Genetic and Structural Variation in the Gastric Cancer Kinome Revealed through Targeted Deep Sequencing

Abstract

Genetic alterations in kinases have been linked to multiple human pathologies. To explore the landscape of kinase genetic variation in gastric cancer (GC), we used targeted, paired-end deep sequencing to analyze 532 protein and phosphoinositide kinases in 14 GC cell lines. We identified 10,604 single-nucleotide variants (SNV) in kinase exons including greater than 300 novel nonsynonymous SNVs. Family-wise analysis of the nonsynonymous SNVs revealed a significant enrichment in mitogen-activated protein kinase (MAPK)-related genes (P < 0.01), suggesting a preferential involvement of this kinase family in GC. A potential antioncogenic role for MAP2K4, a gene exhibiting recurrent alterations in 2 lines, was functionally supported by siRNA knockdown and overexpression studies in wild-type and MAP2K4 variant lines. The deep sequencing data also revealed novel, large-scale structural rearrangement events involving kinases including gene fusions involving CDK12 and the ERBB2 receptor tyrosine kinase in MKN7 cells. Integrating SNVs and copy number alterations, we identified Hs746T as a cell line exhibiting both splice-site mutations and genomic amplification of MET, resulting in MET protein overexpression. When applied to primary GCs, we identified somatic mutations in 8 kinases, 4 of which were recurrently altered in both primary tumors and cell lines (MAP3K6, STK31, FER, and CDKL5). These results demonstrate that how targeted deep sequencing approaches can deliver unprecedented multilevel characterization of a medically and pharmacologically relevant gene family. The catalog of kinome genetic variants assembled here may broaden our knowledge on kinases and provide useful information on genetic alterations in GC. Cancer Res; 71(1); 29-39. Ó2010 AACR.

STK31(TDRD8) is dynamically regulated throughout mouse spermatogenesis and interacts with MIWI protein

“…Interestingly, recent evidence showed that STK31 was also found to be expressed abundantly in colorectal cancer and gastric and esophageal cancer, and thus suggested to be a novel cancer/testis (CT) antigen (Yokoe et al 2008;Zang et al 2011), indicating the acquisition of a gametogenic program in cancer involved in tumorigenesis. It is also noticeable that we did not explore the expression of STK31 during mice prenatal development.…”

MET exon 14 juxtamembrane splicing mutations: clinical and therapeutical perspectives for cancer therapy

“…In the preclinical analysis included in the study, the growth of two patientderived tumor cell lines harboring MET exon 14 deletion (one from gastric and one from colon cancer) were strongly inhibited by both Met TKI and an anti-Met monoclonal antibody (29). Furthermore, two independent preclinical studies reported the presence of MET exon 14 deletion in gastric cancer cell lines (58,59). In particular, a genomewide analysis of 34 gastric cancer cell lines showed that only one cell line (Hs746T) has a splice site mutation of MET exon 14, concurrent with MET amplification and protein overexpression (58).…”

Mutations leading to constitutive active gp130/JAK1/STAT3 pathway

“…Mutations of the Src-like kinase Brk (breast tumor kinase) have been identified at low frequency in different cancers as clear cell renal cell carcinoma [90], gastric cancer [91], head and neck squamous cell carcinoma [92], cutaneous squamous cell carcinoma [93] and pancreatic cancer [94]. The L16F mutant, situated in the SH3 domain, the R131L mutant, located in the SH2 domain, the L343F mutants in the kinase domain and the P450L mutant, located adjacent to the inhibitory tyrosine residue at the C-terminal tail of Brk, have been shown to be able to constitutively activate Brk [95].…”