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

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 immunohis...

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Autores principales: Becht, Etienne, Giraldo, Nicolas A., Lacroix, Laetitia, Buttard, Bénédicte, Elarouci, Nabila, Petitprez, Florent, Selves, Janick, Laurent-Puig, Pierre, Sautès-Fridman, Catherine, Fridman, Wolf H., de Reyniès, Aurélien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073889/
https://www.ncbi.nlm.nih.gov/pubmed/27765066
http://dx.doi.org/10.1186/s13059-016-1070-5
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author Becht, Etienne
Giraldo, Nicolas A.
Lacroix, Laetitia
Buttard, Bénédicte
Elarouci, Nabila
Petitprez, Florent
Selves, Janick
Laurent-Puig, Pierre
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
author_facet Becht, Etienne
Giraldo, Nicolas A.
Lacroix, Laetitia
Buttard, Bénédicte
Elarouci, Nabila
Petitprez, Florent
Selves, Janick
Laurent-Puig, Pierre
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
author_sort Becht, Etienne
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1070-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-50738892016-10-26 Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression Becht, Etienne Giraldo, Nicolas A. Lacroix, Laetitia Buttard, Bénédicte Elarouci, Nabila Petitprez, Florent Selves, Janick Laurent-Puig, Pierre Sautès-Fridman, Catherine Fridman, Wolf H. de Reyniès, Aurélien Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1070-5) contains supplementary material, which is available to authorized users. BioMed Central 2016-10-20 /pmc/articles/PMC5073889/ /pubmed/27765066 http://dx.doi.org/10.1186/s13059-016-1070-5 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Becht, Etienne
Giraldo, Nicolas A.
Lacroix, Laetitia
Buttard, Bénédicte
Elarouci, Nabila
Petitprez, Florent
Selves, Janick
Laurent-Puig, Pierre
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title_full Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title_fullStr Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title_full_unstemmed Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title_short Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
title_sort estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073889/
https://www.ncbi.nlm.nih.gov/pubmed/27765066
http://dx.doi.org/10.1186/s13059-016-1070-5
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