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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

ABSTRACT: Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

PROVIDER: PRJNA532774 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8893740.fastq.gz	Fastqsanger.gz
	SRR8893740_1.fastq.gz	Fastqsanger.gz
	SRR8893740_2.fastq.gz	Fastqsanger.gz
	SRR8893750.fastq.gz	Fastqsanger.gz
	SRR8893750_1.fastq.gz	Fastqsanger.gz

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Project description:Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development in association with clinical response. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.

Project description:Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

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Project description:CD8+ T cells derived from mice with intact NLRP3 signaling in the tumor microenvironment showed an increased expression of coinhibitory receptors PD-1, TIM-3, 2B4 and LAG-3 compared to CD8+ T cells from PancOVA-bearing Nlrp3-/- mice, indicating that NLRP3 inflammasome activation in the tumor microenvironment mediates IL-18 receptor signaling-induced T cell exhaustion. RNAseq was used to characterised molecular pathways involved in T cell plasticity in the presence and absence of intratumoral NLRP3.

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