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: 10610721
• 负责人: Christine M. Lovly
• 金额: $ 31.65万
• 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/10610721
• 关键词: Acceleration; Biochemical; Biological; Biological Assay; Biology; C-terminal; Cancer Patient; Cells; Chimeric Proteins; Chromosomal translocation; Clinic; Clinical; Computer Models; DNA Sequence Alteration; Data; Development; Dimerization; Disease; Doctor of Philosophy; EGFR inhibition; ERBB2 gene; ERBB3 gene; Engineering; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor; ErbB4 gene; Exons; FDA approved; Family; Family member; Future; Genomics; Genotype; Goals; Heterodimerization; Homodimerization; Human; Lung Adenocarcinoma; Lung Neoplasms; Malignant Neoplasms; Malignant neoplasm of lung; Mediating; Methods; Molecular; Mutate; Mutation; Mutation Detection; Nucleic Acid Regulatory Sequences; Oncogenic; Patient Care; Patients; Phenotype; Phosphorylation; Phosphotransferases; Physicians; Polymers; Principal Investigator; Proteins; Receptor Activation; Recurrence; Reporting; Research; Research Personnel; Role; Signal Transduction; Single Nucleotide Polymorphism; Somatic Mutation; Structural Models; Techniques; Test Result; Testing; Therapeutic Agents; Therapeutically Targetable; Translating; Transmembrane Domain; Variant; Work; actionable mutation; cancer therapy; cancer type; clinical diagnostics; clinical practice; clinically significant; diagnostic assay; diagnostic tool; dimer; drug development; drug sensitivity; experimental study; gene panel; genetic variant; in silico; in vivo; inhibitor; innovation; insight; multidisciplinary; next generation sequencing; novel; novel therapeutic intervention; polymerization; precision medicine; prospective; protein structure; receptor; screening; standard of care; structural biology; targeted agent; therapeutic target; tool; 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.

对不确定意义(VU)变体的机械洞察，使用新的EGFR变体作为 范式 调查人员：克里斯汀·M·洛夫利，医学博士，延斯·梅勒，博士 肿瘤基因组改变的前瞻性识别和合理的治疗靶向 使肺癌患者的护理发生了革命性变化，现在已成为公认的肺癌患者护理标准 这种疾病与其他肿瘤类型有关。随着复杂的肿瘤基因分型技术的出现， 新的基因变异正在加速。要实现精准医疗的承诺，当务之急是 需要确定这些变异体的可操作性，以选择靶向抑制剂。这项提议的目的是 是开发一种新的、数据驱动的范式来表征不确定的基因组变体 重要性(VU)和生成关于其功能的可操作的假设。为此，我们 提出一种创新的“个性化结构生物学”方法。这一范式的中心假设是 通过将突变放在蛋白质结构的上下文中并推断，可以最好地理解这种VU 从突变对功能、表型和药物敏感性的结构性后果。 通过对肺癌患者肿瘤的分析，我们鉴定了三个EGFR基因组 以前没有报道的改变：1)EGFR外显子18-25激酶结构域重复，2)EGFR- RAD51融合；3)EGFR跨膜区突变。重要的是，每一种EGFR变体 在临床基因分型报告中被报告为VUS，因为没有关于VUS敏感性的数据 将突变的蛋白质转化为EGFR抑制剂，目前已应用于临床。我们试图研究这些EGFR VU 努力在基本机制水平上了解它们如何激活EGF受体以促进 致癌作用。我们将把结构和计算模型与各种生化、分子、细胞 基于和体内的方法来研究这三种不同变化的功能影响。穿过 这些研究，我们期望能明确以前未知的肺癌致癌机制。 通过这些新的和反复检测到的EGFR变体。重要的是，了解结构和 这些EGFR变异体的功能结果有望为ErbB受体提供新的见解 生物学并揭示FDA批准的药物在肺癌和许多其他肿瘤类型中的新用途 Erbor B(EGFR/HER2/HER3/HER4)更改。此外，拟议研究的一个关键成果是 开发一种创新的、集成的硅胶管道，适用于任何类型的癌症的VUS， 我们将通过RosettaCommons(www.rosettacommons.org)免费提供。因此， 拟议的研究将超越本提案中讨论的三种EGFR变体。与 最近FDA批准了基于NGS的肿瘤检测，VUS的问题将继续增长，因为这些 (&gt；300)基因小组临床诊断分析正在接触到更多的患者。因此，它是 该领域势在必行地产生并系统地整合这种“个性化结构生物学”方法，以 了解VUS的功能意义，以便更好地为所有癌症患者服务。