Mapping Bcl11b binding in in vitro differentiated resident memory T cells [ChIP-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA773116 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16506729_1.fastq.gz | Fastqsanger.gz | |||
| SRR16506729_2.fastq.gz | Fastqsanger.gz | |||
| SRR16506730_1.fastq.gz | Fastqsanger.gz | |||
| SRR16506730_2.fastq.gz | Fastqsanger.gz |
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Project description:The transcription factor (TF) networks that regulate the differentiation of resident versus circulating memory CD8+ T cells are incompletely understood. Here we show that the TF Bcl11b restricts gut resident memory (Trm) cell differentiation, while promoting splenic T central memory (Tcm) and effector memory (Tem) cell differentiation. The reduction of Bcl11b-deficient splenic Tcm and Tem cells was not due to major alterations in their programs, but rather due to the increased homing of their precursors to the small intestine. However, Bcl11b-deficient resident memory precursor cells upregulated residency program, including the TFs Ahr and Prdm1 (encoding Blimp1), and downregulated Tcf7, which restricts the residency program and promotes tissue egress. Bcl11b directly bound at Ahr and Prdm1, as well as at Tcf7 genes. Abrogating Ahr and Prdm1, or restoration of Tcf7 expression in Bcl11b-deficient cells led to partial correction of the excessive resident memory cell differentiation. Functionally, Bcl11b-deficient memory CD8+ T cells had an impaired recall response, but anti-tumor immunity was increased in adoptive cell therapy. Bcl11b also repressed the residency program in human CD8+ T cells and human Bcl11b low tumor-infiltrating lymphocytes showed increased residency gene expression. Thus, Bcl11b plays a critical role in balancing the circulating and tissue residency programs and reveals a potential novel target for cancer immunotherapies.
2023-06-08 | GSE186282 | GEO
Project description:The networks of transcription factors (TFs) that control multipotency versus effector programs in intestinal resident memory T (TRM) cells are poorly understood. Mice with post-activation, conditional deletion of the TF Bcl11b in CD8+ T cells, infected with a food-born pathogen, had increased numbers of intestinal TRM cells, and their precursors and decreased splenic effector cells and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors with no major alterations in their programs. Bcl11b-/- memory CD8+ T cells had an impaired recall response despite their accumulation in the gut. Intestinal Bcl11b-/- TRM cells and their precursors manifested major alterations in the residency program, with diminished expression of multipotency program genes and upregulation of the effector program genes. Integration of transcriptomics with chromatin accessibility, activating histone marks and Bcl11b genome binding showed a link between the reduction in the multipotent program genes with regions of decreased chromatin accessibility and activating histone marks in Bcl11b-/- cells. In contrast, the effector program genes displayed increased activating epigenetic status. We propose that Bcl11b regulates tissue resident TRM program genes and is positioned upstream of Tcf1 and Blimp1 in regulation of multipotency versus effector TRM program, respectively. Rescuing experiments normalized the increased numbers of intestinal Bcl11b-/- TRM cells. Thus, Bcl11b is a frontrunner in the memory tissue residency program and acts early in lineage decision, promoting TRM cell multipotency and restricting effector function.
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Project description:The networks of transcription factors (TFs) that control multipotency versus effector programs in intestinal resident memory T (TRM) cells are poorly understood. Mice with post-activation, conditional deletion of the TF Bcl11b in CD8+ T cells, infected with a food-born pathogen, had increased numbers of intestinal TRM cells, and their precursors and decreased splenic effector cells and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors with no major alterations in their programs. Bcl11b-/- memory CD8+ T cells had an impaired recall response despite their accumulation in the gut. Intestinal Bcl11b-/- TRM cells and their precursors manifested major alterations in the residency program, with diminished expression of multipotency program genes and upregulation of the effector program genes. Integration of transcriptomics with chromatin accessibility, activating histone marks and Bcl11b genome binding showed a link between the reduction in the multipotent program genes with regions of decreased chromatin accessibility and activating histone marks in Bcl11b-/- cells. In contrast, the effector program genes displayed increased activating epigenetic status. We propose that Bcl11b regulates tissue resident TRM program genes and is positioned upstream of Tcf1 and Blimp1 in regulation of multipotency versus effector TRM program, respectively. Rescuing experiments normalized the increased numbers of intestinal Bcl11b-/- TRM cells. Thus, Bcl11b is a frontrunner in the memory tissue residency program and acts early in lineage decision, promoting TRM cell multipotency and restricting effector function.
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Project description:The networks of transcription factors (TFs) that control multipotency versus effector programs in intestinal resident memory T (TRM) cells are poorly understood. Mice with post-activation, conditional deletion of the TF Bcl11b in CD8+ T cells, infected with a food-born pathogen, had increased numbers of intestinal TRM cells, and their precursors and decreased splenic effector cells and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors with no major alterations in their programs. Bcl11b-/- memory CD8+ T cells had an impaired recall response despite their accumulation in the gut. Intestinal Bcl11b-/- TRM cells and their precursors manifested major alterations in the residency program, with diminished expression of multipotency program genes and upregulation of the effector program genes. Integration of transcriptomics with chromatin accessibility, activating histone marks and Bcl11b genome binding showed a link between the reduction in the multipotent program genes with regions of decreased chromatin accessibility and activating histone marks in Bcl11b-/- cells. In contrast, the effector program genes displayed increased activating epigenetic status. We propose that Bcl11b regulates tissue resident TRM program genes and is positioned upstream of Tcf1 and Blimp1 in regulation of multipotency versus effector TRM program, respectively. Rescuing experiments normalized the increased numbers of intestinal Bcl11b-/- TRM cells. Thus, Bcl11b is a frontrunner in the memory tissue residency program and acts early in lineage decision, promoting TRM cell multipotency and restricting effector function.
2023-06-09 | GSE222912 | GEO
Project description:The networks of transcription factors (TFs) that control multipotency versus effector programs in intestinal resident memory T (TRM) cells are poorly understood. Mice with post-activation, conditional deletion of the TF Bcl11b in CD8+ T cells, infected with a food-born pathogen, had increased numbers of intestinal TRM cells, and their precursors and decreased splenic effector cells and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors with no major alterations in their programs. Bcl11b-/- memory CD8+ T cells had an impaired recall response despite their accumulation in the gut. Intestinal Bcl11b-/- TRM cells and their precursors manifested major alterations in the residency program, with diminished expression of multipotency program genes and upregulation of the effector program genes. Integration of transcriptomics with chromatin accessibility, activating histone marks and Bcl11b genome binding showed a link between the reduction in the multipotent program genes with regions of decreased chromatin accessibility and activating histone marks in Bcl11b-/- cells. In contrast, the effector program genes displayed increased activating epigenetic status. We propose that Bcl11b regulates tissue resident TRM program genes and is positioned upstream of Tcf1 and Blimp1 in regulation of multipotency versus effector TRM program, respectively. Rescuing experiments normalized the increased numbers of intestinal Bcl11b-/- TRM cells. Thus, Bcl11b is a frontrunner in the memory tissue residency program and acts early in lineage decision, promoting TRM cell multipotency and restricting effector function.
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Project description:The transcription factor (TF) networks that regulate the differentiation of resident versus circulating memory CD8+ T cells are incompletely understood. Here we show that the TF Bcl11b restricts gut resident memory (Trm) cell differentiation, while promoting splenic T central memory (Tcm) and effector memory (Tem) cell differentiation. The reduction of Bcl11b-deficient splenic Tcm and Tem cells was not due to major alterations in their programs, but rather due to the increased homing of their precursors to the small intestine. However, Bcl11b-deficient resident memory precursor cells upregulated residency program, including the TFs Ahr and Prdm1 (encoding Blimp1), and downregulated Tcf7, which restricts the residency program and promotes tissue egress. Bcl11b directly bound at Ahr and Prdm1, as well as at Tcf7 genes. Abrogating Ahr and Prdm1, or restoration of Tcf7 expression in Bcl11b-deficient cells led to partial correction of the excessive resident memory cell differentiation. Functionally, Bcl11b-deficient memory CD8+ T cells had an impaired recall response, but anti-tumor immunity was increased in adoptive cell therapy. Bcl11b also repressed the residency program in human CD8+ T cells and human Bcl11b low tumor-infiltrating lymphocytes showed increased residency gene expression. Thus, Bcl11b plays a critical role in balancing the circulating and tissue residency programs and reveals a potential novel target for cancer immunotherapies.
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