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

View ORCID ProfileFlorent Petitprez, Sacha Lévy, Cheng-Ming Sun, View ORCID ProfileMaxime Meylan, Christophe Linhard, View ORCID ProfileEtienne Becht, Nabila Elarouci, View ORCID ProfileLubka T. Roumenina, View ORCID ProfileMira Ayadi, View ORCID ProfileCatherine Sautès-Fridman, View ORCID ProfileWolf H. Fridman, View ORCID ProfileAurélien de Reyniès
doi: https://doi.org/10.1101/2020.03.10.985176
Florent Petitprez
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
2Programme Cartes d’Identité des Tumeurs, Ligue Nationale contre le Cancer, F-75013, Paris, France
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  • For correspondence: florent.petitprez@ligue-cancer.net reyniesa@ligue-cancer.net
Sacha Lévy
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Cheng-Ming Sun
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Maxime Meylan
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
2Programme Cartes d’Identité des Tumeurs, Ligue Nationale contre le Cancer, F-75013, Paris, France
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Christophe Linhard
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Etienne Becht
3Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Nabila Elarouci
2Programme Cartes d’Identité des Tumeurs, Ligue Nationale contre le Cancer, F-75013, Paris, France
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Lubka T. Roumenina
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Mira Ayadi
2Programme Cartes d’Identité des Tumeurs, Ligue Nationale contre le Cancer, F-75013, Paris, France
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Catherine Sautès-Fridman
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Wolf H. Fridman
1Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team inflammation, complement and cancer, F-75006, Paris, France
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Aurélien de Reyniès
2Programme Cartes d’Identité des Tumeurs, Ligue Nationale contre le Cancer, F-75013, Paris, France
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  • ORCID record for Aurélien de Reyniès
  • For correspondence: florent.petitprez@ligue-cancer.net reyniesa@ligue-cancer.net
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Abstract

Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases, notably cancer. While numerous methods allow to quantify immune or stromal cells in human tissue samples based on transcriptomic data, very few are available for mouse studies. Here, we introduce murine Microenvironment Cell Population counter (mMCP-counter), a method based on highly specific transcriptomic markers that allow to accurately quantify 12 immune and 4 stromal murine cell populations. We validated mMCP-counter with flow cytometry data. We also showed that mMCP-counter outperforms existing methods. We showed in mouse models of mesothelioma and kidney cancer that mMCP-counter quantification scores are predictive of response to immune checkpoint blockade Finally, we illustrated mMCP-counter’s potential to analyze immune impacts of Alzheimer’s disease. mMCP-counter is available as an R package from GitHub: https://github.com/cit-bioinfo/mMCP-counter.

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Posted March 11, 2020.
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The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Florent Petitprez, Sacha Lévy, Cheng-Ming Sun, Maxime Meylan, Christophe Linhard, Etienne Becht, Nabila Elarouci, Lubka T. Roumenina, Mira Ayadi, Catherine Sautès-Fridman, Wolf H. Fridman, Aurélien de Reyniès
bioRxiv 2020.03.10.985176; doi: https://doi.org/10.1101/2020.03.10.985176
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The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Florent Petitprez, Sacha Lévy, Cheng-Ming Sun, Maxime Meylan, Christophe Linhard, Etienne Becht, Nabila Elarouci, Lubka T. Roumenina, Mira Ayadi, Catherine Sautès-Fridman, Wolf H. Fridman, Aurélien de Reyniès
bioRxiv 2020.03.10.985176; doi: https://doi.org/10.1101/2020.03.10.985176

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