CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive phosphoproteomics and proteomics data for tumor and tumor-adjacent normal tissue across multiple cancer types. This dataset provides an unprecedented opportunity to systematically characterize pan-cancer kinase activities, which is essential for coupling tumor subtypes with kinase inhibitors as potential treatment. In this work, we performed Kinase Enrichment Analysis (KEA) using a CPTAC phosphoproteomics dataset to identify putative differences in kinase state between tumor and normal tissues within and across five types of cancer. We then implemented an interactive web-portal, the ProTrack Kinase Activity Portal (ProKAP), for querying, visualizing, and downloading the derived pan-cancer kinase activity scores together with the corresponding sample metadata, and protein and phosphoprotein expression profiles. To illustrate the usage of this digital resource, we analyzed the association between kinase activity scores and immune subtypes of clear cell renal cell carcinoma (ccRCC) derived from the CPTAC ccRCC study. We found multiple kinases, whose inhibition has been suggested to have therapeutic effect in other tumor types, are highly active in CD8+-enriched ccRCC tumors. The ProTrack Kinase Activity Portal (ProKAP) is available at: https://pancan-kea3.cptac-data-view.org.