1. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes.
- Author
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Wang H, Diaz AK, Shaw TI, Li Y, Niu M, Cho JH, Paugh BS, Zhang Y, Sifford J, Bai B, Wu Z, Tan H, Zhou S, Hover LD, Tillman HS, Shirinifard A, Thiagarajan S, Sablauer A, Pagala V, High AA, Wang X, Li C, Baker SJ, and Peng J
- Subjects
- AMP-Activated Protein Kinases metabolism, Animals, Brain Neoplasms metabolism, Disease Models, Animal, Feedback, Physiological, Glioma metabolism, Mice, Mutation, Oncogene Protein p65(gag-jun) metabolism, Phosphopeptides metabolism, Phosphoproteins metabolism, Proto-Oncogene Proteins c-akt metabolism, Proto-Oncogene Proteins c-myc metabolism, Receptor, Platelet-Derived Growth Factor alpha genetics, Receptor, trkA genetics, Signal Transduction, Systems Biology, Up-Regulation, Brain Neoplasms genetics, Gene Expression Profiling, Glioma genetics, Proteomics
- Abstract
High throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome, phosphoproteome and transcriptome in two high-grade glioma (HGG) mouse models driven by mutated RTK oncogenes, PDGFRA and NTRK1, analyzing 13,860 proteins and 30,431 phosphosites by mass spectrometry. Systems biology approaches identify numerous master regulators, including 41 kinases and 23 transcription factors. Pathway activity computation and mouse survival indicate the NTRK1 mutation induces a higher activation of AKT downstream targets including MYC and JUN, drives a positive feedback loop to up-regulate multiple other RTKs, and confers higher oncogenic potency than the PDGFRA mutation. A mini-gRNA library CRISPR-Cas9 validation screening shows 56% of tested master regulators are important for the viability of NTRK-driven HGG cells, including TFs (Myc and Jun) and metabolic kinases (AMPKa1 and AMPKa2), confirming the validity of the multiomics integrative approaches, and providing novel tumor vulnerabilities.
- Published
- 2019
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