Cellular and Molecular Research, National Cancer Centre, Singapore.
Cancer Res. 2011 Jan 1;71(1):29-39. doi: 10.1158/0008-5472.CAN-10-1749. Epub 2010 Nov 19.
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.
激酶的遗传改变与多种人类病理有关。为了探索胃癌（GC）中激酶遗传变异的全景，我们使用靶向、配对末端深度测序分析了 14 种 GC 细胞系中的 532 种蛋白和磷酸肌醇激酶。我们在激酶外显子中鉴定了 10604 个单核苷酸变异（SNV），包括 300 多个新的非同义 SNV。非同义 SNV 的家族分析显示，丝裂原活化蛋白激酶（MAPK）相关基因显著富集（P < 0.01），提示该激酶家族在 GC 中优先参与。MAP2K4 是一个在 2 个细胞系中反复改变的基因，其潜在的抗癌作用得到了 siRNA 敲低和野生型和 MAP2K4 变异系过表达研究的功能支持。深度测序数据还揭示了涉及激酶的新型大规模结构重排事件，包括 CDK12 和 ERBB2 受体酪氨酸激酶在 MKN7 细胞中的基因融合。整合 SNV 和拷贝数改变，我们确定 Hs746T 是一个同时具有剪接位点突变和 MET 基因组扩增的细胞系，导致 MET 蛋白过表达。当应用于原发性 GCs 时，我们在 8 个激酶中鉴定了体细胞突变，其中 4 个在原发性肿瘤和细胞系中都反复改变（MAP3K6、STK31、FER 和 CDKL5）。这些结果表明，靶向深度测序方法如何能够提供对一个医学上和药理学上相关基因家族前所未有的多层次特征描述。这里组装的激酶组遗传变异目录可能拓宽我们对激酶的认识，并为 GC 中的遗传改变提供有用信息。
