bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bcl6 is the nexus transcription factor of T follicular helper cell (TFH) differentiation via a set of repressor-of-repressor gene circuits
Authors: Choi Jinyong , Diao Huitian , Faliti Caterina E. , Truong Jacquelyn , Rossi Meghan , Bélanger Simon , Yu Bingfei , Goldrath Ananda W. , Pipkin Matthew E. , Crotty Shane 
Published: January 2023

Abstract
T follicular helper (TFH) cells are a distinct type of CD4 T cells that are essential for most antibody and B lymphocyte responses. TFH regulation and dysregulation is involved in a range of diseases. Bcl6 is the lineage defining transcription factor of TFH cells and its activity is essential for TFH cell differentiation and function. However, how Bcl6 controls TFH biology has largely remained unclear, at least in part due to intrinsic challenges of connecting repressors to gene upregulation in complex cell types with multiple possible differentiation fates. Multiple competing models were tested here by a series of experimental approaches. We ruled out the model that TFH is a default pathway of CD4 T cell by utilizing Bcl6 and Blimp1 double deficient mice in acute virus infection and protein immunization. We showed that Bcl6 has a strong negative autoregulatory loop in TFH cells, by generating mice containing a deletion mutation of an 8-nucleotide Bcl6 binding site in the Bcl6 promoter. To determine putative Bcl6 target TFs, we developed an integrated analytic approach using RNA-seq, BCL6 ChIP-seq, and ATAC-seq data and Bcl6 and Blimp1 double KO mice. Using this approach, Runx2, Runx3, and Klf2 were identified as Bcl6-targeted repressors (Bcl6-r TFs) that regulate important TFH genes. Taken together, Bcl6 controls pleiotropic attributes of TFH differentiation and function (migration, costimulation, inhibitory receptors, and cytokines) via multiple repressor-of-repressor gene circuits.
ITK regulates IL-10 production by CD8+ T cells and lung immunopathology during influenza infection
Authors: McGee Michael C , Solouki Sabrina , Limper Candice B , Ye Kaixiong , Nidetz Natalie F. , August Avery , Huang Weishan 
Published: January 2023

Abstract
Influenza (flu) infections cause 250,000 deaths and 3–5 million cases of severe illness during the average flu season. Severe influenza infections are associated with a combination of strong pro-inflammatory and weak anti-inflammatory immune responses. Production of the anti-inflammatory cytokine IL-10 by T cells restricts immunopathology during flu infections, however our knowledge of the signaling pathways regulating IL-10 induction is limited. Using IL-10GFP reporter mouse models, we found that Interleukin-2 inducible T cell kinase (ITK), a critical component in T cell receptor (TCR) signaling, regulates the development of IL-10-producing CD8+ T cells during influenza A infection. Compared to wild type (WT) mice, Itk−/− mice displayed increased morbidity and mortality after influenza infection, accompanied by a significant reduction of IL-10 producing CD8+ T cells in the airways. Using the model antigen ovalbumin (OVA) and transgenic TCR specific for OVA in CD8+ T cells (OTI), along with an allele sensitive mutation in the ITK kinase domain, we determine that ITK regulates IL-10 production in antigen-specific CD8+ T cells in a kinase dependent manner. RNA sequencing and multiparametric flow cytometric analyses revealed that ITK differentially regulates the expression of cell surface markers and transcription factors that are involved in regulating T cell differentiation, effector and memory phenotypes. Together, our data suggests that ITK is a critical regulator of IL-10 production by CD8+ T cells and regulate immunopathology during influenza infection. Modulating ITK signaling may be a strategy for regulating immunopathology due to viral infections.
Dissecting Human Tissue Resident Memory T cell Heterogeneity on the Single Cell Level
Authors: Szabo Peter Anthony , Dogra Pranay , Thapa Puspa , Poon Maya M.L. , Matsumoto Rei , Kubota Masaru , Bush Erin , Sims Peter , Farber Donna L 
Published: January 2023

Abstract
The majority of T cells throughout the human body persist as non-circulating tissue-resident memory T cells (TRM) in lymphoid and mucosal sites, and are vital for orchestrating protective immune responses. However, given the difficulty of sampling healthy human tissues, a full understanding of TRM identity and function across tissue sites remains lacking. Here, we utilize a unique human tissue resource where tissues are obtained from organ donors to dissect CD4+ and CD8+ TRM heterogeneity using high-dimensional flow cytometry and single cell RNA-sequencing (scRNA-seq). We identify remarkable heterogeneity in expression of key surface markers that define TRM, namely CD103, CD101, CD49a, PD-1 and CXCR6, particularly in the lung and the intestines. These phenotypic groups of TRM denote different functional subsets after activation: CD103+ and CD101+ TRM preferentially produce IL-17A, CD49a+ and CXCR6+ TRM show enhanced IFNγ production, and PD-1+ TRM produce granzyme-B. To investigate the transcriptional programming underlying TRM, we profile ~20,000 resting and activated T cells from the lungs and intestines of human organ donors with scRNA-seq and identify TRM based on our previously defined tissue signature. In both tissues, we detect multiple clusters of TRM enriched for expression of individual or a combination of TRM marker genes. Importantly, these clusters show variable expression of genes coding for cytokines (IFNG, IL23A, IL26), transcription factors (TBX21, GATA3, BATF), and cytotoxic molecules (GNLY, GZMs), suggesting differentially regulated TRM subsets. Our results therefore highlight the heterogeneity of TRM across human tissue sites and define the transcriptional programming underlying TRM function.
CD70 contributes to age-associated T cell defects and overwhelming inflammatory responses
Authors: Kong Yaxian , Wang Di , Du Juan , Song Yangzi , Wang Beibei , Song Rui , Zhao Hongxin , Zeng Hui 
Published: January 2023

Abstract
Aging is associated with immune dysregulation, especially T cell disorders, which result in increased susceptibility to various diseases. Previous studies have shown that loss of co-stimulatory receptors or accumulation of co-inhibitory receptors play important roles in T cell senescence. In the present study, CD70, which was generally regarded as a costimulatory molecule, was found to be upregulated on CD4+and CD8+ T cells of elderly individuals. Consistent with its contradictory role in T cell activation, which was reported by recent studies, the findings of this study highlighted an important role of CD70 in T cell senescence. CD70+ T cells from elderly individuals displayed phenotypic features of exhaustion by expressing enhanced levels of numerous inhibitory receptors and elevated susceptibility to apoptosis. In contrast, aged CD70+ T cells also produced higher levels of pro-inflammatory cytokines and expressed more intracellular Granzyme B and perforin, which was consistent with an important feature of senescent cells termed the senescence-associated secretory phenotype (SASP). Importantly, their functional dysregulation associated with aging was reversed by blocking CD70. To the best of our knowledge, this is the first evidence for the involvement of CD70 in immunosenescence. Collectively, this study demonstrated CD70 as a prominent regulator involved in immunosenescence, which led to defects and overwhelming inflammatory responses of T cells during aging. These findings provide a strong rationale for targeting CD70 to prevent dysregulation related to immunosenescence.
Epigenomics of T Cell Activation and Memory
Authors: Barski Artem 
Published: January 2023

Abstract
A characteristic feature of adaptive immunity is the rapid recall response of memory T cells, the ability of memory T cells to produce cytokines in response to pathogen much more rapidly than naïve T cells. We have recently found that this rapid recall ability is associated with epigenetic gene poising. Here, we aim to uncover the mechanism that underlie chromatin remodeling during initial activation of T cells and, thus, contribute to the establishment of memory phenotype. Upon encountering an antigen, naïve T helper cells become activated, differentiate into several lineages and contribute to immune response. Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-Seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, most notably multiple sclerosis, IBD and allergy. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
Pericellular hyaluronan modulates IL-2 responsiveness through CD44
Authors: Martinez Hunter , Marshall Payton L , Kaber Gernot , Nagy Nadine , Bollyky Paul L 
Published: January 2023

Abstract
CD44 is ubiquitously expressed on human T cells. Stimulation through TCR results in upregulation of CD44. Through interactions with an extracellular matrix ligand, hyaluronan, CD44 classically mediates cell-cell contact for promoting adherence and migration. Here we report a distinct function of CD44 in regulating cellular production and responsiveness to the T cell growth factor IL-2. Overexpression of CD44 in IL-2 responsive cell lines results in a decreased responsiveness to IL-2. Upon CD44 cross-linking, we observe an increased sensitivity to IL-2. The enhanced response to IL-2 is accompanied by diminished Socs1 expression. These data suggest interactions between CD44 and pericellular hyaluronan function to alter cellular responses to IL-2. We propose that this is an underappreciated way inflammation, in the form of an extracellular matrix product, contributes to clonal T cell expansion.
Kennedy pathway regulation by miR-16-1/15a cluster family during T cell activation
Authors: Urena Frank R , Horgen F. David , Ma Chi , Hoffmann Fukun W. , Hoffmann Peter R. 
Published: January 2023

Abstract
The Kennedy pathway in the endoplasmic reticulum is vital for the synthesis of phosphatidylethanolamine (PE) that is incorporated into cell membranes and lipid-based signaling molecules. The three steps of the Kennedy pathway are catalyzed by ethanolamine kinase, CTP-phosphoethanolamine Cytidyltransferase, and selenoprotein I (SELENOI). Our data suggest that two of the three enzymes (ethanolamine kinase and SELENOI) included in this pathway are upregulated during T cell activation as a mechanism for increasing PE, to support increased membrane synthesis and lipidated signaling proteins. Moreover, we have analyzed micro-RNAs (miRs) and found that miR-16-1 and miR-15a, which are linked in the genome and are co-expressed, have sequences predicted to target ethanolamine kinase and SELENOI. Thus, we hypothesized that levels of miR-16-1/15a decrease upon T cell activation to allow increased expression of ethanolamine kinase and SELENOI, thereby driving the increased synthesis of PE. Using real-time PCR and western blot analyses, we found that both miR-16-1 and miR-15a decreased, while levels of ethanolamine kinase and SELENOI increased in mouse primary T cells upon T cell receptor (TCR) activation. This coincided with increased levels of different PE species as measured by LC-MS. Overall, these data support the model of miR-16-1/15a regulation of the Kennedy pathway, in which miR-16-1/15a levels are higher in naïve T cells as a means to keep PE synthesis low. Upon TCR engagement, these miRs are reduced and all three enzymes are upregulated, thereby allowing increased PE synthesis required by activated T cells.
Electrophilic nitro-fatty acids suppress psoriasiform dermatitis through the inhibition of STAT3
Authors: Wang Peng , Killeen Meaghan , Freeman Bruce , Falo Louis D. , Schopfer Francisco , Mathers Alicia R 
Published: January 2023

Abstract
Psoriasis is a systemic, immune-mediated disorder, characterized by chronic inflammatory skin and joint manifestations. Electrophilic nitro-fatty acids (NO2-FAs) have been reported to exert potent anti-inflammatory effects in several in vivo murine models of inflammatory diseases, such as chronic kidney disease and cardiovascular disease. To study the therapeutic potential of NO2-FAs on psoriasis, we employed both acute and chronic murine experimental models of psoriasis. Our studies demonstrate that oral treatments of nitro-oleic acid (OA-NO2), prior to imiquimod (IMQ) or rIL-23 treatments, significantly inhibited the induction of psoriasis-like inflammation and inflammatory cytokine production in the skin. Moreover, utilizing transgenic murine models of psoriasis, we determined that OA-NO2 had both a preventative and therapeutic effect on psoriasiform inflammation. Mechanistic in vitro experiments demonstrated that OA-NO2 decreased IL-17A-induced IL-6 expression in normal human dermal fibroblasts through the inhibition of NF-κB phosphorylation. Importantly, OA-NO2 also impaired signal transducers and activators of transcription 3 (STAT3) phosphorylation and translocation to the nucleus. Further mechanistic results indicated that OA-NO2 regulates STAT3 activation by post-translational modification of STAT3 via nitroalkylation. Overall, our results confirm the critical role of STAT3 in psoriasiform dermatitis and highlight the potential of NO2-FAs as therapeutic agents for the treatment of cutaneous inflammatory diseases, such as psoriasis.
Regulation of IDO1 expression and the kynurenine pathway in synovial fibroblasts
Authors: Municio Cristina , Ergueta Sandra , Usategui Alicia , Del Rey Manuel J , Pablos José L , Criado Gabriel 
Published: January 2023

Abstract

Background
Regulation of tryptophan metabolism along the kynurenine pathway by Indoleamine 2,3-dioxygenase (IDO) has been implicated in immune modulation. The purpose of this study was to investigate the mechanisms underlying IDO1 expression and its consequences on the pro-inflammatory and senescent phenotype of human synovial fibroblasts (SF).

Methods
Human SF were acutely treated with TNFα or IL6/sIL6R. Expression of genes implicated in tryptophan metabolism (IDO1, IDO2, KYNU and WARS) and the senescence associated secretory phenotype (SASP) (IL6, IL8, MCP1 y MMP3) were quantified by RT-PCR. IDO1 was silenced by lentiviral vectors. Expression of IDO1 protein was determinated by Western Blot. Production of kynurenine, a surrogate marker of IDO1 activity, was quantified by ELISA. Quantitative data were statistically analyzed by Pearson or Spearman correlation coefficient or Mann-Whitney test where appropriate.

Results
Basal expression of genes involved in Trp metabolism along the kynurenine pathway was comparable in SF regardless of their origin (normal, rheumatoid arthritis and osteoarthritis). Both TNFα and IL6/sIL6R induced Trp degradation and the expression of IDO1, KYNU and WARS, with IL6/sIL6R being more potent, but only IL6/sIL6R was able to induce expression of IDO2. IDO1 silencing specifically promoted an increase in basal IL6 mRNA levels and protein secretion without affecting other SASP components (IL8, MCP1 and MMP3).

Conclusion
Inflammatory cytokines TNFα and IL6/sIL6R induce the expression of enzymes implicated in the kynurenine pathway in SF. IDO1 negatively regulates IL6 production by SF.
Elucidating Topological Regulation of Antigen Receptor Gene Assembly
Authors: Allyn Brittney , Hayer Katharina , Nganga Vincent , Oltz Eugene M. , Bassing Craig 
Published: January 2023

Abstract
The compaction of antigen receptor (AgR) loci is thought to be important for efficient assembly of broad AgR gene repertoires through recombination of V gene segments with distal D and/or J gene segments of the recombination center (RC). Compaction of mammalian genomes occurs through CTCF protein-mediated chromosome looping, as well as by compartmentalization of chromatin based on transcriptional state. The large AgR loci generally have many CBEs strewn throughout their V segment regions positioned in convergent orientation with a few CBEs flanking their RC. The field hypothesizes that distal V CBEs promote recombination of nearby V gene segments by bringing them into proximity with D and J segments through looping to the convergent RC CBEs. To test this hypothesis, we have mutated CBEs within the mouse TCRβ locus. We find that deletion of the Trbv1 CBE, as well as deletion or inversion of the Trbv14 CBE, lowers, but does not ablate, contact and rearrangement of flanking Vβ gene segments with the distal RC. Unexpectedly, deletion of all convergent CBEs of the RC alters Vβ repertoire but has no obvious effect on overall levels of Vβ recombination, implying that compartmentalization might be the dominant mechanism for compaction and recombination of TCRβ loci. Consistent with this scenario, we show that deletion of the Trbv1 promoter inactivates Trbv1 chromatin and ablates interactions between Trbv1 and the RC. Our ongoing work seeks to determine relative roles of chromosome looping and compartmentalization in promoting and shaping AgR gene assembly.
Characterizing Zap70 signaling mutants in primary T cells using CRISPR/Cas9
Authors: Frie Meredith , Ill Riley , Lillemeier Bjorn 
Published: January 2023

Abstract
T cell activation is controlled by a complex series of signaling events that originate from the T cell receptor (TCR) at the plasma membrane. These signaling events are both spatially and temporally regulated to ensure that T cells activate only in a correct and specific context. A key aspect of T cell activation is the ability of the TCR to recognize peptides with specific affinities while simultaneously discounting a large proportion of MHC-TCR interactions with lower affinities. Our lab has identified Zap70 interaction dynamics with phosphorylated motifs in the TCR as a key mediator of T cell activation thresholds. However, studying these signaling events within primary T cells remains challenging because manipulating the signaling threshold through germline mutations will cause abnormal T cell development and selection in the thymus.
To investigate the role of Zap70 in regulating the activation threshold in mature, peripheral T cells, we have developed a CRISPR/Cas9 expression system in primary murine T cells. Using a retroviral construct, we can simultaneously knock down endogenous Zap70 and replace its expression with ectopic Zap70 mutants with differing TCR interaction dynamics and signal transduction. Ectopic Zap70 is expressed up to 41 days after infection and 33 days after adoptive transfer to Rag1−/− mice. In addition, the primary cells are sensitive to antigenic stimulation comparable to uninfected primary T cells. Using this system, we can both dissect the mechanisms by which Zap70-TCR dynamics regulate signal transduction and determine whether manipulating Zap70-TCR dynamics can affect T cell activity under various pathological conditions.
PSGL-1-directed regulation of calcium signaling modulates PD-1 expression following T cell activation
Authors: Otero Dennis C , Ma Jiadai , Hope Jennifer L , Bradley Linda M 
Published: January 2023

Abstract
We previously identified PSGL-1 (P-selectin glycoprotein-1) as a T cell-intrinsic, cell surface checkpoint inhibitor during chronic viral infection. In this model, we found that cross-linking PSGL-1 with antibody reduced signaling through the T cell receptor (TCR) in exhausted T cells and further upregulated PD-1 expression. However, the mechanism responsible for PD-1 regulation by PSGL-1 remained to be described. Here we show that, in naïve T cells, PSGL-1 ligation results in enhanced PD-1 expression following activation through the T cell receptor. Furthermore, naïve T cells lacking PSGL-1 fail to upregulate PD-1 to the same extent as wild type T cells following activation. Strikingly we have discovered that T cells lacking PSGL-1 showed reduced calcium signaling. In T cells, the calcium/calcineurin/NFAT pathway is important for induction of many genes including PD-1. Consequently, PSGL-1 deficient T cells also exhibit reduced nuclear translocation of NFAT explaining the reduced PD-1 expression. Conversely, we found that ligating PSGL-1 enhanced NFAT nuclear translocation with TCR signaling thus contributing to upregulation of PD-1. Therefore, by regulating calcium signaling through the T cell receptor, PSGL-1 modulates the extent of PD-1 expression early in activation and subsequently influencing the extent of T cell exhaustion. Further studies aim to elucidate how PSGL-1 regulates calcium signaling through the T cell receptor.
Insights from an in vitro derived T cell receptor
Authors: Alonso Jesus A , Singh Nishant K , Kranz David M , Evavold Brian D , Baker Brian M 
Published: January 2023

Abstract
Heterodimeric alpha-beta T cell receptors (TCRs) play a key role in cell-mediated immune responses of adaptive immunity. T cells continuously probe peptides presented by major histocompatibility complex (MHC) found on the cell surface. T cell activation initiates through the binding of antigenic peptides on MHCs. Yeast display technology has proven an effective way to gain insight into the underpinnings of peptide-MHC specificity enabling the switching of TCR affinity and specificity to unrelated antigens through directed evolution. Interestingly, in vitro directed evolution also generates mutants that lose peptide specificity. Here, we provide further detail of one of these cross-reactive TCRs, S3–4, which binds tightly but with a highly unusual geometry. Despite binding with an affinity that is characteristic of a strong agonist, S3–4’s odd binding geometry does not support T cell signaling. Further investigation with functional experiments and 2D kinetics shows that lack of signaling by S3–4 is ultimately attributable to the TCR’s inability to reach ligand. Although S3–4 is an example from a constrained system generated outside the bounds of usual immune function, our results show how unusual binding can influence T cell function and further demonstrate how divergences between 3D and 2D binding parameters can emerge.