Analysis of Pathogenic Variants Correctable With CRISPR Base Editing Among Patients With Recessive Inherited Retinal Degeneration
Analysis of Pathogenic Variants Correctable With CRISPR Base Editing Among Patients With Recessive Inherited Retinal Degeneration
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DOI：
10.1001/jamaophthalmol.2020.6418
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发表时间：
2021-01-28
影响因子：
8.1
通讯作者：
MacLaren, Robert E.
中科院分区：
文献类型：
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作者：
Fry, Lewis E.;McClements, Michelle E.;MacLaren, Robert E.
重要性 许多常见的遗传性视网膜疾病不容易用基因疗法治疗。使用碱基编辑器进行基因编辑可以有针对性地修复 DNA 和 RNA 中的单核苷酸转换变体。目前尚不清楚有多少患者具有可通过碱基编辑策略纠正的致病性变异。 目的 评估与遗传性视网膜变性相关的常见大隐性遗传基因中适合碱基编辑的致病性单核苷酸变异的患病率和谱。 设计、设置和参与者在这项回顾性横断面研究中，对 2013 年 7 月至 12 月期间具有与遗传性视网膜变性相关的基因双等位基因致病性变异的患者进行了无法识别的记录使用来自牛津大学医院医学遗传学实验室、莱顿开放变异数据库和之前发表的研究的数据对 2019 年进行了分析。对六个候选基因（ABCA4、CDH23、CEP290、EYS、MYO7A 和 USH2A）进行了检查，这些基因被确定为最常见的隐性基因，其编码序列无法在单个腺相关病毒载体中传递。数据分析时间为 2020 年 4 月 16 日至 5 月 11 日。 主要结果和测量 具有可通过碱基编辑策略纠正的致病性转变变异的等位基因的比例以及具有碱基可编辑等位基因的患者的比例。 结果 莱顿开放变异数据库中共有 12 369 个等位基因，以及通过牛津大学医院医学遗传学的遗传服务接受诊断的 179 名患者实验室进行了分析。莱顿开放变异数据库中包含的候选基因中，可编辑变异占所有致病变异的 53%。可编辑的致病等位基因的比例因基因而异； ABCA4 中 63.1% 的等位基因、CDH23 中 62.7% 的等位基因、MYO7A 中 53.8% 的等位基因、CEP290 中 41.6% 的等位基因、USH2A 中 37.3% 的等位基因和 EYS 中 22.2% 的等位基因是可编辑的。每个基因的 5 个最常见的可编辑致病变异占每个基因内所有致病等位基因的平均值 (SD) 19.1% (9.5%)。在牛津队列中，179 名患者中有 136 名 (76.0%) 至少有 1 个可编辑等位基因。 107 名基因 ABCA4 具有双等位基因致病变异的患者中，共有 53 名患者 (49.5%) 和 56 名 USH2A 基因双等位基因致病变异患者中的 16 名 (28.6%) 具有 5 个最常见可编辑等位基因中的 1 个。 结论和相关性 本研究发现，适合碱基编辑的致病变异通常发生在遗传性视网膜变性中。这些发现如果推广到其他队列，将提供一种开发碱基编辑疗法的方法，以治疗不适合基因治疗的视网膜变性。
IMPORTANCE Many common inherited retinal diseases are not easily treated with gene therapy. Gene editing with base editors may allow the targeted repair of single-nucleotide transition variants in DNA and RNA. It is unknown how many patients have pathogenic variants that are correctable with a base editing strategy.OBJECTIVE To assess the prevalence and spectrum of pathogenic single-nucleotide variants amenable to base editing in common large recessively inherited genes that are associated with inherited retinal degeneration.DESIGN, SETTING, AND PARTICIPANTS In this retrospective cross-sectional study, nonidentifiable records of patients with biallelic pathogenic variants of genes associated with inherited retinal degeneration between July 2013 and December 2019 were analyzed using data from the Oxford University Hospitals Medical Genetics Laboratories, the Leiden Open Variation Database, and previously published studies. Six candidate genes (ABCA4, CDH23, CEP290, EYS, MYO7A, and USH2A), which were determined to be the most common recessive genes with coding sequences not deliverable in a single adeno-associated viral vector, were examined. Data were analyzed from April 16 to May 11, 2020.MAIN OUTCOMES AND MEASURES Proportion of alleles with a pathogenic transition variant that is potentially correctable with a base editing strategy and proportion of patients with a base-editable allele.RESULTS A total of 12 369 alleles from the Leiden Open Variation Database and 179 patients who received diagnoses through the genetic service of the Oxford University Hospitals Medical Genetics Laboratories were analyzed. Editable variants accounted for 53% of all pathogenic variants in the candidate genes contained in the Leiden Open Variation Database. The proportion of pathogenic alleles that were editable varied by gene; 63.1% of alleles in ABCA4, 62.7% of alleles in CDH23, 53.8% of alleles in MYO7A, 41.6% of alleles in CEP290, 37.3% of alleles in USH2A, and 22.2% of alleles in EYS were editable. The 5 most common editable pathogenic variants of each gene accounted for a mean (SD) of 19.1% (9.5%) of all pathogenic alleles within each gene. In the Oxford cohort, 136 of 179 patients (76.0%) had at least 1 editable allele. A total of 53 of 107 patients (49.5%) with biallelic pathogenic variants in the gene ABCA4 and 16 of 56 patients (28.6%) with biallelic pathogenic variants in the gene USH2A had 1 of the 5 most common editable alleles.CONCLUSIONS AND RELEVANCE This study found that pathogenic variants amenable to base editing commonly occur in inherited retinal degeneration. These findings, if generalized to other cohorts, provide an approach for developing base editing therapies to treat retinal degeneration not amenable to gene therapy.