Simultaneous Enumeration of Cancer and Immune Cell Types from Bulk Tumor Gene Expression Data

Overview

Journal Elife

Specialty Biology

Date 2017 Nov 14

PMID 29130882

Citations 696

Authors

Julien Racle

Kaat de Jonge

Petra Baumgaertner

Daniel E Speiser

David Gfeller

Affiliations

Soon will be listed here.

Abstract

Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).

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