Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment

Published: 17 November 2023| Version 2 | DOI: 10.17632/2wwjdppm7f.2
Maarten Slagter


RNASeq data accompanying the publication 'Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment' which will be published in the journal Cancer Cell. This repository contains preprocessed/quantified RNASeq data for a range of 'experiments' that we labelled with 4-digit identifiers. There's bulk (directories named exp_5092, exp_5892, exp_7296) and single cell (the remaining directories) RNASeq here. Meta data, in GEO submission/Excel format, describing the exact experimental conditions of each experiment, is included within each of the experiment directories. For the matched raw sequencing data, please see the mirror repository on the GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE220738 Paper abstract Cells in the tumor microenvironment (TME) influence each other through secretion and sensing of soluble mediators, such as cytokines and chemokines. While signaling of interferon γ (IFNγ) and tumor necrosis factor α (TNFα) is integral to anti-tumor immune responses, our understanding of the spatiotemporal behavior of these cytokines is limited. Here, we describe a single cell transcriptome-based approach to infer which signal(s) an individual cell has received. We demonstrate that, contrary to expectations, CD8+ T cell-derived IFNγ is the dominant modifier of the TME relative to TNFα. Furthermore, we demonstrate that cell pools that show abundant IFNγ sensing are characterized by decreased expression of transforming growth factor beta (TGFβ)-induced genes, consistent with IFNγ-mediated TME remodeling. Collectively, these data provide evidence that CD8+ T cell-secreted cytokines should be categorized into local and global tissue modifiers, and describe a broadly applicable approach to dissect cytokine and chemokine modulation of the tumor microenvironment.



Antoni van Leeuwenhoek Nederlands Kanker Instituut, Leids Universitair Medisch Centrum, Technische Universiteit Delft


RNA Sequencing, Single-Cell RNA Sequencing