Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Top Cited Papers
Open Access
- 20 October 2016
- journal article
- method
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 17 (1), 1-20
- https://doi.org/10.1186/s13059-016-1070-5
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.Keywords
Funding Information
- Inserm
- Université Paris Descartes
- Université Pierre et Marie Curie
- CARPEM
- Labex Immuno-Oncology (LAXE62_9UMS872 FRIDMAN)
- Fondation ARC pour la Recherche sur le Cancer (FR)
- Cancéropôle Ile-de-France
- Institut National Du Cancer (FR) (2011-1-PLBIO-06-INSERM 6-1,PLBIO09-088-IDF-KROEMER)
- Universidad de los Andes School of Medicine
- Colciencias
- Ecole doctorale Physiologie, physiopathologie et thérapeutique
This publication has 27 references indexed in Scilit:
- Landscape of tumor-infiltrating T cell repertoire of human cancersNature Genetics, 2016
- Immune Contexture, Immunoscore, and Malignant Cell Molecular Subgroups for Prognostic and Theranostic Classifications of CancersAdvances in Immunology, 2016
- Dendritic Cells in Tumor-Associated Tertiary Lymphoid Structures Signal a Th1 Cytotoxic Immune Contexture and License the Positive Prognostic Value of Infiltrating CD8+ T CellsCancer Research, 2014
- Inferring tumour purity and stromal and immune cell admixture from expression dataNature Communications, 2013
- DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq dataBioinformatics, 2013
- Leukocyte Complexity Predicts Breast Cancer Survival and Functionally Regulates Response to ChemotherapyCancer Discovery, 2011
- Frozen robust multiarray analysis (fRMA)Biostatistics, 2010
- A New Perspective on Transcriptional System Regulation (TSR): Towards TSR ProfilingPLOS ONE, 2008
- Effector Memory T Cells, Early Metastasis, and Survival in Colorectal CancerThe New England Journal of Medicine, 2005
- Culture of Human Endothelial Cells Derived from Umbilical Veins. IDENTIFICATION BY MORPHOLOGIC AND IMMUNOLOGIC CRITERIAJCI Insight, 1973