title: Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.
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 stratifications associated with overall survival in lung adenocarcinoma and colorectal and breast cancer.
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.|Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.
authors.forename: Etienne
authors.initials: E
authors.lastname: Becht
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.
authors.forename: Nicolas A
authors.initials: NA
authors.lastname: Giraldo
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.
authors.forename: Laetitia
authors.initials: L
authors.lastname: Lacroix
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.
authors.forename: Bénédicte
authors.initials: B
authors.lastname: Buttard
authors.affiliation: Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.
authors.forename: Nabila
authors.initials: N
authors.lastname: Elarouci
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.|Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Petitprez
authors.affiliation: Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM, Université Toulouse III, Toulouse, France.|Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France.
authors.forename: Janick
authors.initials: J
authors.lastname: Selves
authors.affiliation: INSERM, UMR_S1147, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Laurent-Puig
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Sautès-Fridman
authors.affiliation: INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.|Université Paris Descartes, Paris, France.|Université Pierre et Marie Curie, Paris, France.
authors.forename: Wolf H
authors.initials: WH
authors.lastname: Fridman
authors.affiliation: Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France. aurelien.DeReynies@ligue-cancer.net.
authors.forename: Aurélien
authors.initials: A
authors.lastname: de Reyniès
mesh_terms: D000230:Adenocarcinoma / Q000276:immunology / Q000473:pathology; D000077192:Adenocarcinoma of Lung; D014408:Biomarkers, Tumor; D001943:Breast Neoplasms / Q000276:immunology / Q000473:pathology; D058948:Cell Tracking / Q000379:methods*; D015179:Colorectal Neoplasms / Q000276:immunology / Q000473:pathology; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008175:Lung Neoplasms / Q000276:immunology / Q000473:pathology; D012333:RNA, Messenger / Q000096:biosynthesis; D017154:Stromal Cells / Q000276:immunology / Q000473:pathology*; D059467:Transcriptome / Q000235:genetics; D059016:Tumor Microenvironment / Q000235:genetics* / Q000276:immunology
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger
keywords: Deconvolution; Gene signatures; Transcriptomic markers; Tumor microenvironment