GEO DataSets

(Submitter supplied) Epigenetic changes, including histone methylation, control T cell differentiation and memory formation, though the enzymes that mediate these processes are not clear. We show that UTX, a histone H3 lysine 27 (H3K27) demethylase, promotes the generation of T follicular helper (Tfh) cells, a CD4+ T cell subset essential for B cell antibody generation and clearance of chronic viral infections. Mice with T cell specific UTX deletion (UTX TKO mice) had fewer Tfh cells, showed defective germinal center formation, lacked virus-specific IgG production, and were unable to resolve chronic lymphocytic choriomeningitis virus infection. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Persistent virus infections can cause pathogenesis that is debilitating or lethal. During these infections, virus-specific T cells fail to protect due to weakened antiviral activity or failure to persist. These outcomes are governed epigenetically, though it is unknown which enzymes contribute to T cell loss or impaired function over time. Here, we show that T cell receptor-stimulated CD8+ T cells increase their expression of UTX (Ubiquitously transcribed Tetratricopeptide repeat, X-chromosome), an enzyme involved in demethylating histone-3 lysine-27 (H3K27), and reduce genome-wide H3K27-me3. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL21103 GPL19057

23 Samples

Download data: BED, BW, TXT

(Submitter supplied) CD4 T follicular helper (Tfh) cells provide the required signals to B cells for germinal center reactions that are necessary for longlived antibody responses. However, it remains unclear whether there are CD4+ memory T cells committed to the Tfh lineage after antigen clearance. Using adoptive transfer of antigen-specific memory CD4+ subpopulations (based on CXCR5 and Ly6c expression)in the LCMV infection model, we found that there are distinct memory CD4+ T cell populations with commitment to the Tfh and Th1 lineages. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

22 Samples

Download data: CEL, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

12 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: To compare the transcriptomes of activated CD4 T effector cell populations in the presence and absence of STAT3 at 8 days post-infection using high-throughput RNA sequencing analysis. Methods: Cell sorting of the populations was done using the markers Ly6c and PSGL-1

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Follicular helper T cells (TFH), known as the primary helpers of the germinal center (GC) reaction, promote the humoral immune response to defend against various pathogens. Under conditions of infection by different types of pathogens, many shared transcription factors (TFs), such as Bcl-6, TCF-1 and Maf, are broadly expressed in TFH cells, orchesting TFH cell differentiation and function. In addtion, TFH cells also coexpress environmentally specific TFs as their conventional T cell counterparts (such as T-bet, GATA-3 or ROR-γt, which are expressed in Th1, Th2 or Th17 cells, respectively). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL

(Submitter supplied) In mice chronically infected with lymphocytic choriomeningitis virus (LCMV), we defined a subset of exhausted CD8+ T cells abundantly expressing chemokine receptor CXCR5. These CXCR5+ CD8+ T cells were preferentially localized in B cell follicles, expressing less inhibitory receptors while exhibiting more potent cytolytic activity compared to the CXCR5- subset. Furthermore, we identified Id2-E2A axis as the regulator for the generation of this subset. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT, XLSX

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

40 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK, TXT

(Submitter supplied) Microarray experiments were performed to elucidate the transcriptome changes due to EZH2 deficiency in follicular T helper (TFH) cells. These data suggest TFH-lineage associated genes are down-regulated in EZH2-null TFH cells, indicating that EZH2 primes TFH differentiation by regulating canonical genes of TFH cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) Although the methylation status of histone H3K27 plays a critical role in CD4+ T cell differentiation and its function, the role of Utx, histone H3K27 demethylase, in the CD8+ T cell-dependent immune response remains unclear. We therefore generated T cell-specific Utx knockout (Utx KO) mice to determine the role of Utx in CD8+ T cells. Wild-type (WT) and Utx KO mice were infected with Listeria monocytogenes expressing OVA to analyze the immune response of Ag-specific CD8+ T cells upon primary and secondary infections. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

2 Samples

Download data: WIG

(Submitter supplied) We report CD2AP KO TFH cells in LCMVc13 infection have enhanced cytokine production and cell cycling characteristics compared to WT cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

4 Samples

Download data: TXT

(Submitter supplied) In this project we analyze the transcriptome of the human multiple myeloma isogenic cell lines ARP-1 (UTX wild-type) and ARD (UTX null). The transcriptome is studied at baseline, upon restoration of UTX levels in ARD cells for 3 and 6 days, and upon treatment of the cell lines with the EZH2 inhibitor GSK343. Moreover, we analyzed the transcriptome of a ARD resistant cell line that we generated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

22 Samples

Download data: CSV

(Submitter supplied) CD4 T cells responses induced by LM61 immunization are heterogeneous in phenotype. The majority consists of Th1 cells, but there is also a consistent population of Tfh-differentiated cells and a minor population of Treg cells. Tfh-differentiated cells, alongside Th1 cells expand upon LCMV challenge.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TSV

(Submitter supplied) Vaccination induced CD4 T cells prevent B cell decimation by turning on a germinal center like transcriptional program. This cellular differentiation is similiar to the one observed when type I interferon receptor-deficient (IFNAR-/-) instead of wt mice are used as recipients.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TSV

(Submitter supplied) The KDM6 histone demethylases (UTX/KDM6A and JMJD3/KDM6B) mediate removal of repressive histone H3K27me3 marks to establish transcriptionally permissive chromatin. Loss of UTX in female mice is embryonic lethal. Unexpectedly, male UTX-null mice escape embryonic lethality due to expression of UTY, a paralog lacking H3K27-demethylase activity. This suggests that UTX plays an enzyme-independent role in development, and challenges the need for active H3K27-demethylation in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

8 Samples

Download data: BW, TXT

(Submitter supplied) T follicular helper (Tfh) cells are essential for germinal center B cell responses; however, the molecular mechanism underlying Tfh cell programming, in particular, the initial Tfh cell development, remains largely unknown. Here, we show that in vivo, despite enhanced non-Tfh effector functions, the deletion of transcription factor Bach2 still results in preferential Tfh cell differentiation. Mechanistically, the deletion of Bach2 leads to the induction of CXCR5 expression even before the up-regulation of Ascl2. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: XLSX

(Submitter supplied) In response to infection, antigen-specific CD8+ T cells are primed in the T cell zone of secondary lymphoid organs and differentiate into cytotoxic effector T (TC) cells. Concurrently, CD4+ T cells differentiate into follicular helper T (TFH) cells that localize to B cell follicles and promote protective antibody responses. During unresolved infections, however, some viruses including human immunodeficiency virus (HIV) or Epstein–Barr virus (EBV) escape immune control and persist in TFH cells and B cells, respectively. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

1 Sample

Download data: BW

(Submitter supplied) Lymphocytic Choriomeningitis Virus (LCMV) specific CD8+ T cells (P14) were transferred into congenic WT mice followed by LCMV(DOCILE) infection. CXCR5-expressing (CXCR5+) or CXCR5 non-expressing (CXCR5-) P14 were purified on day 8 after infection, and total mRNA were sequenced from these populations. mRNA of P14 from uninfected mice (Naive P14) was also sequenced.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

8 Samples

Download data: TXT

(Submitter supplied) Follicular helper T cells (TFH cells) are the prototypic helper T cell subset specialized to enable B cells to form germinal centers (GCs) and produce high-affinity antibodies. We found that expression of microRNAs (miRNAs) by T cells was essential for TFH cell differentiation. More specifically, we show that after immunization of mice with protein, the miRNA cluster miR-17~92 was critical for robust differentiation and function of TFH cells in a cell-intrinsic manner that occurred regardless of changes in proliferation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

8 Samples

Download data: TXT

(Submitter supplied) To elucidate the effect of Utx, histone demethylase, on CD8 Tcell diferentiation, The gene expression were measured in WT and Utx KO CD8 T cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT