Distribution and pathogenicity of nsSNPs in receptor tyrosine kinases (RTKs) in patients with colorectal cancer.

Abstract

e15012 Background: Non-synonymous single nucleotide polymorphisms (nsSNPs) occur along the entire sequence of RTKs and can promote oncogenic activity. As prior “hot-spot” testing was limited to the tyrosine kinase domain (TKD), next-generation sequencing (NGS) allows the discovery of novel extra-TKD variants. Methods: We analyzed all nsSNPs in 29 RTKs of colon cancer patients (pts) who received tumor profiling (2013-2015) with Caris NGS. Mutations were classified by location including the TKD, extracellular domain (ECD), transmembrane domain (TM), juxtamembrane domain (JM) and carboxy-terminal (CT) regions. nsSNPs underwent in silico analysis using PolyPhen-2 (Harvard) to predict if damaging (pnsSNP). Results: 110 pts were identified with a median age of 58 years (range 37-86); 55% male; 57% white, 41% black. 51 were KRAS+, 12 BRAF+, 5 NRAS+ and 5 were microsatellite unstable (MSI-H); 67 were left-sided, 31 right-sided, 10 transverse and 2 unknown. A total of 171 nsSNPs and 7 pathogenic mutations (Pmut) were detected: ERBB2 (ECD S310F, TKD V777L and TKD V842I), ERBB3 (ECD A232V and TKD Q809R), FGFR2 (ECD S252L) and RET (TKD L790F). 83/110 (76%) pts had ≥1 RTK mutation (median 1; range 0-9). 72/171 (42%) variants were pnsSNPs and found in 50 (45%) pts; 14% of pts had ≥2. All 29 RTKs had nsSNPs with median 6 (range 2-12); 24/29 RTKs had a Pmut or pnsSNP (median 2; range 0-8). RTKs with the most nsSNPs were EPHA5 (8/10 were pnsSNPs), PDGFA (7/8), ALK (6/8), ERBB4 (5/8), NTRK3 (5/6), cKIT (4/9), ROS1 (3/12), PDGFRB (3/6) and FGFR1 (3/6). nsSNPs were distributed across all RTK domains: 50% were ECD (30/86 pnsSNPs), 27% TKD (28/46), 13% CT (7/22), 5% JM (6/9) and 5% TM (1/8). No significant difference was seen between pnsSNP incidence and sidedness or KRAS/BRAF/NRAS status. In MSI-H pts, 13/22 variants were pnsSNPs (median 2; 1-5); 4/5 MSI-H were right-sided (Fisher’s exact p < 0.01). Conclusions: > 70% colon cancer pts had ≥1 mutation in 29 RTKs with > 70% outside the TKD, and > 40% pnsSNPs. MSI-H had a higher incidence of pnsSNPs; further study is warranted to determine their significance and actionability.