analyses incritically ill COVID-19 patients. Molecular Therapy-Nucleic Acids 29,
342-353 (2022).
Tomiyama T, Yamamoto T, Takahama S, Toshima T, Itoh S, Harada
N, Shimokawa M, Okuzaki D, Mori M, Yoshizumi T. Up-regulated
LRRN2 expression as a marker for graft quality in living donor livertransplantation. Hepatology Communications 6, 2836-2849 (2022).

168

131

Piboonprai K, Millius A, Shimoda M, Tanaka H, Akira S, Maeda K.
Breaking self-regulation of Regnase-1 promotes its own protein
expression. Genes to Cells 28, 383-389 (2023).

Tomofuji Y, et al. Identification of serum metabolome signaturesassociated with retinal and renal complications of type 2 diabetes.
Communications Medicine 3, 5 (2023).

132

Qiuping L, Pan P, Zhenzhen L, Zhen Z, Xuezhu Z, Shuting L.
Acupuncture regulates the Th17/Treg balance and improvescognitive deficits in a rat model of vascular dementia. Heliyon 9,
e13346 (2023).

169

Tsujimoto K, Jo T, Nagira D, Konaka H, Park JH, Yoshimura S, Ninomiya
A, Sugihara F, Hirayama T, Itotagawa E, Matsuzaki Y, Takaichi Y, Aoki
W, Saita S, Nakamura S, Ballabio A, Nada S, Okada M, Takamatsu H,
Kumanogoh A. The lysosomal Ragulator complex activates NLRP3
inflammasome in vivo via HDAC6. EMBO Journal 42, e111389 (2023).

133

Ramdas S, et al. A multi-layer functional genomic analysis tounderstand noncoding genetic variation in lipids. American Journalof Human Genetics 109, 1366-1387 (2022).

134

Ryoden Y, Nagata S. The XK plasma membrane scramblase andthe VPS13A cytosolic lipid transporter for ATP-induced cell death.
Bioessays 44, e2200106 (2022).

135

Sakoguchi A, Arase H. Mechanisms for Host Immune Evasion
Mediated by Plasmodium falciparum-Infected Erythrocyte Surface
Antigens. Frontiers in Immunology 13, 901864 (2022).

136

Sanidad KZ, Amir M, Ananthanarayanan A, Singaraju A, Shiland NB,
Hong HS, Kamada N, Inohara N, Nunez G, Zeng MY. Maternal gut
microbiome-induced IgG regulates neonatal gut microbiome andimmunity. Science Immunology 7, eabh3816 (2022).

145

Shimizu T, Schutt CR, Izumi Y, Tomiyasu N, Omahdi Z, Kano K,
Takamatsu H, Aoki J, Bamba T, Kumanogoh A, Takao M, Yamasaki
S. Direct activation of microglia by ?-glucosylceramide causes
phagocytosis of neurons that exacerbates Gaucher disease.
Immunity 56, 307 (2023).

150

Sonehara K, et al. A common deletion at BAK1 reduces enhancer
activity and confers risk of intracranial germ cell tumors. Nature
Communications 13, 4478 (2022).

151

Song WL, Li XY, Cao HY, Wang TT, Sun YH, Fan QJ, Zahid D, Li M, Li WZ.
Taurine promotes B-cell activation by interaction with the V-H/V-L
framework regions of B-cell receptor. Immunology (2023).

152

Suenaga T, Mori Y, Suzutani T, Arase H. Regulation of Siglec-7mediated varicella-zoster virus infection of primary monocytes bycis-ligands. Biochemical and Biophysical Research Communications
613, 41-46 (2022).

153

Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M,
McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi
M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara
N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts toacquire host-derived nutrients during dietary nutrient restriction.
Cell Reports 40, 111093 (2022).

154

Sun X, Hosomi K, Shimoyama A, Yoshii K, Lan HWX, Wang YR,
Yamaura H, Nagatake T, Ishii KJ, Akira S, Kiyono H, Fukase K,
Kunisawa J. TLR4 agonist activity of Alcaligenes lipid a utilizes
MyD88 and TRIF signaling pathways for efficient antigen
presentation and T cell differentiation by dendritic cells. International
Immunopharmacology 117, 109852 (2023).

170

Tsujioka H, Yamashita T. Utilization of ethanolamine phosphate
phospholyase as a unique astrocytic marker. Frontiers in Cellular
Neuroscience 17, 1097512 (2023).

171

Tuipulotu DE, et al. Immunity against Moraxella catarrhalis requires
guanylate-binding proteins and caspase-11-NLRP3 inflammasomes.
EMBO Journal 42, (2023).

172

Wang QBS, et al. The whole blood transcriptional regulation
landscape in 465 COVID-19 infected samples from Japan COVID-19
Task Force. Nature Communications 13, 4830 (2022).

191

173

Wang YC, Menon AK, Maki Y, Liu YS, Iwasaki Y, Fujita M, Guerrero
PA, Silva DV, Seeberger PH, Murakami Y, Kinoshita T. Genome-wide
CRISPR screen reveals CLPTM1L as a lipid scramblase required for
efficient glycosylphosphatidylinositol biosynthesis. Proceedings of
the National Academy of Sciences USA 119, e2115083119 (2022).

The articles were published between April, 2022 and March, 2023.
The data were acquired using Web of ScienceTM Core Collection
on May 29, 2023, and sorted by alphabetical order of the firstauthors.

Information

108

116

Noda Y, Shiroyama T, Masuhiro K, Amiya S, Enomoto T, Adachi Y, Hara
R, Niitsu T, Naito Y, Miyake K, Koyama S, Hirata H, Nagatomo I, Takeda Y,
Kumanogoh A. Quantitative evaluation of emphysema for predicting
immunotherapy response in patients with advanced non-small-celllung cancer. Scientific Reports 12, 8881 (2022).

109

Access Map

By Hankyu Railway
15 min. walk east from Kita-Senri Station on the Hankyu Senri Line.
By Osaka Monorail
25 min. walk from Handai-byoin-mae Station on the Osaka Monorail.
By Hankyu Bus
Rout 1: Get on the bus bound for “Handai Honbu Mae” or “Ibaraki Mihogaoka” from SenriChuo Station. Get off at Handai Honbu Mae, walk 15 min.
Rout 2: Get on the bus bound for “Onohara Higashi, Fuji Kasai” from Senri-Chuo Station.
Get off at “Handai-guchi”, walk 5 min.
By Kintetsu Bus
Get on the bus bound for “Handai Honbu Mae” or “Ibaraki Mihogaoka” from Hankyu
Ibarakishi Station (via JR Ibaraki Station). Get off at “Handai Honbu Mae”, walk 15 min.

SUITA CAMPUS Osaka University

Information● Access from the Nearest Station

Handai-guchi
Ibaraki Mihogaoka

Graduate School of Medicine

Senri Gate

Osaka Monorail
Handai-byoin-mae Station

Graduate School of Engineering

Handai Honbu Mae

HankyuKita-Senri Station

ADDRESSTEL

FAX
E-mail110

IFReC Research Building,
Osaka University 3-1 Yamadaoka, Suita,
565-0871, Osaka, Japan
General Affairs: +81-6-6879-4275
Accounting: +81-6-6879-4917
Research Planning & Management Office:+81-6-6879-4777+81-6-6879-4272
ifrec-office@ifrec.osaka-u.ac.jp

Graduate School of
Frontier Bioscience

Main Gate
Kita Fire
Station

Han

kyu

Rai

RIKEN

lwa

y

111