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Genome Biol. 2016 Oct 20;17(1):218.

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.

Author information

1
INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.
2
Université Paris Descartes, Paris, France.
3
Université Pierre et Marie Curie, Paris, France.
4
Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.
5
Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM, Université Toulouse III, Toulouse, France.
6
Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France.
7
INSERM, UMR_S1147, Paris, France.
8
Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France. aurelien.DeReynies@ligue-cancer.net.

Abstract

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.

KEYWORDS:

Deconvolution; Gene signatures; Transcriptomic markers; Tumor microenvironment

PMID:
27765066
PMCID:
PMC5073889
DOI:
10.1186/s13059-016-1070-5
[Indexed for MEDLINE]
Free PMC Article

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