Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma

• Type of Material: Article
• Authors: Yu-Hsiu T. Lin, University of California San Francisco; Gregory P. Way, University of Pennsylvania; Benjamin G. Barwick, Emory University; Margarette C. Mariano, University of California San Francisco; Makeba Marcoulis, University of California San Francisco; Ian D. Ferguson, University of California San Francisco; Christoph Driessen, Kantonsspital St. Gallen; Lawrence Boise, Emory University; Casey S. Greene, University of Pennsylvania; Arun P. Wiita, University of California San Francisco
• Language: English
• Date: 2019-11-12
• Publisher: AMER SOC HEMATOLOGY
• Publication Version: Final Published Version
• Copyright Statement: © 2019 by The American Society of Hematology
• Final Published Version (URL): http://dx.doi.org/10.1182/bloodadvances.2019000303
• Title of Journal or Parent Work: BLOOD ADVANCES
• Volume: 3
• Issue: 21
• Start Page: 3214
• End Page: 3227
• Grant/Funding Information: This work was supported by the Damon Runyon Cancer Research Foundation Dale Frey Breakthrough Award (DFS 14-15), the National Institutes of Health (National Cancer Institute grants K08CA184116 and R01CA226851; and National Institute of General Medical Sciences grant DP2OD022552), and the UCSF Stephen and Nancy Grand Multiple Myeloma Translational Initiative (A.P.W.); the MMRF Answer Fund and the National Institutes of Health (National Cancer Institute grant P30 CA138292) (L.H.B.); and American Cancer Society postdoctoral fellowship PF-17-109-1-TBG (B.G.B.). G.P.W. was supported in part by a training grant from the National Institutes of Health (National Human Genome Research Institute grant T32 HG000046). This work was funded in part by a grant from the Gordon and Betty Moore Foundation (GBMF 4552) (C.S.G.).
• Keywords: CELL-LINE; ACTIVATING MUTATIONS; Life Sciences & Biomedicine; SENSITIVITY; PROGRESSION; Science & Technology; DEPENDENCIES; N-RAS; INHIBITOR; DRIVERS; Hematology; NRAS; K-RAS
• Research Categories: Health Sciences, Rehabilitation and Therapy; Biology, Cell; Biology, Genetics; Health Sciences, Oncology

Abstract

A major driver of multiple myeloma (MM) is thought to be aberrant signaling, yet no kinase inhibitors have proven successful in the clinic. Here, we employed an integrated, systems approach combining phosphoproteomic and transcriptome analysis to dissect cellular signaling in MM to inform precision medicine strategies. Unbiased phosphoproteomics initially revealed differential activation of kinases across MM cell lines and that sensitivity to mammalian target of rapamycin (mTOR) inhibition may be particularly dependent on mTOR kinase baseline activity. We further noted differential activity of immediate downstream effectors of Ras as a function of cell line genotype. We extended these observations to patient transcriptome data in the Multiple Myeloma Research Foundation CoMMpass study. A machine-learning–based classifier identified surprisingly divergent transcriptional outputs between NRAS- and KRAS-mutated tumors. Genetic dependency and gene expression analysis revealed mutated Ras as a selective vulnerability, but not other MAPK pathway genes. Transcriptional analysis further suggested that aberrant MAPK pathway activation is only present in a fraction of RAS-mutated vs wild-type RAS patients. These high-MAPK patients, enriched for NRAS Q61 mutations, have inferior outcomes, whereas RAS mutations overall carry no survival impact. We further developed an interactive software tool to relate pharmacologic and genetic kinase dependencies in myeloma. Collectively, these predictive models identify vulnerable signaling signatures and highlight surprising differences in functional signaling patterns between NRAS and KRAS mutants invisible to the genomic landscape. These results will lead to improved stratification of MM patients in precision medicine trials while also revealing unexplored modes of Ras biology in MM.