期刊
GENOME BIOLOGY
卷 17, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13059-016-1070-5
关键词
Transcriptomic markers; Gene signatures; Deconvolution; Tumor microenvironment
资金
- Institut National de la Sante et de la Recherche Medicale
- University Paris-Descartes
- University Pierre et Marie Curie
- Institut National du Cancer [2011-1-PLBIO-06-INSERM 6-1, PLBIO09-088-IDF-KROEMER]
- CARPEM (CAncer Research for PErsonalized Medicine)
- Labex Immuno-Oncology [LAXE62_9UMS872 FRIDMAN]
- Fondation ARC pour la recherche sur le cancer
- Canceropole Ile-de-France
- Universidad de los Andes School of Medicine
- Colciencias
- CARPEM post-doctorate fellowship
- PPATH doctorate fellowship
We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data. We present in vitro mRNA mixture and ex vivo immunohistochemical data that quantitatively support the validity of our method's estimates. Additionally, we demonstrate that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches. MCP-counter is applied to draw a global picture of immune infiltrates across human healthy tissues and non-hematopoietic human tumors and recapitulates microenvironment-based patient stratifications associated with overall survival in lung adenocarcinoma and colorectal and breast cancer.
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