articleGenome MedicineMay 24, 2019GOLD OA

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

FFFrancesca FinotelloCMClemens MayerCPChristina PlattnerGLGerhard LaschoberDRDietmar Rieder

Innsbruck Medical University · Universität Innsbruck · +8 more institutions

PubMed
Indexed incrossrefdoajpubmed

Abstract

We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability:…

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Topics & keywords

Topics
Keywords
  • Immune system
  • Flow cytometry
  • Cancer research
  • Biology
  • Cytotoxic T cell
  • Deconvolution
  • Computational biology
  • Immunology
UN Sustainable Development Goals
  • Good health and well-being
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