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

Becht, Étienne; Giraldo, Nicolás A.; Lacroix, Laetitia; Buttard, Bénédicte; Elarouci, Nabila; Petitprez, Florent; Sèlves, Janick; Laurent‐Puig, Pierre; Sautès‐Fridman, Catherine; Fridman, Wolf H.; Reyniès, Aurélien de

doi:10.1186/s13059-016-1070-5

articleGenome biologyOct 20, 2016GOLD OA

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

ÉBÉtienne Becht NANicolás A. Giraldo LLLaetitia Lacroix BBBénédicte Buttard NENabila Elarouci

Délégation Paris 5 · Université Paris Cité · +7 more institutions

PubMed

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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…

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Topics

Keywords

Biology
Stromal cell
Immune system
Tumor microenvironment
Population
Transcriptome
Adenocarcinoma
Gene expression

UN Sustainable Development Goals

Good health and well-being

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