Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK.
Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK.
Sci Signal. 2018 Apr 17;11(526):eaan6776. doi: 10.1126/scisignal.aan6776.
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.
癌症基因组学的一个主要挑战是从给定肿瘤中的许多中性“乘客”突变中识别“驱动”突变。为了识别否则会在突变噪声中丢失的驱动突变，我们通过对激酶活性至关重要的基序来过滤基因组数据。在我们筛选的第一步中，我们使用来自癌症细胞系百科全书和癌症基因组图谱的数据来识别在激酶结构域内或之前发生截断突变的激酶。对前 30 种肿瘤抑制激酶进行了比对，并根据氨基酸保守性和突变频率确定了功能丧失（LOF）突变的热点。新的 LOF 突变的功能后果通过生化验证得到证实，并用 LOF 热点残基的前 15 位在泛癌分析中定义肿瘤抑制激酶组。排名列表显示 MAP2K7（JNK 通路的重要介质）是胃癌的候选肿瘤抑制剂，尽管其突变频率在这种癌症类型的突变噪声范围内。MAP2K7 的大多数突变使其催化活性丧失，并且在 MAP2K7 或下游激酶 JNK 中存在 LOF 突变的胃癌细胞中重新激活 JNK 通路抑制集落形成和软琼脂中的生长，证明了在胃癌中失活 JNK 通路的功能相关性。总之，我们的数据突出了一种广泛适用的策略，可以识别功能性癌症驱动突变，并将 JNK 途径定义为胃癌中的肿瘤抑制途径。
