MCP-counter, a software tool allowing to assess the abundance of microenvironment cell populations using gene expresssion

Developed through a collaboration between the CIT team and Pr Hervé Fridman’s lab, MCP-counter software allows, given a transcriptome profile, to robustly measure the abundance of 10 microenvironment cellular populations (T cells, T CD8 cells, NK cells, cytotoxic lymphocytes, B lineage, monocytic lineage, myeloid dendritic cells, neutrophils, endothelial cells, fibroblasts). The authors illustrate the interest of using MCP-counter to study the tumoral microenvironement. By analyzing around 20.000 tumor transcriptomes related to 32 cancer types, they show that MCP-counter faithfully reproduces what is described in the literature concerning these various types of microenvironment populations and their prognostic value. They also show that classifying tumors according to the abundance of these 10 populations allows  identifying classes with distinct prognosis. This work has been accepted for publication in Genome Biology (Becht et al. Genome Biology 2016). Using MCP-counter, these authors had previously shown (Becht et al. Clin. Cancer Res. 2016) that in colorectal cancer the information obtained on these 10 microenvironment cell populations was of great interest to guide the choice of immunotherapies .InfoDuJour_201601_MCPcounter_AdR_en