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

• 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
• 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

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）是一种致命的遗传疾病，目前在全球范围内影响约100,000人。 CF是引起的 通过一系列功能丧失突变，损害了囊性纤维化的生物发生和/或功能 跨膜电导调节剂（CFTR）离子通道，其中大多数增强其错误折叠和 降解。最近的药物发现工作产生了一套批准的小分子“校正器” 增强不折叠的CFTR变体和恢复电导到CFTR电导的“增强器”的表达 门控有缺陷的变体。这些分子的组合最近彻底改变了治疗 约90％的CF患者至少有一份经过良好研究的ΔF508CFTR副本，这是高度的 高加索人之间的渗透。但是，当前组合疗法的效率在 约有10％的患者具有稀有，未表征的CF变体的潜水员组合 药理学特性（“ Theratype”）。努力扩大当前治疗剂的标签并最大化 可治疗的CF基因型的数量，尤其是在非白人种群中，受到大型限制 CF变体的数量和当前方法的有限吞吐量。识别响应的稀有CF变体 随着新的纠正剂和/或潜在者的增益，治疗性鸡尾酒可能会变得更加挑战 赞同。应对这一挑战需要新技术，以实现有效的生化和/或 稀有CF变体的药理分析。在下文中，我们建议用独特的 新兴遗传，生化和计算方法的融合。我们显示突变扫描的深度扫描 （DMS）可用于比较校正子对数百个并行中数百种变体的影响。 我们的初步发现为CF变体的不同理论提供了前所未有的瞥见 识别具有独特的生化和/或药物特性的众多变体。我们首先提出 扩展这些投资，以衡量完整的CFTR2错过的响应 变体到一组结构上多样的校正分子。然后，我们将表征 具有不同校正响应的变体，以识别CFTR相互作用，使这些小的效果拮抗 分子。然后，我们将与DMS融合CRISPR/ CAS9技术，以确定这些相互作用如何影响 使用最先进的结构建模方法，我们将 识别与拮抗相互作用相关的CFTR蛋白中的结构缺陷 并在CFTR变体类型中出发。然后，我们将利用机器学习根据CF进行分类 他们观察到的药物特性。最后，我们将评估批准的校正器对 使用行业标准短路电流分析的先前未表征变体的功能性能 在Fischer大鼠甲状腺和人类气道上皮细胞中。这些调查将在一起有助于扩大清单 可治疗的CF基因型，并提供了优化CF药物靶向的新工具。