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Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (ATAC-Seq)

ABSTRACT: Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (ATAC-Seq)

PROVIDER: PRJNA828189 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18821687_1.fastq.gz	Fastqsanger.gz
	SRR18821687_2.fastq.gz	Fastqsanger.gz
	SRR18821688_1.fastq.gz	Fastqsanger.gz
	SRR18821688_2.fastq.gz	Fastqsanger.gz
	SRR18821689_1.fastq.gz	Fastqsanger.gz

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Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells

Project description:Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells

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Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (RNA-Seq)

Project description:Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (RNA-Seq)

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Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (scRNA-Seq)

Project description:Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (scRNA-Seq)

| PRJNA828188 | ENA

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (RNA-Seq)

Project description:T cell exhaustion is a major impediment to anti-tumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here we show that the biology of tumor-associated macrophages (TAM) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAM reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique long-lasting antigen-specific synaptic interactions that fail to activate T cells, but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor.

2022-04-26 | GSE201071 | GEO

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (ATAC-Seq)

2022-04-26 | GSE201072 | GEO

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells (scRNA-Seq)

2022-04-26 | GSE201073 | GEO

Spatiotemporal co-dependency between macrophages and exhausted CD8<sup>+</sup> T cells in cancer.

Project description:T cell exhaustion is a major impediment to antitumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here, we show that the biology of tumor-associated macrophages (TAMs) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAMs reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique, long-lasting, antigen-specific synaptic interactions that fail to activate T cells but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor.

| S-EPMC9197962 | biostudies-literature

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-04-26 | GSE201074 | GEO

Transcription profiling of mouse naive, effector, memory and exhausted virus-specific CD8 T cells after chronic viral infection

Project description:CD8 T cells normally differentiate from resting naÃ¯ve T cells into function effector and then memory CD8 T cells following acute infections. During chronic viral infections, however, virus-specific CD8 T cells often become exhausted. We used microarrays to examine the gene expression differences between naive, effector, memory and exhausted virus-specific CD8 T cells following lymphocytic choriomeningitis virus infection. Experiment Overall Design: Three or four independent samples were sorted by flow cytometry for each cell type (naive, effector, memory and exhausted) virus-specific CD8 T cells. RNA was extracted and hybridized to Affymetrix microarrays.

2008-06-16 | E-GEOD-9650 | biostudies-arrayexpress

CD39 expression identifies terminally exhausted CD8+ T cells

Project description:Exhausted T cells express multiple co-inhibitory molecules that impair their function and limit immunity to chronic viral infection. Defining novel markers of exhaustion is important both for identifying and potentially reversing T cell exhaustion. Herein, we show that the ectonucleotidse CD39 is a marker of exhausted CD8+ T cells. CD8+ T cells specific for HCV or HIV express high levels of CD39, but those specific for EBV and CMV do not. CD39 expressed by CD8+ T cells in chronic infection is enzymatically active, co-expressed with PD-1, marks cells with a transcriptional signature of T cell exhaustion and correlates with viral load in HIV and HCV. In the mouse model of chronic Lymphocytic Choriomeningitis Virus infection, virus-specific CD8+ T cells contain a population of CD39high CD8+ T cells that is absent in functional memory cells elicited by acute infection. This CD39high CD8+ T cell population is enriched for cells with the phenotypic and functional profile of terminal exhaustion. These findings provide a new marker of T cell exhaustion, and implicate the purinergic pathway in the regulation of T cell exhaustion. CD8+ T cells from subjects with HCV infection were sorted and pelleted and re-suspended in TRIzol (Invitrogen). RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined with a Nanodrop spectrophotometer or Ribogreen RNA quantification kits (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified with the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer's instructions. After fragmentation and biotinylation, cDNA was hybridized to HG-U133A 2.0 microarrays (Affymetrix).

2015-09-08 | E-GEOD-72752 | biostudies-arrayexpress

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