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 (1, 2) , Sacha Levy (1) , Chengming Sun (1) , Maxime Meylan (1, 2) , Christophe Linhard (1) , Etienne Becht (3) , Nabila Elarouci (2) , David Tavel (2) , Lubka T. Roumenina (1) , Mira Ayadi (2) , Catherine Sautes-Fridman (1) , Wolf Herman Fridman (1) , Aurelien de Reynies (2)

1 CRC (UMR_S_1138 / U1138) - Centre de Recherche des Cordeliers
2 CIT - (le programme) Cartes d'identité des tumeurs
3 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]

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.

Mots clés: Immune composition; Heterogeneous tissue; Tumor microenvironment; Immune checkpoint blockade; Alzheimer's disease

Domaines: Sciences du Vivant [q-bio]; Cancer

Florent Petitprez, Sacha Levy, Chengming Sun, Maxime Meylan, Christophe Linhard, et al.. The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Genome Medicine, 2020, 12 (1), ⟨10.1186/s13073-020-00783-w⟩. ⟨hal-02975516⟩