The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression

Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from transcriptomic data, few are available for mouse studies. We introduce murine Microenvironm...

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Autores principales: Petitprez, Florent, Levy, Sacha, Sun, Cheng-Ming, Meylan, Maxime, Linhard, Christophe, Becht, Etienne, Elarouci, Nabila, Tavel, David, Roumenina, Lubka T., Ayadi, Mira, Sautès-Fridman, Catherine, Fridman, Wolf H., de Reyniès, Aurélien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541325/
https://www.ncbi.nlm.nih.gov/pubmed/33023656
http://dx.doi.org/10.1186/s13073-020-00783-w
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author Petitprez, Florent
Levy, Sacha
Sun, Cheng-Ming
Meylan, Maxime
Linhard, Christophe
Becht, Etienne
Elarouci, Nabila
Tavel, David
Roumenina, Lubka T.
Ayadi, Mira
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
author_facet Petitprez, Florent
Levy, Sacha
Sun, Cheng-Ming
Meylan, Maxime
Linhard, Christophe
Becht, Etienne
Elarouci, Nabila
Tavel, David
Roumenina, Lubka T.
Ayadi, Mira
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
author_sort Petitprez, Florent
collection PubMed
description Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from transcriptomic data, few are available for mouse studies. We introduce murine Microenvironment Cell Population counter (mMCP-counter), a method based on highly specific transcriptomic markers that accurately quantify 16 immune and stromal murine cell populations. We validated mMCP-counter with flow cytometry data and showed that mMCP-counter outperforms existing methods. We showed that mMCP-counter scores are predictive of response to immune checkpoint blockade in cancer mouse models and identify early immune impacts of Alzheimer’s disease.
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spelling pubmed-75413252020-10-08 The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression Petitprez, Florent Levy, Sacha Sun, Cheng-Ming Meylan, Maxime Linhard, Christophe Becht, Etienne Elarouci, Nabila Tavel, David Roumenina, Lubka T. Ayadi, Mira Sautès-Fridman, Catherine Fridman, Wolf H. de Reyniès, Aurélien Genome Med Method Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases. While numerous methods can quantify immune or stromal cells in human tissue samples from transcriptomic data, few are available for mouse studies. We introduce murine Microenvironment Cell Population counter (mMCP-counter), a method based on highly specific transcriptomic markers that accurately quantify 16 immune and stromal murine cell populations. We validated mMCP-counter with flow cytometry data and showed that mMCP-counter outperforms existing methods. We showed that mMCP-counter scores are predictive of response to immune checkpoint blockade in cancer mouse models and identify early immune impacts of Alzheimer’s disease. BioMed Central 2020-10-06 /pmc/articles/PMC7541325/ /pubmed/33023656 http://dx.doi.org/10.1186/s13073-020-00783-w Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
spellingShingle Method
Petitprez, Florent
Levy, Sacha
Sun, Cheng-Ming
Meylan, Maxime
Linhard, Christophe
Becht, Etienne
Elarouci, Nabila
Tavel, David
Roumenina, Lubka T.
Ayadi, Mira
Sautès-Fridman, Catherine
Fridman, Wolf H.
de Reyniès, Aurélien
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title_full The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title_fullStr The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title_full_unstemmed The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title_short The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
title_sort murine microenvironment cell population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541325/
https://www.ncbi.nlm.nih.gov/pubmed/33023656
http://dx.doi.org/10.1186/s13073-020-00783-w
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