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Mus musculus

ABSTRACT: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (ATAC-seq for in-vitro experiments)

PROVIDER: PRJNA359351 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5134650_1.fastq.gz	Fastqsanger.gz
	SRR5134650_2.fastq.gz	Fastqsanger.gz
	SRR5134651_1.fastq.gz	Fastqsanger.gz
	SRR5134651_2.fastq.gz	Fastqsanger.gz
	SRR5134652_1.fastq.gz	Fastqsanger.gz

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Mus musculus

Project description:Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (ATAC-seq for in-vivo experiments)

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Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells

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Project description:Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (OT-I vs P14 RNA-seq)

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Project description:Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (anti-PD-L1 vs Control IgG RNA-seq)

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Chromatin accessibility analysis of tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. [ATACseq]

Project description:To identify unique chromatin regions predicting the anti-tumor efficacy of Nrf2-deleted smart CD8+ T cell therapy, we performed an assay for transposase-accessible chromatin sequencing (ATAC-seq) using tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. From the analysis of ATAC-seq data, we identified quantitatively distinct open regions of chromatin that distinguish Nrf2-deficient CD8+ T cells or WT CD8+ T cells.

2024-04-01 | GSE229990 | GEO

CD8+ T cell-derived Fgl2 regulates immunity in a cell-autonomous manner

Project description:The regulatory circuits dictating CD8+ T cell responsiveness vs. exhaustion during anti-tumor immunity are incompletely understood. Here, we report that tumor-infiltrating antigen-specific PD-1+ TCF-1- CD8+ T cells express the immunosuppressive cytokine Fgl2. Conditional deletion of Fgl2 from antigen-specific CD8+ T cells prolonged CD8+ T cell persistence, decreased phenotypic and transcriptomic signatures of T cell exhaustion, and improved tumor control. Melanoma patients who died of their disease exhibited increased expression of Fgl2 in tumor-infiltrating CD8+ T cells as compared to those who survived. PD-1+CD8+ T cell-derived Fgl2 also negatively regulated virus-specific T cell responses in a model of chronic viral infection. Mechanistically, the enhanced responsiveness of Fgl2-deficient CD8+ T cells is underpinned by the interaction of Fgl2 with CD8+ T cell-expressed FcγRIIB, ligation of which results in caspase 3/7-mediated apoptosis. These data illuminate a novel cell-autonomous regulatory axis by which PD-1+ CD8+ T cell responses are regulated in vivo.

2024-01-05 | GSE252556 | GEO

TET2-mutant clonal hematopoiesis prevents T-cell exhaustion and suppresses cancer metastasis [RNA-seq]

Project description:TET2-mutant clonal hematopoiesis (CH) is associated with reduced cancer metastasis in human cohorts. Using mouse models of colorectal cancer liver metastasis, we demonstrate that Tet2-deficient hematopoietic cells suppress metastatic tumor burden by preventing CD8+ T-cell exhaustion. Bulk RNA-seq of sorted CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) from Vav1CreTet2KO, Cd4CreTet2KO, and Tet2fl/fl control mice was performed to characterize transcriptional changes associated with Tet2 loss in tumor-infiltrating T cells.

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3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer [Hi-C]

Project description:CD8+ T cell responses are essential for anti-tumor immunity, but chronic antigen exposure in cancer can lead to T cell exhaustion, marked by high PD-1 expression. Recent studies have identified progenitor-like CD8+ T cells (Tprog cells) within tumor-infiltrating lymphocytes (TILs) that sustain antitumor responses. These cells can differentiate into terminally exhausted cells (Tterm cells), losing their proliferative and effector functions. Immunotherapy aims to enhance CD8+ TILs functionality, promoting their transition from Tprog to Tterm cells. However, the mechanisms behind this exhaustion remain unclear. Single-cell RNA sequencing and ATAC-seq have revealed distinct profiles and chromatin accessibility between progenitor and terminally exhausted states. Histone modifications predict a loss of enhancer-promoter contacts during this transition. Chromatin structure plays a crucial role in T cell differentiation. We constructed a high-resolution 3D genome map of CD8+ T cell subsets and, through multi-omics integration, identified chromatin structure changes linked to T cell exhaustion, including alterations in topologically associating domains (TADs) and chromatin loops, providing new insights into the genetic basis of CD8+ T cell exhaustion in cancer.

2025-10-01 | GSE299305 | GEO

3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer

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Single-cell ATAC sequencing of SIINFEKL-reactive T cells in GL261 murine brain tumors in MHC class II deficient tumor-mircoenvironments

Project description:Single cell ATAC sequencing of SIINFEKL-reactive immune cell from intracranial murine GL261-SIINFEKL tumors 20 days after inoculation. SIINFEKL-reactive T cells were sorted based on dextramer staining. We show that loss of major histocompatibility complex (MHC) class II (MHCII)-restricted antigen presentation on bbm drives dysfunctional intratumoral tumor-reactive CD8+ T cell states through increased chromatin accessibility and expression of Tox, a critical regulator of T cell exhaustion.

2023-01-11 | E-MTAB-12512 | biostudies-arrayexpress

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