Computational Deconvolution of Tumor-Infiltrating Immune Components with Bulk Tumor Gene Expression Data

Methods Mol Biol. 2020;2120:249-262. doi: 10.1007/978-1-0716-0327-7_18.

Abstract

Tumor-infiltrating immune cells play critical roles in immune-mediated tumor rejection and/or progression, and are key targets of immunotherapies. Estimation of different immune subsets becomes increasingly important with the decreased cost of high-throughput molecular profiling and the rapidly growing amount of cancer genomics data. Here, we present Tumor IMmune Estimation Resource (TIMER), an in silico deconvolution method for inference of tumor-infiltrating immune components. TIMER takes bulk tissue gene expression profiles measured with RNA-seq or microarray to evaluate the abundance of six immune cell types in the tumor microenvironment: B cell, CD4+ T cell, CD8+ T cell, neutrophil, macrophage, and dendritic cell. We further introduce its associated webserver for convenient, user-friendly analysis of tumor immune infiltrates across multiple cancer types.

Keywords: Cancer immunotherapy; Deconvolution; Infiltrating immune cells; Interactive website; RNA-seq; Tumor immune interaction.

MeSH terms

  • B-Lymphocytes / immunology
  • B-Lymphocytes / metabolism
  • CD4-Positive T-Lymphocytes / immunology
  • CD4-Positive T-Lymphocytes / metabolism
  • CD8-Positive T-Lymphocytes / immunology
  • CD8-Positive T-Lymphocytes / metabolism
  • Computer Simulation
  • Dendritic Cells / immunology*
  • Dendritic Cells / metabolism
  • Gene Expression Profiling / methods*
  • Genomics / methods
  • Humans
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Lymphocytes, Tumor-Infiltrating / metabolism
  • Neoplasms / genetics*
  • Neoplasms / immunology
  • Neutrophils / immunology*
  • Neutrophils / metabolism
  • Software
  • Tumor Microenvironment
  • Tumor-Associated Macrophages / immunology*
  • Tumor-Associated Macrophages / metabolism