Molecular and Pharmacological Modulators of the Tumor Immune Contexture Revealed by Deconvolution of RNA-seq Data

Overview

Journal Genome Med

Publisher Biomed Central

Specialty Genetics

Date 2019 May 26

PMID 31126321

Citations 735

Authors

Francesca Finotello

Clemens Mayer

Christina Plattner

Gerhard Laschober

Dietmar Rieder

Hubert Hackl

Anne Krogsdam

Zuzana Loncova

Wilfried Posch

Doris Wilflingseder

Sieghart Sopper

Marieke Ijsselsteijn

Thomas P Brouwer

Douglas Johnson

Yaomin Xu

Yu Wang

Melinda E Sanders

Monica V Estrada

Paula Ericsson-Gonzalez

Pornpimol Charoentong

Justin Balko

Noel Filipe da Cunha Carvalho de Miranda

Zlatko Trajanoski

Affiliations

Soon will be listed here.

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: quanTIseq is available at http://icbi.at/quantiseq .

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