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Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell RNA-seq of human breast tumor samples with exhausted and non-exhausted immune environments

ABSTRACT: Fresh human breast tumor tissue was dissociated into single cells and viably frozen. Patient samples were annotated as having an ""exhausted"" or ""non-exhausted"" immune environment based on CyTOF characterization of T cell phenotypes (Wagner et al, Cell 2019). 14 samples (7 exhausted, 7 non-exhausted) were selected for scRNA-seq (without prior cell type enrichment) with the goal to compare the two immune environment types and to comprehensively characterize exhaustion-associated features of the tumor microenvironment.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Sandra Tietscher

PROVIDER: E-MTAB-10607 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cancer-associated fibroblast classification in single-cell and spatial proteomics data.

Cords Lena L Tietscher Sandra S Anzeneder Tobias T Langwieder Claus C Rees Martin M de Souza Natalie N Bodenmiller Bernd B

Nature communications 20230718 1

Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour microenvironment, where they have critical effects on tumour evolution and patient prognosis. To define CAF phenotypes, we analyse a single-cell RNA sequencing (scRNA-seq) dataset of over 16,000 stromal cells from tumours of 14 breast cancer patients, based on which we define and functionally annotate nine CAF phenotypes and one class of pericytes. We validate this classification system in four additional cancer ...[more]

PMID: 37463917

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