title: 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.
authors.affiliation: Cellular and Molecular Research, National Cancer Centre, Singapore.
authors.forename: Zhi Jiang
authors.initials: ZJ
authors.lastname: Zang
authors.forename: Choon Kiat
authors.initials: CK
authors.lastname: Ong
authors.forename: Ioana
authors.initials: I
authors.lastname: Cutcutache
authors.forename: Willie
authors.initials: W
authors.lastname: Yu
authors.forename: Shen Li
authors.initials: SL
authors.lastname: Zhang
authors.forename: Dachuan
authors.initials: D
authors.lastname: Huang
authors.forename: Lian Dee
authors.initials: LD
authors.lastname: Ler
authors.forename: Karl
authors.initials: K
authors.lastname: Dykema
authors.forename: Anna
authors.initials: A
authors.lastname: Gan
authors.forename: Jiong
authors.initials: J
authors.lastname: Tao
authors.forename: Siyu
authors.initials: S
authors.lastname: Lim
authors.forename: Yujing
authors.initials: Y
authors.lastname: Liu
authors.forename: P Andrew
authors.initials: PA
authors.lastname: Futreal
authors.forename: Heike
authors.initials: H
authors.lastname: Grabsch
authors.forename: Kyle A
authors.initials: KA
authors.lastname: Furge
authors.forename: Liang Kee
authors.initials: LK
authors.lastname: Goh
authors.forename: Steve
authors.initials: S
authors.lastname: Rozen
authors.forename: Bin Tean
authors.initials: BT
authors.lastname: Teh
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
mesh_terms: D000595:Amino Acid Sequence; D045744:Cell Line, Tumor; D018628:Gene Dosage; D014644:Genetic Variation; D006801:Humans; D020935:MAP Kinase Signaling System / Q000235:genetics; D008969:Molecular Sequence Data; D011494:Protein Kinases / Q000737:chemistry / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction; D013274:Stomach Neoplasms / Q000201:enzymology / Q000235:genetics* / Q000473:pathology
chemical_list: D011494:Protein Kinases