Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases

Hudson, A. M. et al. (2018) Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases. Science Signaling, 11(526), eaan6776. (doi: 10.1126/scisignal.aan6776) (PMID:29666306)

Abstract

A major challenge in cancer genomics is identifying “driver” mutations from the many neutral “passenger” mutations within a given tumor. To identify driver mutations that would otherwise be lost within mutational noise, we filtered genomic data by motifs that are critical for kinase activity. In the first step of our screen, we used data from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas to identify kinases with truncation mutations occurring within or before the kinase domain. The top 30 tumor-suppressing kinases were aligned, and hotspots for loss-of-function (LOF) mutations were identified on the basis of amino acid conservation and mutational frequency. The functional consequences of new LOF mutations were biochemically validated, and the top 15 hotspot LOF residues were used in a pan-cancer analysis to define the tumor-suppressing kinome. A ranked list revealed MAP2K7, an essential mediator of the c-Jun N-terminal kinase (JNK) pathway, as a candidate tumor suppressor in gastric cancer, despite its mutational frequency falling within the mutational noise for this cancer type. The majority of mutations in MAP2K7 abolished its catalytic activity, and reactivation of the JNK pathway in gastric cancer cells harboring LOF mutations in MAP2K7 or the downstream kinase JNK suppressed clonogenicity and growth in soft agar, demonstrating the functional relevance of inactivating the JNK pathway in gastric cancer. Together, our data highlight a broadly applicable strategy to identify functional cancer driver mutations and define the JNK pathway as tumor-suppressive in gastric cancer.

• Item Type: Articles
• Additional Information: Funding: This research was fully supported by Cancer Research UK and the National Cancer Institute.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Miller, Professor Crispin

Creator Roles

Miller, C.: Formal analysis

• Authors: Hudson, A. M., Stephenson, N. L., Li, C., Trotter, E., Fletcher, A. J., Katona, G., Bieniasz-Krzywiec, P., Howell, M., Wirth, C., Furney, S., Miller, C. J., and Brognard, J.
• College/School: College of Medical Veterinary and Life Sciences > School of Cancer Sciences
• Journal Name: Science Signaling
• Publisher: American Association for the Advancement of Science
• ISSN: 1945-0877
• ISSN (Online): 1937-9145