Integrated clinical, genetic and functional analysis of the ABCA4 locus

ABCA4 基因座的综合临床、遗传和功能分析

• 批准号: 10636782
• 负责人: RANDO L ALLIKMETS
• 金额: $ 43.38万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10636782
• 关键词: 220kDa rod outer segment rim protein; Address; Affect; Age; Alleles; Atrophic; Biological Assay; CRISPR/Cas technology; Cell Culture Techniques; Cell Line; Clinical; Clinical Data; Clinical Treatment; Clinical Trials; Code; Collection; Consensus Sequence; Counseling; Coupled; Data; Defect; Diagnosis; Diagnostic; Disease; Enhancers; Family; Flecks; Frequencies; Future; Gene Expression; Genes; Genetic; Genetic Databases; Genetic Screening; Genetic Variation; Genomics; Genotype; Goals; Image; Introns; Knowledge; Link; Lipofuscin; Messenger RNA; Methodology; Methods; Modality; Mus; Mutate; Mutation; Onset of illness; Outcome Study; Pathogenicity; Patient Care; Patient Selection; Patients; Pattern; Penetrance; Persons; Phenotype; Population; Prognosis; RNA; RNA Splicing; Reporter; Research; Rest; Retina; Retinal Degeneration; Retinal Diseases; Retinitis Pigmentosa; Severities; Site; Stargardt' s disease; Statistical Data Interpretation; Structure; Subgroup; Testing; United States; Untranslated RNA; Variant; cell type; clinical care; clinical database; clinical heterogeneity; clinical phenotype; clinical prognosis; cohort; combinatorial; cone-rod dystrophy; design; diagnostic accuracy; disease diagnosis; disease heterogeneity; disorder subtype; genetic analysis; genetic approach; genetic testing; genotyped patients; improved; in silico; induced pluripotent stem cell; insight; molecular modeling; mutant; novel; patient screening; predictive modeling; prognostic; programs; promoter; segregation; therapy design; translational study

Mutations in the ABCA4 gene are responsible for a wide variety of retinal degeneration phenotypes, including Stargardt disease (STGD), cone-rod dystrophy (CRD) and retinitis pigmentosa (RP). Different combinations of >900 ABCA4 mutant alleles result in distinct phenotypes in a continuum of disease manifestations. Variation in the ABCA4 locus has emerged as the most prevalent cause of Mendelian retinal disease, with an estimated 1/20 people across all populations carrying a potential disease-associated variant in this gene. Genetic analyses of ABCA4-associated retinal disease have been substantially advanced in recent years. New methods, such as direct sequencing of the entire genomic ABCA4 locus, have allowed detecting up to 80% of the disease-associated ABCA4 alleles, including 2 (both) mutations in ~65-75% of patients. Of these 75% are in the coding region and 25% in introns, more than half of which are outside of splice consensus sequences. Of the rest, 1 mutation is detected in ~20% of patients while no disease-associated alleles are found in another 10% of screened patients with phenotypes compatible with the ABCA4 disease. These data suggest that many (rare) disease-associated ABCA4 alleles are yet to be identified and, most importantly, unequivocally confirmed by adequate functional analyses. We will test the hypothesis that a combination of advanced genetic screening coupled with advanced functional analyses of ABCA4 alleles from non-coding sequences is necessary to unequivocally determine the ABCA4-associated disease load. The proposed research program, based on large, comprehensively characterized familial cohort of ABCA4 disease, is using integrated approaches of genetic analyses, quantified clinical data and functional analyses to generate a predictive model for ABCA4 disease. The ultimate goal of the proposed project is to complete the analysis of the ABCA4 locus. The research program is organized into two Specific Aims. In the first Aim, we propose a novel combinatorial pipeline utilizing our existing clinical and genetic databases, accumulated knowledge, and advanced in silico methodology to predict most disease-associated variants in the coding and non-coding sequences of the entire ABCA4 locus. In the second Aim we will confirm or reject the variants in non-coding sequences for disease association by functional testing ABCA4 RNA from mutated iPSC lines for splicing and expression defects. The outcome of these studies will substantially aid in disease diagnosis, prognosis and will serve as a platform for selecting patients for emerging clinical trials geared to delay the onset, or arrest the progression, of ABCA4-associated diseases.

ABCA4基因突变导致多种视网膜变性表型， 包括Stargardt病(STGD)、视锥-视杆细胞营养不良(CRD)和视网膜色素变性(RP)。不同 &gt；900 ABCA4突变等位基因组合在一系列疾病中导致不同的表型 表现形式。ABCA4基因座的变异已成为孟德尔视网膜最常见的原因 疾病，估计在所有人口中有1/20的人携带潜在的疾病相关变异 这个基因。近些年来，ABCA4相关视网膜疾病的基因分析有了很大进展 好几年了。新的方法，如直接对整个基因组ABCA4基因座进行测序，已经能够检测到 高达80%的疾病相关ABCA4等位基因，包括约65%-75%的患者中的两个(两者)突变。的 这75%位于编码区，25%位于内含子，其中一半以上位于剪接外 共识序列。在其余的患者中，约20%的患者检测到1个突变，而没有与疾病相关的 在另外10%的表型与ABCA4疾病相容的筛查患者中发现了等位基因。 这些数据表明，许多(罕见的)与疾病相关的ABCA4等位基因尚未被识别，而且大多数 重要的是，充分的功能分析明确证实了这一点。我们将检验一个假设，即 ABCA4等位基因的高级遗传筛选与高级功能分析相结合 非编码序列是明确确定ABCA4相关疾病负荷所必需的。这个 建议的研究计划，基于ABCA4疾病的大型、全面特征的家族队列， 正在使用基因分析、量化临床数据和功能分析的集成方法来生成 ABCA4病的预测模型。拟议项目的最终目标是完成对 ABCA4基因座。 这项研究计划分为两个具体目标。在第一个目标中，我们提出了一部小说 利用我们现有的临床和基因数据库、积累的知识和 先进的计算机方法，可预测编码和非编码中的大多数疾病相关变体 整个ABCA4基因座的序列。在第二个目标中，我们将确认或拒绝非编码的变体 通过功能测试来自突变的IPSC株系的ABCA4 RNA用于剪接和 表情缺陷。这些研究的结果将大大有助于疾病的诊断、预后和意愿 作为为新出现的临床试验挑选患者的平台，旨在推迟发病，或阻止 ABCA4相关疾病的进展。

项目成果

Longitudinal Analysis of a Resolving Foveomacular Vitelliform Lesion in ABCA4 Disease.

• DOI: 10.1016/j.oret.2022.04.005
• 发表时间: 2022-09
• 期刊: OPHTHALMOLOGY RETINA
• 影响因子: 4.5
• 作者: Lee, Winston;Su, Pei -Yin;Zernant, Jana;Nagasaki, Takayuki;Tsang, Stephen H.;Allikmets, Rando
• 通讯作者: Allikmets, Rando

The human ATP-binding cassette (ABC) transporter superfamily.

• DOI: 10.1002/humu.24418
• 发表时间: 2022-09
• 期刊: HUMAN MUTATION
• 影响因子: 3.9
• 作者: Dean, Michael;Moitra, Karobi;Allikmets, Rando
• 通讯作者: Allikmets, Rando

Reevaluating the Association of Sex With ABCA4 Alleles in Patients With Stargardt Disease.

重新评估 Stargardt 病患者中性别与 ABCA4 等位基因的关联。

• DOI: 10.1001/jamaophthalmol.2021.0460
• 发表时间: 2021
• 期刊: JAMA ophthalmology
• 影响因子: 8.1
• 作者: Lee,Winston;Zernant,Jana;Nagasaki,Takayuki;Allikmets,Rando
• 通讯作者: Allikmets,Rando

Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability.

• DOI: 10.1016/j.xhgg.2023.100237
• 发表时间: 2023-10-12
• 期刊: HUMAN GENETICS AND GENOMICS ADVANCES
• 作者: Corradi, Zelia;Khan, Mubeen;Hitti-Malin, Rebekkah;Mishra, Ketan;Whelan, Laura;Cornelis, Stephanie S.;Hoyng, Carel B.;Kampjarvi, Kati;Klaver, Caroline C. W.;Liskova, Petra;Stoehr, Heidi;Weber, Bernhard H. F.;Banfi, Sandro;Farrar, G. Jane;Sharon, Dror;Zernant, Jana;Allikmets, Rando;Dhaenens, Claire-Marie;Cremers, Frans P. M.
• 通讯作者: Cremers, Frans P. M.