Dissecting gastric cancer clonality with genomic analyses and patient xenografts

摘要 胃癌是全球癌症死亡的第三大原因，有超过720，000人 每年都死于这种疾病。这种恶性肿瘤的生存率仍然很低：只有4%的患者 转移性胃癌在诊断后存活5年。有趣的是，最近的胃癌基因组研究 已经表明这种恶性肿瘤是高度异质性的，每个肿瘤都有数百个突变。是 然而，这些突变是如何组成胃肿瘤亚克隆细胞群的尚不清楚。 了解胃肿瘤的亚克隆组织是很重要的，因为这些信息对于 设计最佳的分子检测方法，指导精准医疗。在本研究中，我们将 研究胃癌克隆性的区域和时间变化，以了解肿瘤内 异质性和亚克隆结构，并鉴定携带驱动突变的肿瘤亚克隆 作为治疗的目标虽然亚克隆结构的研究尚未在胃癌中进行， 最近对其他癌症类型的研究，如肺和肾肿瘤，产生了有趣的，但对比鲜明的 结果虽然驱动突变倾向于存在于大多数肺肿瘤亚克隆中，但多个和年轻的肺肿瘤亚克隆可能存在于肺肿瘤亚克隆中。 携带不同驱动子的亚克隆是肾肿瘤的特征。因此，虽然肺癌和肾癌 显示了广泛的肿瘤内异质性，这些结果表明，有限的取样（即单一活检）可能 适用于肺癌的分子指导治疗，但更广泛的多区域采样 并且分析将需要用于肾癌的分子诊断。在这里，我们旨在提高我们的 了解胃癌克隆性及其与分子诊断的相关性， 30例胃癌肿瘤的区域测序，并通过评估组织学和遗传学水平， 当它们被植入免疫抑制的NSG小鼠时，匹配的肿瘤的相似性。我们的指导 一种假说认为，胃癌中广泛的肿瘤内异质性导致了复杂的肿瘤模式 无性系构型本研究的主要目的如下：（1）利用细胞克隆技术研究胃癌细胞克隆多样性， 多区域测序和（2）评估原发性癌症和非原发性癌症之间的组织学和基因组相似性。 来源于患者来源的异种移植模型的肿瘤。这些实验对于阐明 胃癌克隆进化模式及其在精准医学中的影响和相关性。特别是， 我们将揭示胃癌亚克隆中驱动突变的分布， 设计进一步的临床前研究和临床试验的基础，有效地靶向这些突变， 胃癌生存率急需改善。我们的发现也将与解决癌症有关 在美国，胃癌的发病率在西班牙裔美国人中占很大比例。

Abstract Gastric cancer is the third leading cause of cancer mortality worldwide, with over 720,000 individuals succumbing to this disease each year. Survival to this malignancy remains dismal: only 4% of patients with metastatic gastric cancer are alive 5 years after diagnosis. Interestingly, recent gastric cancer genomic studies have shown that this malignancy is highly heterogeneous, with every tumor having hundreds of mutations. It is not known, however, how these mutations are organized into gastric tumor subclonal cell populations. Understanding the subclonal organization of gastric tumors is important as such information will be essential to design optimal molecular testing methods that guide precision medicine. In the present study, we will investigate regional and temporal changes in gastric cancer clonality to understand the levels of intra-tumor heterogeneity and subclonal architecture, and to identify tumor subclones carrying driver mutations that can be targeted for therapy. Although subclonal architecture studies have not yet been carried out in gastric cancer, recent studies in other cancer types, such as lung and renal tumors, have produced interesting, yet contrasting results. While driver mutations tend to be present in most lung tumor subclones, multiple and younger subclones carrying different drivers are characteristic of renal tumors. Thus, while both lung and renal cancer show extensive intra-tumor heterogeneity, these results suggest that limited sampling (i.e. a single biopsy) may be appropriate for molecularly-guided therapies in lung cancer but that more extensive multiregional sampling and analyses will be required for molecular diagnostics in renal cancer. Here we aim to improve our understanding of gastric cancer clonality and its relevance for molecular diagnostics by performing multi- regional sequencing of 30 gastric cancer tumors and by evaluating the levels of histological and genetic similarities of matching tumors when they are implanted into immunosuppressed NSG mice. Our guiding hypothesis is that extensive intra-tumor heterogeneity in gastric cancers leads to complex patters of tumor clonal architecture. Our aims in the study are as follows: (1) To investigate gastric cancer clonal diversity using multiregional sequencing and (2) To assess histological and genomic similarities between primary cancers and tumors derived from patient-derived xenograft models. These experiments will be crucial to elucidate the patterns of gastric cancer clonal evolution and their impact and relevance in precision medicine. In particular, we will uncover the distribution of driver mutations in gastric cancer subclones and will provide a very strong basis to design further preclinical studies and clinical trials that efficiently target such mutations, leading to much needed improvements in gastric cancer survival. Our findings will be also relevant to address cancer disparities in the country as gastric cancer disproportionally affects U.S. Hispanics.