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: 10379353
• 负责人: Christine M. Lovly
• 金额: $ 31.96万
• 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/10379353
• 关键词: 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; 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; Nucleic Acid Regulatory Sequences; Oncogenic; Patient Care; Patients; Phenotype; Phosphorylation; Phosphotransferases; Physicians; 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; Translating; Transmembrane Domain; Variant; Work; actionable mutation; base; 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; 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.

使用新型EGFR变体作为一种不确定意义的变体（VU）的机械洞察力 范例 调查人员：医学博士Christine M. Lovly，博士和Jens Meil​​er，博士 肿瘤基因组改变的前瞻性鉴定和合理的治疗靶向具有 彻底改变了肺癌患者的护理 这种疾病和其他肿瘤类型。随着复杂的肿瘤基因分型的出现，发现 新颖的遗传变异正在加速。为了实现精确医学的承诺，有一个紧急的 需要定义这些变体以选择靶向抑制剂的可行性。该提议的目的 是为了开发一种新颖的，数据驱动的范例来表征不确定的基因组变异 意义（VU）并产生有关其功能的可行假设。为此，我们 提出了一种创新的“个性化结构生物学”方法。该范式的中心假设是 通过将突变放置在蛋白质结构的背景下并推断，可以最好地理解该VU 突变对功能，表型和药物敏感性的结构后果。 通过分析肺癌患者的肿瘤，我们确定了三个EGFR基因组 以前尚未报道的改变：1）EGFR外显子18-25激酶结构域重复，2）EGFR- RAD51融合和3）EGFR跨膜结构域突变。重要的是，这些EGFR变体中的每一个 据报道是临床基因分型报告的VUS，因为没有有关有关的敏感性的数据 现在用于临床实践中的EGFR抑制剂的突变蛋白质。我们试图研究这些EGFR vus 努力在基本机械级别上了解它们如何激活EGF受体以促进 肿瘤发生。我们将将结构和计算建模与各种生化，分子，细胞整合 基于体内的方法来研究这三个不同变化的功能效应。通过 这些研究，我们期望定义肺癌定义的先前未识别的肿瘤发生机制 通过这些新颖的并经常检测到的EGFR变体。重要的是，了解结构和 这些EGFR变体的功能后果有望为ERBB受体提供新的见解 生物学并揭示了FDA批准的肺癌和许多其他肿瘤类型的新用途 Harbor Erbb（EGFR/HER2/HER3/HER4）的改动。此外，提议的研究的关键可交付 是在任何类型的癌症中适用于VU的硅管道中的创新性的开发， 我们将通过Rosettacommons（www.rosettacommons.org）免费提供。因此， 拟议的研究将超出本提案中讨论的三个EGFR变体的研究。与 FDA最近批准了基于NGS的肿瘤测试，随着这些大型的VUS问题，VUS的问题将继续增长 （> 300）基因面板临床诊断测定法已达到较高的患者体积。因此，是 势在必行的领域生成并系统地将这种“个性化结构生物学”方法整合到 了解VU的功能意义，以便为所有癌症患者提供服务。