Single-cell lineage mapping of a diverse virus-specific naïve CD4 T cell repertoire
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE158896 | GEO | 2020/11/10
REPOSITORIES: GEO
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Project description:In vitro cultures remain crucial for studying the fundamental mechanisms of human T cell development. Here, we introduce a novel in vitro cultivation system based on ThymoSpheres (TS): dense spheroids of DLL4 expressing stromal cells and human hematopoietic precursor cells (HPCs), in the absence of thymic epithelial cells. These spheroids are subsequently cultured at the air-liquid interphase. TS generate large numbers of mature T cells, are easy to manipulate, scalable, and can be repeatably sampled to monitor T cell differentiation. The mature T cells generated from primary human HPCs were extensively characterized using single-cell RNA and combinedT cell receptor (TCR) sequencing. These predominantly CD8α T cells exhibit transcriptional and CDR3 characteristics recently described in a human polyclonal αβ unconventional T cell (UTC) lineage. This includes the expression of hallmark genes associated with agonist selection, such as IKZF2(Helios), and expression of various Natural Killer (NK) receptors. The TCR repertoire of these UTCs is polyclonal and enriched for CDR3-associated autoreactive features and early rearrangements of the TCRα chain. In conclusion, TS cultures offer an intriguing platform to study the development of this human polyclonal UTC lineage and its inducing selection mechanisms.
2024-09-16 | GSE269574 | GEO
Project description:Genetic techniques such as antibody phage display have indicated an oligoclonal autoantibody response in various autoimmune diseases including pemphigus. These techniques have limited sampling of B cell clones. Characterization by mass spectometry of pemphigus serum autoantibodies affinity-purified on the autoantigen desmoglein indicates a much more polyclonal response. Conversely, many genetically detectable anti-desmoglein B cells do not contribute detectably to the serum antibody response. There is no convergence of the autoantibody response among patients, as determined by CDR3 sequence or heavy chain variable gene usage, implying targeting of these genes will not be a useful therapeutic strategy. Longitudinal analysis of autoantibodies over years indicates that, although many antibody clones persist, the proportion of each clonal antibody changes. These studies indicate a dynamic and very diverse autoantibody response not revealed by genetic studies, and explain why similar overall anti-desmoglein titers may give variable disease activity.
2016-11-30 | MSV000080368 | MassIVE
Project description:ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells Day2 (D2), Day5 (D5), Day8 (D8) post-LCMV-Armstrong infection, as well as EZH2-null (KO) TFH and TH1 at Day8 post-LCMV-infection. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. H3K27me3-ChIP-seq was performed in WT TFH and TH1 cells to confirm the deposition of the histone marks at those loci.
2018-12-31 | GSE120532 | GEO
Project description:We co-cultured T cells with Mo-DCs exposed to ConA for 24 h and used multiplex PCR and next-generation sequencing to detect the TCRα repertoire.The length of the amino acids of CDR3 in each group was 4–59 amino acids, and all presented a normal distribution. Moreover, the length of the amino acids of CDR3 was not different between ConA and control groups. The number of clonotypes and unique clonotypes in the ConA group was increased significantly compared with that in control groups. However, the difference of high-frequency CDR3 amino-acid clonotypes between ConA and control groups was not significant (cutoff = 0.2%). Our results for the V and J gene segments of TCR diversity showed a marked increase in the number of clonotypes in the ConA group. The Shannon–Wiener Diversity Index of ConA was lower than that in the control group, and the top-20 V and J gene segments of ConA showed a higher usage frequency than that in the control group, but the difference between ConA and the control group was not significant. Collectively, these data indicated that ConA could reduce CDR3 diversity and augment usage of high-frequency CDR3.
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Project description:Single-cell lineage mapping of a diverse virus-specific naïve CD4 T cell repertoire
| PRJNA666915 | ENA
Project description:TFH and Th1 cells generated after viral or intracellular bacterial infections are critical for the control of infections and the development of immunological memories. However, the mechanisms that govern the choice of activated CD4 T cells to the two alternative fates remain unclear. Here, we found that reciprocal expression of TCF1 and Blimp1 between viral-specific TFH and Th1 cells started early after infection. TCF1 was intrinsically required for the differentiation of TFH cells. In the absence of TCF1, TFH cells failed to maintain their transcriptional and metabolic signatures, distinct from those in Th1 cells. Mechanistically, TCF1 functioned through forming negative feedback loops with IL-2 and Blimp1 signaling. Thus, we have demonstrated an essential role of TCF1 in TFH-cell differentiation. Tcf7 deficient and WT SMARTA CD4 T cells were isolated from mice 8 days after Lymphocytic Choriomeningitis Virus (LCMV) infection. TFH and Th1 cells were separated by FACS.
2015-09-18 | E-GEOD-65660 | biostudies-arrayexpress
Project description:CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation. Analysis of in vivo polyclonal GC Tfh vs Tfh vs Non-Tfh eight days after LCMV viral infection. Analysis of in vivo follicular helper CD4 T cells (CXCR5high GL7low), versus germinal center follicular helper CD4 T cells (CXCR5hi GL7hi), versus non-follicular helper CD4 T cells (CXCR5low) eight days after viral infection.
2010-04-28 | E-GEOD-21380 | biostudies-arrayexpress
Project description:Transcriptional regulation of cell fate decisions in the immune system endows cells with specialized function; an iterative process that adapts to the changing landscape of infections. As coordinators of the immune system, T helper cells of the CD4+ lineage possess the ability to differentiate into an array of functional cell states in order to guide the response towards antibody production via the formation of T follicular helper (Tfh) cells or inflammation by the generation of T effector (Teff) cells. Tfh–Teff cell fate choice is mediated by the BCL6–Blimp-1 counter-antagonistic gene regulatory module, polarizing Tfh and Teff cells, respectively. A key question is how T helper cells establish and negotiate BCL6–Blimp-1 counter antagonism to control the output of Tfh and Teff cells. We show that the T cell receptor (TCR)-signal induced transcription factor, IRF4, is necessary for the generation of both BCL6-expressing Tfh cells and Blimp-1-expressing Teff cells. Importantly, we show that increasing TCR signal strength augments the amounts of IRF4 expressed as well as Teff cell fate trajectories that occur at the expense of Tfh cells. Using an orthogonal genetic system, based on a tet-inducible allele of Irf4, we demonstrate that increasing IRF4 expression during priming redirected Tfh cell fate choices towards those of Teff. Importantly, promotion of Teff cell fate trajectories by increased IRF4 expression occurred independently of IL-2 signals. At the molecular level, we link greater IRF4 abundance with its recruitment to low affinity DNA binding sites embedded within regulatory elements affiliated with the Teff gene program, including Blimp-1. Together, these results demonstrate that the Irf4 locus functions as the “reader” of TCR signal strength, in turn, the concentration dependent activity of the IRF4 transcription factor “writes” T helper cell fate choice.
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Project description:Ets1 can directly bind key TFH genes, regulating their expression . Loss of Ets1 results in the pre-mature expression of TFH-genes in Non-TFH cells. We wished to analyze if loss of Ets1 correlated with changes in chromatin accessibility especially in TFH gene loci.
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