Defining the impact of mutant oncogene zygosity

项目摘要/摘要 癌基因突变编码的蛋白质具有增强健康的功能获得的生物学特性。 从历史上看，癌基因的杂合突变被认为足以诱发癌症的发生或 促进癌症进展。然而，致癌基因突变往往与广泛的基因组收益并存。 和损失。然而，癌症基因组的这两个基本特性之间的相互作用很差。 明白了。我们最近发现，KRAS G12D拷贝数增加，WT随后丢失 白血病中的KRAS等位基因导致竞争适合度增加，代价是MAP激酶途径增加 依赖。在随后的初步研究中，我们发现以功能增益为目标的合子变化 癌基因突变在癌症演变过程中经常被选中，并具有预后和治疗作用 这意味着什么。这些发现暗示了WT等位基因对突变癌基因的更广泛的生长抑制作用。 功能，并强调对医生和患者进行前瞻性识别的潜在临床重要性 精确肿瘤学背景下突变癌基因合性的变化。然而，如果没有原则性的方法 为了表征癌基因突变等位基因失衡的程度和意义，我们的 对癌基因生物学和治疗的理解将会扩大。因此，我们提出了功能和翻译 对突变癌基因合性改变决定不同肿瘤的假说进行基因组研究 癌症的生物学和治疗敏感性。在目标1中，我们前瞻性地利用了7万人的队列 将癌症患者的序列与详细的临床和治疗注释联系起来，以确定患病率和 致癌突变等位基因失衡的机制。我们将确定等位基因不平衡的程度 代表了治疗敏感性的预测性生物标志物，并为科学研究创造了公共资源 社区促进对突变癌基因合性的更广泛的机制研究。我们的初步数据显示 在大约一半的RAS突变肿瘤中，这种竞争性的适应性导致WT RAS的丢失。因此，在 目的2我们利用单细胞特性的进展来确定这种连续遗传进化的起源， 建立针对突变体的独立产生的分子变化的年表和适合度收益 从KRAS突变癌症患者的转移瘤中分离的单个细胞中存在野生型KRAS等位基因。 最后，在目标3中，我们使用工程细胞系统和患者来源的异种移植物来研究肿瘤。 雌激素受体基因常见缺失的WT等位基因对ESR1-突变体ER+的抑制作用 转移性乳腺癌，首次将这一现象扩展到突变的RAS之外。总而言之， 拟议的研究试图确定突变癌基因变化的生物学和临床意义。 奇奇斯。通过与我们的机构临床测序计划的整合，我们预计我们的 这些发现将改变临床试验的设计，并改进广泛适用的治疗敏感性生物标记物 在分子定义的癌症患者群体中。

PROJECT SUMMARY/ABSTRACT Mutations in oncogenes encode proteins with gain-of-function biological properties that enhance fitness. Historically, heterozygous mutations in oncogenes have been viewed as sufficient to induce cancer initiation or promote cancer progression. However, oncogenic driver mutations often co-exist with extensive genomic gains and losses. Yet, the interplay between these two fundamental properties of cancer genomes is poorly understood. We recently showed that increased KRAS G12D copy number and subsequent loss of the WT KRAS allele in leukemias leads to increased competitive fitness at the cost of increased MAP kinase pathway dependence. In subsequent preliminary studies, we showed that zygosity changes targeting gain-of-function oncogenic mutations are frequently selected for during cancer evolution and have prognostic and therapeutic implications. These findings allude to broader growth suppressive effects of the WT allele on mutant oncogene function and underscore the potential clinical importance of prospectively identifying for physicians and patients changes in mutant oncogene zygosity within the context of precision oncology. Yet, without principled methods for characterizing the extent and significance of oncogenic mutant allele imbalance, the gap in our understanding of oncogene biology and therapy will widen. We therefore propose functional and translational genomic investigations to test the hypothesis that changes in mutant oncogene zygosity dictates distinct tumor biology and therapeutic sensitivities in cancer. In Aim 1, we leverage a cohort of 70,000 prospectively sequenced cancer patients linked to detailed clinical and treatment annotation to establish the prevalence and mechanisms of oncogenic mutant allele imbalance. We will identify the degree to which allelic imbalance represents a predictive biomarker of therapeutic sensitivity and create a public resource for the scientific community to foster broader mechanistic studies of mutant oncogene zygosity. Our preliminary data indicates that competitive fitness drives the loss of WT RAS in approximately half of all RAS-mutant tumors. Thus, in Aim 2 we utilize advances in single-cell characterization to define the origins of such serial genetic evolution, establishing the chronology and fitness gains of independently arising molecular changes targeting the mutant and wildtype KRAS alleles in single cells isolated from metastatic tumors of KRAS-mutant cancer patients. Finally, in Aim 3 we use engineered cellular systems and patient-derived xenografts to study the tumor suppressive effect of the commonly deleted WT allele of the estrogen receptor (ER) gene in ESR1-mutant ER+ metastatic breast cancers, extending this phenomenon beyond mutant RAS for the first time. In sum, the proposed studies seek to establish the biological and clinical significance of changes to mutant oncogene zygosity. Through the integration with our institutional clinical sequencing initiative, we anticipate that our findings will alter the design of clinical trials and refine broadly applicable biomarkers of therapeutic sensitivity in molecularly defined populations of cancer patients.