Mechanistic insights into Variants of Uncertain Significance (VUS) using novel EGFR variants as a paradigm

使用新型 EGFR 变体作为范例对意义不确定的变体 (VUS) 进行机制洞察

• 批准号: 10598265
• 负责人: Christine M. Lovly
• 金额: $ 5.08万
• 依托单位: VANDERBILT UNIVERSITY MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-19 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10598265
• 关键词: Biochemical; Biology; Cancer Patient; Cells; Clinical; Computer Models; DNA Sequence Alteration; Data; Development; Disease; Doctor of Philosophy; ERBB2 gene; ERBB3 gene; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor; ErbB4 gene; Exons; FDA approved; Genotype; Malignant neoplasm of lung; Methods; Molecular; Mutate; Mutation; Patient Care; Patients; Phenotype; Phosphotransferases; Proteins; Recurrence; Reporting; Research; Research Personnel; Structural Models; Testing; Transmembrane Domain; Variant; actionable mutation; base; cancer type; clinical diagnostics; clinical practice; diagnostic assay; drug sensitivity; gene panel; genetic variant; in silico; in vivo; inhibitor; innovation; insight; novel; precision medicine; prospective; protein structure; receptor; standard of care; structural biology; therapeutic target; tumor; tumorigenesis; variant of unknown significance

Mechanistic insights into Variants of Uncertain Significance (VUS) using novel EGFR variants as a paradigm Investigators: Christine M. Lovly, MD, PhD and Jens Meiler, PhD The prospective identification and rational therapeutic targeting of tumor genomic alterations has revolutionized the care of patients with lung cancer and is now the accepted standard of care for patients with this disease and with other tumor types. With the advent of sophisticated tumor genotyping, the discovery of novel genetic variants is accelerating. In order to realize the promise of precision medicine, there is an urgent need to define the actionability of these variants to select targeted inhibitors. The objective of this proposal is to develop a novel, data-driven paradigm for characterizing genomic Variants of Uncertain Significance (VUS) and generating actionable hypotheses about their functions. For this purpose, we propose an innovative `Personalized Structural Biology' approach. The central hypothesis of this paradigm is that VUS can be best understood by placing the mutation into the context of protein structures and inferring from the structural consequences of the mutation on function, phenotype, and drug sensitivity. By analyzing the tumors of patients with lung cancer, we have identified three EGFR genomic alterations that have not previously been reported: 1) EGFR exon 18-25 Kinase Domain Duplication, 2) EGFR- RAD51 fusions, and 3) EGFR transmembrane domain mutations. Importantly, each of these EGFR variants was reported as a VUS on clinical genotyping reports because there were no data regarding the sensitivity of the mutated proteins to EGFR inhibitors now used in clinical practice. We sought to study these EGFR VUS in an effort to understand on a fundamental mechanistic level how they activate the EGF receptor to promote oncogenesis. We will integrate structural and computational modeling with various biochemical, molecular, cell based, and in vivo approaches to investigate the functional effects of these three distinct alterations. Through these studies, we expect to define previously unrecognized mechanisms of oncogenesis in lung cancer defined by these novel and recurrently detected EGFR variants. Importantly, understanding the structural and functional consequences of these EGFR variants is expected to provide novel insights into ErbB receptor biology and reveal new uses for FDA approved agents in lung cancer and many other tumor types which harbor ErbB (EGFR/HER2/HER3/HER4) alterations. Furthermore, a key deliverable of the proposed studies is the development of an innovative, integrated in silico pipeline that is applicable to VUS in any type of cancer, which we will make freely available via RosettaCommons (www.rosettacommons.org). Thereby, the impact of the proposed research will go beyond that of the three EGFR variants discussed in this proposal. With the recent FDA approval of NGS-based tumor testing, the problem of VUS will continue to grow as these large (>300) gene panel clinical diagnostic assays are reaching higher volumes of patients. Therefore, it is imperative the field generate and systematically integrate such `personalized structural biology' methods to understand the functional significance of VUS in order to best serve all cancer patients.

使用新型EGFR变体作为不确定意义变体（VUS）的机制见解 范式 研究者：克莉丝汀M. Lovly，MD，PhD和Jens Meiler，PhD 肿瘤基因组改变的前瞻性鉴定和合理的治疗靶向， 彻底改变了肺癌患者的护理，现在是肺癌患者接受的护理标准。 这种疾病和其他类型的肿瘤。随着复杂的肿瘤基因分型的出现， 新的基因变异正在加速。为了实现精准医疗的承诺，迫切需要 需要定义这些变体的作用能力以选择靶向抑制剂。本提案的目的 是开发一种新的，数据驱动的范式，用于表征不确定的基因组变异 重要性（VUS）和产生关于其功能的可行假设。为此，我们 提出创新的“个性化结构生物学”方法。这一范式的核心假设是 VUS可以通过将突变置于蛋白质结构的背景下并推断 从功能，表型和药物敏感性的突变的结构后果。 通过分析肺癌患者的肿瘤，我们已经确定了三个EGFR基因组， 既往未报告的改变：1）EGFR外显子18-25激酶结构域重复，2）EGFR- RAD 51融合，和3）EGFR跨膜结构域突变。重要的是，这些EGFR变体中的每一种 在临床基因分型报告中被报告为VUS，因为没有关于 突变的蛋白质EGFR抑制剂现在用于临床实践。我们试图研究这些EGFR VUS， 努力了解在一个基本的机械水平上，他们如何激活EGF受体，以促进 肿瘤发生我们将把结构和计算建模与各种生物化学、分子、细胞 基于，并在体内的方法来研究这三个不同的改变的功能效果。通过 通过这些研究，我们希望能够明确以前未被认识到的肺癌发生机制。 通过这些新的和反复检测的EGFR变体。重要的是，了解结构和 这些EGFR变体的功能结果有望为ErbB受体提供新的见解 并揭示FDA批准的药物在肺癌和许多其他肿瘤类型中的新用途， 携带ErbB（EGFR/HER 2/HER 3/HER 4）改变。此外，拟议研究的一个关键交付成果是， 是开发一种创新的、集成的计算机管道，适用于任何类型癌症的VUS， 我们将通过RosettaCommons（www.rosettacommons.org）免费提供。因此， 所提议的研究将超出本提议中讨论的三种EGFR变体。与 尽管FDA最近批准了基于NGS的肿瘤检测，但随着这些大规模的肿瘤检测，VUS的问题将继续增长。 （>300）基因组临床诊断测定正在达到更高数量的患者。因此有 该领域必须产生并系统地整合这种“个性化结构生物学”方法， 了解VUS的功能意义，以便为所有癌症患者提供最佳服务。