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

被引：2696

作者：

Becht, Etienne ^{[1
,2
,3
,4
]}

Giraldo, Nicolas A. ^{[1
,2
,3
]}

Lacroix, Laetitia ^{[1
,2
,3
]}

Buttard, Benedicte ^{[1
,2
,3
]}

Elarouci, Nabila ^{[4
]}

Petitprez, Florent ^{[1
,2
,3
,4
]}

Selves, Janick ^{[5
,6
]}

Laurent-Puig, Pierre ^{[7
]}

Sautes-Fridman, Catherine ^{[1
,2
,3
]}

Fridman, Wolf H. ^{[1
,2
,3
]}

de Reynies, Aurelien ^{[4
]}

机构：

[1] INSERM UMR S 1138, Canc Immune Control & Escape, Cordeliers Res Ctr, Paris, France

[2] Univ Paris 05, Paris, France

[3] Univ Paris 06, Paris, France

[4] Ligue Natl Canc, Programme Cartes Identite Tumeurs, Paris, France

[5] Univ Toulouse 3, Ctr Rech Cancerol Toulouse, UMR 1037, INSERM, Toulouse, France

[6] Ctr Hosp Univ Toulouse, Dept Pathol, Toulouse, France

[7] INSERM, UMR S1147, Paris, France

来源：

GENOME BIOLOGY | 2016年 / 17卷

关键词：

Transcriptomic markers; Gene signatures; Deconvolution; Tumor microenvironment; TERTIARY LYMPHOID STRUCTURES; CONTEXTURE; DECONVOLUTION; LANDSCAPE;

D O I：

10.1186/s13059-016-1070-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

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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