bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Transcription Factors Thpok And Runx3 Identify Two Distinct CD4−CD8− Double Negative T Cell Populations And Respectively Define Their Commitment In The Helper Or Cytotoxic Fate
Authors: Thiault Nicolas , Verstichel Greet , Seumois Gregory , Vijayanand Pandurangan , Kronenberg Mitchell , Cheroutre Hilde 
Published: January 2023

Abstract
In the small intestine epithelium, the major TCRab population is the double negative (DNT) cells lacking the expression of either CD4 or CD8. In contrast to the conventional selected cells, the DNT cells undergo an agonist selection, which leads to their functional education and capacity to migrate to intestine.
DNT cells also possess the capacity to reach the liver, where we observed a heterogeneity of the DNT cells populations, based on expression of ThPOK and Runx3. In the gut, the latter is only expressed by the DNT cells. GSEA analysis and cytokines intra-cellular staining have shown that ThPOK+ DNT cells and Runx3 DNT cells are strongly divergent in their biological function. ThPOK+ DNT cells signature is enriched in genes expressed by CD4 T helper cells with a strong production of the inflammatory cytokine Il-17 whereas Runx3+ DNT cells signature is enriched in gene upregulated in CD8 T cytotoxic cells. In the thymus, based on the expression of these two transcription factors, we also found distinct DNT populations. Adoptive transfer, as well as hanging drop fetal thymus culture have demonstrated that solely Runx3+ DNT cells in the thymus are the precursors of the Runx3+ DNT cells in the gut. Furthermore, we demonstrated in the thymus both DNT cells populations are selected upon an agonist interaction with a self-antigen presented by developing thymocytes, for the development of ThPOK+ DNT cells, and TECs for Runx3+ DNT cells. RNA-seq experiment of thymic DNT populations revealed that the agonist selection process results in their differential functional education since T helper pathways are upregulated in ThPOK+ DNT cells whereas pathways involved in function and differentiation of cytotoxic cells are upregulated in Runx3+ DNT cells.
Quantitative Expression of GATA3 Specifies Lineage Fates and Functions of Innate Lymphoid Cells
Authors: Zheng Mingzhu , Zhong Chao , Cui Kairong , Martins Andrew , Hu Gangqing , Li Dan , Tessarollo Lino , Kozlov Serguei , Keller Jonathan , Tsang John , Zhao Keji , Zhu Jinfang (Jeff) 
Published: January 2023

Abstract
Innate lymphoid cells (ILCs) are the innate counterparts of the CD4 T helper cells of the adaptive system. While the CD4 T cell development and differentiation have been well studied, the development of ILC subsets is far from clear. Lymphoid tissue inducer (LTi) population is the founding member of ILCs, however, recent study has shown that these cells are not derived from a PLZF-expressing ILC common progenitor that generates other ILCs. The transcription factor(s) determining the fate of non-LTi progenitor versus LTi progenitor are unknown. Here we report that GATA3 is absolutely required for the generation of PLZF-expressing non-LTi progenitors, which express high level of GATA3, but not for the generation of RORgammat-expressing LTi progenitors consistent with low levels of GATA3 expression in these progenitors. Nevertheless, low level of GATA3 expression by LTi progenitors is critical for the generation of functional LTi cells. Thus, quantitative expression of GATA3 functionally determines the fates and functions of distinct ILC progenitors.
Inflammation-Induced Tumorigenesis: Diminished Noncanonical NF-κB Signaling is Associated with Pathogenesis of Colitis-associated Colorectal Cancer
Authors: Morrison Holly , Mounzer Christina , Eden Kristin , Baumgarner Katherine , Brown Stephan , Holl Eda , Allen Irving C 
Published: January 2023

Abstract
Colitis-associated colorectal cancer (CAC) is mediated by inflammation-induced tumorigenesis, causing DNA damage in susceptible cell populations. Dysregulation of inflammatory pathways in the colon is attributed to cancer pathogenesis and such signaling is attributed to NF-κB signaling. Transcription factor NF-κB is the master regulator of gene transcription and is activated through one of two pathways. Our focus is on the understudied noncanonical NF-κB signaling pathway, including NF-κB inducing kinase (NIK). NIK must be stabilized for activation of this pathway. Noncanonical signaling is attributed to the production of pro-inflammatory cytokines, recruitment of immune cells, and cell proliferation. We hypothesize that this pathway maintains gut homeostasis and when dysregulated causes cell populations to become tumorigenic. The objective of this study is to validate the clinical relevance of noncanonical signaling. We observe that diminished noncanonical signaling via whole-body Nik knockout mice results in reduced stem cell marker expression, enhanced proliferative capacity, altered microbiome composition, and increased susceptibility towards inflammation-induced tumorigenesis in the colon. Using CAC mouse models, conditional knockout strains show deletion of noncanonical signaling in epithelial cells results in increased susceptibility to colorectal tumorigenesis. Likewise, human colonic biopsy samples collected from CAC patients show significantly decreased expression levels of genes related to the noncanonical NF-kB pathway. This data suggests that the noncanonical NF-κB pathway has a protective role against colorectal cancer by regulating immune system homeostasis in the GI tract.
Influence of proton pump inhibitor or rebamipide use on gut microbiota of rheumatoid arthritis patients
Authors: Kim Ji-Won , Jeong Yunju , Yoon Jun Sik , Ji Geun Eog , Park Sung-Hwan 
Published: January 2023

Abstract

Objective
Patients with rheumatoid arthritis (RA) commonly use gastrointestinal (GI) protective drugs for treatment and prevention of peptic ulcer disease. However, how these drugs affect gut microbiota is unknown in RA patients. The objective of this study was to examine the gut microbiota of RA patients according to their use of GI protective drugs, such as proton pump inhibitors (PPIs), H2-receptor antagonists, and rebamipide.

Methods
Fecal samples were obtained from 15 healthy controls (HCs) and 32 RA patients who were receiving PPI, H2-receptor antagonist, or rebamipide. Bacterial DNA was extracted from the fecal samples and 16S rRNA sequencing was performed. Microbial composition and function were analyzed using QIIME and PICRUSt.

Results
RA patients showed reduced diversity and altered composition of the gut microbiota compared with HCs. Gut microbiota of RA patients receiving acid-suppressing drugs, particularly PPI, was distinct from that of RA patients receiving rebamipide (PPI versus rebamipide, p=0.005). Streptococcus was enriched in RA patients receiving PPI, whereas Clostridium bolteae was enriched in RA patients receiving rebamipide. Gut microbiota of PPI-users was highly expressing the microbial functional pathway involved in virulence factors production. This featured microbial function was positively correlated with the relative abundance of Streptococcus, the differentially abundant taxa of PPI-users.

Conclusions
Gut microbiota of RA patients receiving PPI was distinguished from those receiving rebamipide. Enriched virulent function in gut microbiota of PPI-users suggests that PPIs should not be overprescribed in RA patients.
Comparative Profiling of the Immune System in Sarcoidosis via CITE-Seq and Flow Cytometry
Authors: Magallon Roman E. , Knapp Jennifer R. , Harmacek Laura D. , Tu Ting-Hui Clair , Vestal Brian , Gillespie May , MacPhail Kristyn , Li LI , Elliot Jill , Barkes Briana , Maier Lisa , Sommer Anne , Grewal Pineet , Koth Laura , Arger Nicholas , Werner Brenda , Powers Linda , Hamzeh Nabeel , Breslin Linda , Chen Edward , Danhorn Thomas , Leach Sonia M , Fingerlin Tasha E. , O’Connor Brian P. 
Published: January 2023

Abstract
CITE-Seq enables simultaneous single cell transcriptome and proteome analysis via combining single cell RNA-seq with oligo-labeled antibodies. Conventional techniques such as flow or mass cytometry have caveats including the number of epitopes accurately detected or an inability to recover samples for transcriptome analysis. These limitations are prohibitive for multivariate analysis of limited clinical samples. We developed a CITE-seq assay that enables comprehensive immune cell profiling of Sarcoidosis. Sarcoidosis is a granulomatous lung disease characterized by abnormal CD4+ T cell Th1 activity. However, the disease etiology and course are variable and the underlying molecular drivers remain unknown. The long-term goal of this study is to utilize CITE-seq to identify immune molecular pathways of Sarcoidosis pathogenesis. In our initial studies, we analyzed PBMC’s by CITE-seq vs. flow cytometry and observed similar cell profiles. However, the synergy of protein detection coupled with transcriptome analysis via CITE-seq enhanced cell subset identification vs. flow or scRNA-seq alone. We utilized CITE-seq in an ongoing longitudinal study of Sarcoidosis subjects to enhance resolution of the immune components contributing to disease. We compared CITE-seq to a flow cytometry panel analyzing the differential contributions of various CD4+ T cell lineages. The enhanced granularity provided by CITE-seq elucidated molecular pathways associated with disease pathogenesis. Thus, moving forward CITE-seq can provide the resolution and multivariate data collection required to identify the inflammatory drivers of Sarcoidosis.
Adipose Tissue-Derived Mesenchymal Stem Cells’ Acellular Product Extracellular Vesicles as a Potential Therapy for Crohn Disease
Authors: Li Yan , Altemus Jessica , Lightner Amy 
Published: January 2023

Abstract
The breakdown of gastrointestinal tract immune homeostasis leads to Crohn’s disease (CD). Mesenchymal stem cells (MSCs) have demonstrated clinical efficacy in treating CD in clinical trials, but there is little known about the mechanism of healing. Considering the critical roles of macrophage polarization and T cell activation in CD, and immunomodulatory properties of MSCs, we sought to decipher the interaction between adipose derived MSCs, macrophages and T cells including their cytokine production, regulation of differentiation and pro-/anti-inflammatory function.
When MSC derived EVs from inflamed Crohn’s mesentery were added to monocyte culture, monocytes rapidly differentiated into M1 macrophages (CD68+) from myeloid progenitors. When MSC derived EVS from control patients, regardless of the adipose source of MSCs (subcutaneous fat, omentum, normal mesentery), monocytes selectively differentiated into M2 macrophages (Arg-1+). Adoptive transfer of these differentiated M2 macrophages, effectively reversed T cell activation, proliferation, and cytokine production. Control patient isolated MSC derived EVs significantly suppressed T cells function with significantly decreased levels of inflammatory cytokines, as compared to diseased mesentery MSC derived EVs. This T cells inhibition was a result of NO synthase, arginase, and reduced ERK induced inflammatory signaling.
MSCs alter macrophage polarization and subsequent T cell activation. Healthy MSCs have the ability to drive monocytes to a M2 subset which then effectively reverses T cell function. This mechanism supports why MSCs are effective for regulating CD progression and offers pathways for the evaluation of various MSC sources for optimal efficacy.
Hemagglutinin as potential in vivo driver of DQ6-restricted clonal expansion of CD4+ T cells cross-reactive with hypocretin in narcolepsy
Authors: Jiang Wei , Birtley James R. , Hung Shu-Chen , Wang Weiqi , Chiou Shin-Heng , Davis Mark M , Stern Lawrence J. , Mellins Elizabeth D 
Published: January 2023

Abstract
Narcolepsy is a sleeping disorder, caused by selective loss of neurons secreting a wake-promoting hormone, hypocretin (HCRT). Increased narcolepsy incidence was noted in China after the peak of 2009 H1N1 pandemic influenza (pH1N1) cases and in Europe after Pandemrix vaccine administration. The causes of HCRT neuron depletion and its relationship with pH1N1 are unknown. As narcolepsy susceptibility is associated with HLA-DQ6 and with a TCR α gene (J24) polymorphism, we hypothesized that abnormally expanded J24+/CD4+ T cells in DQ6+ subjects mediate autoimmunity against HCRT neurons and that molecular mimicry (epitopes in pH1N1 and self-antigens) drives T cell expansion via DQ6 presentation. We reported the in vivo expansion of DQ6/HCRT87–97–reactive J24+/CD4+ clones using a J24 allele and an un-conventional phenotype in patients compared to related clones in DQ6+ controls. Here, DQ6/peptide binding and crystal structure identify an epitope, HA274–287 from pH1N1 hemagglutinin, with homology to HCRT87–97 and another peptide, HCRT1–13. DQ6/HA274–287 tetramers isolated &gt;2000 tetramer+/CD4+ T cells in DQ6+ subjects. Single-cell sequencing of TCRs and 25 phenotypic transcripts identify a DQ6/HA274–287 tetramer+/J24+ clone with the identical TCR clonotype (TCR27) and phenotype as the expanded DQ6/HCRT87–97–reactive J24+ clones previously found in the same patient. Control-derived TCR27+ clones identified by DQ6/HCRT1–13 or DQ6/HCRT25–37 tetramers are unexpanded and lack expression of any of the phenotypic genes. Our findings show that DQ6+ subjects carry J24+/CD4+ cells, both public and cross-reactive (e.g TCR27). TCR27 expansion in patients argues for molecular mimicry as a factor in narcolepsy immunopathogenesis.
Inflammatory environments disrupt both bone formation and bone resorption
Authors: Chu Pei-Wen , Chen Yu-Hsu , Chen Chien-Hui , Chen Shau-Kwaun 
Published: January 2023

Abstract
Inflammation has been associated with bone diseases such as osteoporosis and osteoarthritis. Bone loss were reported in the patients of several inflammatory diseases, such as rheumatoid arthritis, systemic lupus erythematosus, inflammatory bowel disease. However, how inflammation influence bone metabolism remains elusive. The bone loss in inflammatory environments are widely considered as the results of osteoclast overactivation which leads to excessive bone resorption. We previously discovered that osteoclasts induced from RAW macrophage treated with RANKL exhibited different cell properties and gene expression profile with undifferentiated macrophage. In this research we examined the excessive bone resorption hypothesis in in vitro systems. RANKL stimulated differentiation of RAW cells into bone-resorptive osteoclasts, and induction of pre-osteoblasts (MC-3T3 E1) into mature osteoblasts are utilized in this research. Inflammatory environments are mimic by treating cultured osteoclast or osteoblast with conditioned medium collected from bone marrow derived macrophage primed with LPS or interferon-γ. The pro-inflammatory cytokines inhibit the proliferation and disrupt the expression of genes that are needed for bone formation, such as osteocalcin and collagen. On the other hand, inflammatory environments did not activate osteoclast, nor promote bone resorption. Instead, pro-inflammatory cytokines inhibit osteoclastogenesis and bone resorption, induce mitochondrial dysfunctions and lead to apoptosis of osteoclast. These results indicated that the bone loss developed in the inflammatory environments might be due to the disruption of both bone formation and bone resorption.
HERV1-env dependent unfolded protein response activation is a potential initiator of autoreactivity in autoimmune liver disease
Authors: Ekong Udeme D , Yao Jie , Knight James , Mehta Sameet , Avitzur Yaron , Martinez Mercedes , Lobritto Steve J , Mason Andrew 
Published: January 2023

Abstract
Regulatory T cells are not terminally differentiated but can acquire effector properties. Here we report Human Endogenous Retrovirus 1 (HERV1-env) induction of endoplasmic reticulum (ER) stress with Unfolded Protein Response (UPR) activation, through its interaction with ATF6. UPR activation cleaves ATF6 to its α and β isoforms. ATF6α up-regulates RORC, STAT3 and TBX21 and induces IL-17A and INF-γ production in regulatory T cells by binding to promoter sequences. Silencing of HERV1-env results in partial recovery of regulatory T cell suppressive function and abrogation of apoptosis. These findings identify ER stress and UPR activation as key factors driving regulatory T cell plasticity.
Characterizing Infection of B Lymphocytes with Measles Virus
Authors: Melot Logan , Coughlin Melissa , Rota Paul , Bankamp Bettina 
Published: January 2023

Abstract
Wild-type (w.t.) measles virus (MeV) infection generates a state of immunosuppression, which does not occur after vaccination with live attenuated vaccine. MeV has been shown to alter the function of immune cells such as dendritic cells and lymphocytes. Though altered B cell functions contribute to immune suppression, the pathogenesis of measles infection of B cells is not understood. Here, we characterized the differences in viral replication and cytokine expression in human B cells infected with vaccine (Edmonston-Zagreb [EZ]) or w.t. MeV. To measure viral replication, human B cells were infected with an EZ virus expressing GFP and the number of GFP expressing cells and mean fluorescence intensity (MFI) were measured after 24 hours. To measure differences in cytokine responses following infection of B cells with EZ or w.t., transcription of IL-1β, IL-6, IL-10, TNFα, IFNβ, and IFNγ was measured at 24, 48, and 72 hours after infection by quantitative RT-PCR. The number of B cells expressing GFP and the MFI increased 3-fold from 0 to 24 hours after infection. Preliminary data suggested that IL-1β transcription is higher in w.t. infected B cells, while IL-6 and IL-10 transcription were higher in EZ-infected B cells. Measles virus replication was detected 24 hours after infection of isolated, human B cells. The differential expression of cytokines in B cells suggest differences in the B cell response to infection with w.t and vaccine strains of MeV. Differential cytokine expression in w.t. infected B cells could play a role in the development of immune cell dysregulation, and the mechanism could be elucidated through further functional studies of infected B cells.
The dual role of alkylated trehalose copolymers as C-Type Lectin Receptor agonists and excipients
Authors: Mancini Rock , Davaritouchaee Maryam , Hendricksen Aaron , Nielsen Amy 
Published: January 2023

Abstract
In nature, trehalose plays many roles, from bacterial signaling and immune cell activation through C-Type Lectin Receptors (CLRs) activated by trehalose-6,6′-dimycolate (cord factor), to the excipient properties of trehalose, which stabilizes organisms against extreme environmental conditions. To-date, our molecular understanding of trehalose has enabled the creation of synthetic trehalose analogues that are superior to the natural systems: trehalose-6,6′-dibehenate is an optimally active motif that retains CLR agonism, and polymers of 4,6-O-(4-vinylbenzylidene)-α,α-trehalose far out-perform the natural excipient abilities of trehalose. Here we report our results from combining these benefits to create synthetic copolymers of 4,6-O-(4-vinylbenzylidene)-trehalose and 4′,6′-O-(4-vinylbenzylidene)-trehalose-6-behenate by Reversible Addition-Fragmentation Chain Transfer Polymerization. The resulting alkylated trehalose copolymers are well defined (PDI &lt; 1.4) with incorporation of behenic acid dispersed throughout the entire length of polymer as measured by DOSY-NMR. Overall, the copolymers retain the excipient properties of trehalose and enhance their ability to act as CLR agonists. A systematic exploration of the macromolecular parameters that drive CLR agonism (DP, PDI, and end-group chemistry), particularly through Dectin-1 and MINCLE, will be presented. These results suggest that alkylated trehalose copolymers could find use as dual vaccine adjuvants and stabilizing excipients.
Macrophage production and activity of innate immune proteins C1q, C1r, and C1s are modulated in response to molecular patterns
Authors: De Silva Angele M , Gallardo Ary , Fraser Deborah A 
Published: January 2023

Abstract
Pattern recognition receptors of the complement system, such as C1q, are vital for clearance of foreign and altered-self targets. C1q has a dual role in vivo: activating the inflammatory classical complement pathway via C1 complex formation (C1qC1r2C1s2) and opsonization in the absence of C1r and C1s which is anti-inflammatory. We hypothesize that macrophages encountering foreign targets will increase levels of C1 subunits to activate C1 and mount an inflammatory response while macrophages encountering damaged-self targets may only increase C1q production to promote anti-inflammatory responses and clearance. Human monocyte derived macrophages (HMDM) were incubated with LPS, E. coli bioparticles, oxLDL, apoptotic cells or polarized into M1 or M2 HMDMs. RNA was isolated for qPCR and supernatant for Luminex protein analysis, ELISA, and C1(q) hemolytic titers. Data show that M1 HMDM increase C1r and C1s mRNA, and produce higher levels of active C1 than M0 HMDM. In contrast, there is no change in gene or protein expression of C1 subunits in M2 HMDM. HMDM treatment with foreign targets revealed a trend of increased C1r and C1s mRNA, and decreased C1q mRNA, but not at the protein level. Treatments with damaged-self targets varied; as hypothesized, C1q gene and protein expression increases in response to apoptotic cells, however there are no substantial changes in treatments with oxLDL. Significant levels of active C1q, but not C1, were detected in response to LPS, oxLDL, and apoptotic cells. Data suggests there is modulation of C1 subunit production and activity in response to different targets. C1q production in the absence of C1r and C1s may be important in resolving inflammation during clearance of apoptotic cells, thus avoiding autoimmunity.
TLR2-Tpl2-dependent ERK Signaling Drives Opposite IL-12 Regulation in Dendritic Cells and Macrophages
Authors: Groft Sarah Grace , Nagy Nancy , Shukla Supriya , Harding Clifford V , Boom W Henry 
Published: January 2023

Abstract
This study investigated responses to TLR2-driven ERK signaling in dendritic cells versus macrophages. TLR2 signaling was induced with Pam3Cys, and the role of ERK signaling was interrogated pharmacologically with a MEK1/2 inhibitor (U0126) or genetically using bone-marrow-derived macrophages or dendritic cells from Tpl2−/− mice. We assessed cytokine production via ELISA and mRNA levels by qRT-PCR. In macrophages, blockade of ERK signaling by pharmacologic or genetic approaches inhibited IL-10 production and increased IL-12p40 production significantly. In dendritic cells, blockade of ERK signaling similarly inhibited IL-10 production but decreased IL-12p40 production, opposite to the effect of ERK signaling blockade in macrophages. This difference in IL-12p40 regulation correlated with differential expression of transcription factors cFos and IRF1, which are known to regulate IL-12. Thus, the impact of ERK signaling in response to TLR2 stimulation differs between macrophages and dendritic cells, potentially regulating their distinctive functions in the immune system. ERK-mediated suppression of IL-12p40 in macrophages may prevent excess inflammation and associated tissue damage following TLR2-stimuation, while ERK-mediated induction of IL-12p40 in dendritic cells may promote priming of Th1 responses. Greater understanding of the role that ERK signaling plays in different immune cell types may inform the development of host-directed therapy for a number of infectious pathogens.