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内的许多中性“乘客”突变中识别“驱动”突变。为了识别可能在突变噪音中丢失的驱动突变，我们通过对激酶活性至关重要的基序过滤了基因组数据。在筛选的第一步中，我们使用来自癌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短突变的激酶。对排名前 30 的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 LOF 突变的功能后果经过生化验证，前 15 个热点 LOF 残基用于泛癌分析，以定义肿瘤抑制激酶组。一份排名列表显示，c-Jun N 末端激酶 (JNK) 通路的重要介质 MAP2K7 作为胃癌的候选肿瘤抑制因子，尽管其突变频率落在该癌症类型的突变噪声范围内。 MAP2K7 的大多数突变消除了其催化活性，并且在 MAP2K7 或下游激酶 JNK 中含有 LOF 突变的胃癌细胞中，JNK 通路的重新激活抑制了软琼脂中的克隆形成和生长，这证明了胃中 JNK 通路失活的功能相关性。癌症。总之，我们的数据强调了一种广泛适用的策略，用于识别功能性癌症驱动突变并将 JNK 通路定义为胃癌的肿瘤抑制通路。