By manually mining literature, Kondratova and Czerwinska et al. created an integrated signaling network meta-map of molecular mechanisms involved in the innate immune response in cancer, including cell type-specific maps and signaling pathways, iteratively integrated into functional phenotype modules and biological processes. This online, open-source, analytic platform enables visualization and interpretation of TME activity and evaluation of innate immune response signatures associated with patient survival. Using the maps to interpret scRNAseq data from melanoma revealed expected macrophage and NK cell anti- and pro-tumor subpopulations.
The lack of integrated resources depicting the complexity of the innate immune response in cancer represents a bottleneck for high-throughput data interpretation. To address this challenge, we perform a systematic manual literature mining of molecular mechanisms governing the innate immune response in cancer and represent it as a signalling network map. The cell-type specific signalling maps of macrophages, dendritic cells, myeloid-derived suppressor cells and natural killers are constructed and integrated into a comprehensive meta map of the innate immune response in cancer. The meta-map contains 1466 chemical species as nodes connected by 1084 biochemical reactions, and it is supported by information from 820 articles. The resource helps to interpret single cell RNA-Seq data from macrophages and natural killer cells in metastatic melanoma that reveal different anti- or pro-tumor sub-populations within each cell type. Here, we report a new open source analytic platform that supports data visualisation and interpretation of tumour microenvironment activity in cancer.
Author Info: (1) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. (2) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 7500
Author Info: (1) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. (2) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. Universite Paris Descartes, Centre de Recherches Interdisciplinaires, Paris, France. (3) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. Universite Paris Descartes, Centre de Recherches Interdisciplinaires, Paris, France. (4) Institut Curie, PSL Research University, Inserm, U932, 75005, Paris, France. (5) Institut Curie, PSL Research University, Inserm, U932, 75005, Paris, France. (6) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. (7) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. (8) Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005, Paris, France. inna.kuperstein@curie.fr.
