Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.

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State: Public
Version: Final published version
Serval ID
serval:BIB_D4CC1AFA4588
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Journal
eLife
Author(s)
Racle J., de Jonge K., Baumgaertner P., Speiser D.E., Gfeller D.
ISSN
2050-084X (Electronic)
ISSN-L
2050-084X
Publication state
Published
Issued date
13/11/2017
Peer-reviewed
Oui
Volume
6
Pages
1-25
Language
english
Notes
Publication types: Journal Article ; Validation Studies ; Research Support, Non-U.S. Gov't
Publication Status: epublish
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).
Keywords
Cell Count/methods, Colorectal Neoplasms/pathology, Flow Cytometry, Gene Expression Profiling/methods, Humans, Immunohistochemistry, Melanoma/pathology, Pathology, Molecular/methods, Sequence Analysis, RNA, cancer biology, cell fraction predictions, computational biology, gene expression, human, systems biology, tumor immune microenvironment
Pubmed
Web of science
Open Access
Yes
Create date
16/11/2017 21:44
Last modification date
20/08/2019 15:54
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