Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

Effective therapies for pancreatic ductal adenocarcinoma (PDAC) have been largely elusive. Prior proteogenomic studies of PDAC have been limited to bulk samples limiting the ability to define tumor-intrinsic targets and understanding tumor heterogeneity. Here, we perform Multiplexed kinase Inhibitor Beads and Mass Spectrometry (MIB-MS) on 102 patient derived xenografts (PDX) derived from 14 unique primary PDAC to define the tumor-intrinsic kinome landscape. Our findings uncover three kinome subgroups making up two dominant tumor-intrinsic kinome subtypes that we call kinotypes. The kinotypes show enrichment of different kinase classes and explain the biological differences in previously described molecular subtypes, basal-like and classical. The kinotype characterizing basal-like tumors shows enrichment of receptor tyrosine kinases, whereas the kinotype characterizing classical tumors is enriched in understudied kinases involved in Wnt signaling and immune pathways. We validate our findings in two clinical trials and show that only patients with basal-like kinotype tumors, who are thought to be refractory to chemotherapy, derive significant benefit from EGFR inhibitors. Our results provide a comprehensive tumor-intrinsic kinome landscape of PDAC that strongly supports actionable kinotype specific kinase targets, potential for sensitive quantitation of patient samples, and provides a roadmap for the use of kinase inhibitors for the treatment of PDAC. RNAseq of 13 Pancreatic ductal adenocarcinoma (PDAC) tumor lines from PDX models with replicates for each sample Raw FASTQ files are not uploaded because the samples are from human patients and there is a concern of patient-privacy.