Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
F Finotello, C Mayer, C Plattner, G Laschober… - Genome medicine, 2019 - Springer
Genome medicine, 2019•Springer
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 …
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 …
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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