Abstract
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.
Highlights
The activity of Phagocytosis and Exocytosis module is not significantly different between the two groups, this module is rather activated in the NK Group 1 compared to the NK Group 2 (Supplementary Fig. 6B). These results demonstrate that the NK Group 1 is characterized by upregulation of biological functions related to NK cell recruitment and activation, coinciding with upregulation of the mechanisms responsible for tumor killing
The attempt to modulate the interactions within the tumor microenvironment lies on the basis of new anticancer immune checkpoint inhibition therapy
Our first goal was to preserve the natural multidimensionality of the biological knowledge available for the different cell types in the innate component of the tumor microenvironment (TME)
Summary
The most stable component was used as a way to order the cells based on some latent process that we aim to interpret using innate immune maps
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