Rational optimization of combinatorial therapies for the treatment of rare cystic fibrosis variants

合理优化治疗罕见囊性纤维化变异的组合疗法

基本信息

批准号：
10736732
负责人：
Lars Plate
金额：
$ 68.77万
依托单位：
PURDUE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-09-01 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10736732
关键词：
Address Affect Autophagocytosis Binding Sites Biochemical Biogenesis CRISPR/Cas technology Caucasians Cells Classification Clinical Cluster Analysis Clustered Regularly Interspaced Short Palindromic Repeats Combined Modality Therapy Computing Methodologies Cystic Fibrosis Cystic Fibrosis Transmembrane Conductance Regulator Defect Delta F508 mutation Disease Drug Combinations Eligibility Determination Epithelial Cells Exhibits FDA approved Genetic Genetic Diseases Genetic Variation Genotype Goals Human In complete remission Inbred F344 Rats Industry Standard Investigation Ion Channel Knock-out Label Link Machine Learning Marketing Measurement Measures Medical Methods Modeling Molecular Chaperones Mutation Nature Patients Persons Pharmaceutical Preparations Pharmacology Population Property Proteins Proteomics Refractory Regulator Genes Residual state Shapes Structural Models Structural defect Surveys System Techniques Testing Therapeutic Thyroid Gland Validation Variant Work airway epithelium combinatorial cystic fibrosis patients drug discovery drug efficacy functional restoration improved loss of function mutation molecular modeling molecular phenotype monolayer mutation screening new therapeutic target novel novel strategies personalized intervention pharmacologic predicting response protein structure proteostasis rare variant response small molecule targeted treatment tool trait variant of unknown significance

项目摘要

Abstract Cystic fibrosis (CF) is a lethal genetic disease that currently affects ~100,000 people worldwide. CF is caused by a spectrum of loss-of-function mutations that compromise the biogenesis and/ or function of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel, most of which enhance its misfolding and degradation. Recent drug discovery efforts have yielded a suite of approved small molecule “correctors” that enhance the expression of misfolded CFTR variants and “potentiators” that restore conductance to CFTR variants with defective gating. Combinations of these molecules have recently revolutionized the treatment of the ~90% of CF patients bearing at least one copy of the well-studied ΔF508 CFTR variant, which is highly penetrant among Caucasians. However, the efficacy of current combinatorial therapies varies widely among the ~10% of patients bearing diverse combinations of rare, uncharacterized CF variants with divergent pharmacological properties (“theratype”). Efforts to expand the labels of current therapeutics and maximize the number of treatable CF genotypes, in particular amongst non-white populations, are constrained by the large number of CF variants and the limited throughput of current methods. Identifying rare CF variants that respond to therapeutic cocktails is likely to become even more challenging as new correctors and/ or potentiators gain approval. Addressing this challenge requires new techniques that enable efficient biochemical and/ or pharmacological profiling of rare CF variants. In the following, we propose to address this challenge with a unique fusion of emerging genetic, biochemical, and computational methods. We show how deep mutational scanning (DMS) can be used to compare the effects of correctors on the expression of hundreds of variants in parallel. Our preliminary findings provide an unprecedented glimpse of the divergent theratypes of CF variants while identifying numerous variants with unique biochemical and/ or pharmacological properties. We first propose to expand on these investigations in order to measure the response of the complete set of CFTR2 missense variants to a panel of structurally diverse corrector molecules. We will then characterize the interactomes of variants with distinct corrector responses to identify CFTR interactions that antagonize the effects of these small molecules. We will then fuse CRISPR/ Cas9 technology with DMS to determine how these interactions impact the spectrum of CF variant theratypes. Using state-of-the-art structural modeling approaches, we will then identify structural defects in the CFTR protein that are associated with the formation of antagonistic interactions and deviations in CFTR variant theratype. We will then utilize machine learning to classify CF variants based on their observed pharmacological properties. Finally, we will assess the effects of approved correctors on the functional properties of previously uncharacterized variants using industry-standard short-circuit current analysis in Fischer Rat Thyroid and human airway epithelial cells. Together, these investigations will help expand the list of treatable CF genotypes and provide new tools to optimize the targeting of CF drugs.

抽象的囊性纤维化 (CF) 是一种致命的遗传性疾病，目前影响全球约 100,000 人。通过一系列损害囊性纤维化的生物发生和/或功能的功能丧失突变跨膜电导调节器（CFTR）离子通道，其中大部分增强其错误折叠和最近的药物发现工作已经产生了一套经批准的小分子“校正剂”。增强错误折叠的 CFTR 变体和恢复 CFTR 电导的“增强剂”的表达这些分子的组合最近彻底改变了门控缺陷的治疗方法。约 90% 的 CF 患者至少携带一份经过充分研究的 ΔF508 CFTR 变体，该变体高度然而，当前组合疗法的疗效在不同人群中差异很大。约 10% 的患者携带罕见、未表征的 CF 变异的不同组合，且具有不同的变异药理学特性（“治疗类型”）。努力扩大当前治疗的标签并最大化可治疗的 CF 基因型的数量，特别是在非白人群体中，受到大量的限制 CF 变体的数量和当前方法的有限吞吐量识别罕见的 CF 变体响应。随着新的校正剂和/或增强剂的获得，治疗性鸡尾酒可能会变得更具挑战性解决这一挑战需要能够实现高效生化和/或的新技术。罕见 CF 变体的药理学分析在下文中，我们建议通过独特的方法来应对这一挑战。我们展示了新兴遗传、生化和计算方法的融合。 (DMS) 可用于并行比较校正器对数百个变体表达的影响。我们的初步研究结果让我们对 CF 变体的不同治疗类型有了前所未有的了解，同时我们首先建议识别具有独特生化和/或药理学特性的众多变体。扩展这些研究以测量整套 CFTR2 错义的响应然后我们将表征一组结构多样的校正分子的变体。具有不同校正反应的变体，以识别对抗这些小影响的 CFTR 相互作用然后，我们将 CRISPR/Cas9 技术与 DMS 融合，以确定这些相互作用如何影响。然后，我们将使用最先进的结构建模方法来了解 CF 变异疗法的范围。鉴定 CFTR 蛋白中与拮抗相互作用形成相关的结构缺陷然后，我们将利用机器学习根据 CFTR 变异体对 CF 变异体进行分类。最后，我们将评估批准的校正剂对药物的影响。使用行业标准短路电流分析来分析以前未表征的变体的功能特性费舍尔大鼠甲状腺和人类气道上皮细胞的研究将有助于扩大这一范围。确定可治疗的 CF 基因型，并提供优化 CF 药物靶向的新工具。