Premature termination codon (PTC) mutations in the ATP-Binding Cassette, Sub-Family A, Member 7 gene (ABCA7) have recently been identified as intermediate-to-high penetrant risk factor for late-onset Alzheimer’s disease (LOAD). High variability, however, is observed in downstream ABCA7 mRNA and protein expression, disease penetrance, and onset age, indicative of unknown modifying factors. Here, we investigated the prevalence and disease penetrance of ABCA7 PTC mutations in a large early onset AD (EOAD)—control cohort, and examined the effect on transcript level with comprehensive third-generation long-read sequencing. We characterized the ABCA7 coding sequence with next-generation sequencing in 928 EOAD patients and 980 matched control individuals. With MetaSKAT rare variant association analysis, we observed a fivefold enrichment (p = 0.0004) of PTC mutations in EOAD patients (3%) versus controls (0.6%). Ten novel PTC mutations were only observed in patients, and PTC mutation carriers in general had an increased familial AD load. In addition, we observed nominal risk reducing trends for three common coding variants. Seven PTC mutations were further analyzed using targeted long-read cDNA sequencing on an Oxford Nanopore MinION platform. PTC-containing transcripts for each investigated PTC mutation were observed at varying proportion (5–41% of the total read count), implying incomplete nonsense-mediated mRNA decay (NMD). Furthermore, we distinguished and phased several previously unknown alternative splicing events (up to 30% of transcripts). In conjunction with PTC mutations, several of these novel ABCA7 isoforms have the potential to rescue deleterious PTC effects. In conclusion, ABCA7 PTC mutations play a substantial role in EOAD, warranting genetic screening of ABCA7 in genetically unexplained patients. Long-read cDNA sequencing revealed both varying degrees of NMD and transcript-modifying events, which may influence ABCA7 dosage, disease severity, and may create opportunities for therapeutic interventions in AD.

ATP结合盒，亚家族A，成员7基因（ABCA7）中的过早终止密码子（PTC）突变最近已被确定为迟发性阿尔茨海默氏病（LOAD）的中度至高渗透性危险因素。但是，在下游ABCA7 mRNA和蛋白表达，疾病渗透性和发病年龄中观察到高变异性，这表明未知的修饰因子。在这里，我们调查了一个大型早期AD（EOAD）对照人群中ABCA7 PTC突变的患病率和疾病穿透力，并使用全面的第三代长读测序技术研究了其对转录水平的影响。我们表征了ABCA7928位EOAD患者和980位匹配的对照个体进行了新一代测序。通过MetaSKAT稀有变异关联分析，我们观察到了五倍的富集（p EOAD患者（3％）与对照组（0.6％）的PTC突变= 0.0004）。仅在患者中观察到10个新的PTC突变，并且PTC突变携带者通常具有增加的家族性AD负荷。此外，我们观察到三种常见编码变体的名义风险降低趋势。在牛津纳米孔MinION平台上使用靶向的长读cDNA测序进一步分析了七个PTC突变。对于每个调查的PTC突变，均以不同比例（占总读取计数的5–41％）观察到含PTC的转录本，这意味着不完整的无义介导的mRNA衰变（NMD）。此外，我们区分并分阶段了几个以前未知的替代剪接事件（最多30％的转录本）。结合PTC突变，其中一些新颖的ABCA7同工型具有挽救有害的PTC效应的潜力。总之，ABCA7 PTC突变在EOAD中起重要作用，需要对遗传原因不明的患者进行ABCA7的基因筛查。长期阅读cDNA序列揭示了NMD的程度和转录修饰事件的变化，这可能会影响ABCA7的剂量，疾病的严重程度，并可能为AD的治疗性干预创造机会。