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 Med. 2020 Oct 6;12(1):86. doi: 10.1186/s13073-020-00783-w.

Abstract

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.

Keywords: Alzheimer’s disease; Heterogeneous tissue; Immune checkpoint blockade; Immune composition; Tumor microenvironment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alzheimer Disease / etiology
  • Alzheimer Disease / metabolism
  • Alzheimer Disease / pathology
  • Animals
  • Biomarkers
  • Cellular Microenvironment / drug effects
  • Cellular Microenvironment / genetics*
  • Cellular Microenvironment / immunology
  • Computational Biology / methods
  • Databases, Genetic
  • Female
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Immune Checkpoint Inhibitors / pharmacology
  • Immune Checkpoint Proteins / metabolism
  • Leukocytes / drug effects
  • Leukocytes / immunology
  • Leukocytes / metabolism*
  • Mice
  • ROC Curve
  • Single-Cell Analysis
  • Stromal Cells / drug effects
  • Stromal Cells / metabolism*
  • Stromal Cells / pathology
  • Transcriptome*

Substances

  • Biomarkers
  • Immune Checkpoint Inhibitors
  • Immune Checkpoint Proteins