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

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.