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Updated: Mar 13, 2026
Predictive Immune Modeling of Solid Tumors
Published on: February 25, 2020
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Etienne Becht1,2,3,4, Nicolas A Giraldo1,2,3, Laetitia Lacroix1,2,3
1INSERM UMR_S 1138, Cancer, Immune Control and Escape, Cordeliers Research Centre, Paris, France.
Insights
We developed Microenvironment Cell Populations-counter (MCP-counter) to quantify immune and stromal cells from gene expression data. This method accurately estimates cell abundance and improves upon existing computational approaches for cancer research.
Area of Science:
- Bioinformatics
- Immunology
- Computational Biology
Background:
- Accurate quantification of immune and stromal cells in tumor microenvironments is crucial for understanding cancer progression and treatment response.
- Existing computational methods for estimating cell populations from transcriptomic data have limitations.
Purpose of the Study:
- To introduce and validate the Microenvironment Cell Populations-counter (MCP-counter) method for robustly quantifying cell populations from transcriptomic data.
- To compare MCP-counter with existing computational approaches and highlight its advantages.
Main Methods:
- Development of the MCP-counter algorithm utilizing transcriptomic data.
- Validation using in vitro mRNA mixtures and ex vivo immunohistochemical data.
- Application to analyze immune infiltrates in human healthy tissues and tumors.
Main Results:
- MCP-counter accurately quantifies eight immune and two stromal cell populations.
- The method demonstrates superior performance compared to previous computational approaches.
- Analysis of human tissues revealed distinct immune infiltration patterns in tumors and recapitulated survival-associated patient stratifications.
Conclusions:
- MCP-counter provides a robust and validated method for estimating cell populations from transcriptomic data.
- The tool offers valuable insights into the tumor microenvironment and its impact on patient survival.
- MCP-counter facilitates large-scale analysis of immune infiltrates across diverse human tissues and cancers.
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.
