De Roeck Arne, Van den Bossche Tobi, van der Zee Julie, Verheijen Jan, De Coster Wouter, Van Dongen Jasper, Dillen Lubina, Baradaran-Heravi Yalda, Heeman Bavo, Sanchez-Valle Raquel, Lladó Albert, Nacmias Benedetta, Sorbi Sandro, Gelpi Ellen, Grau-Rivera Oriol, Gómez-Tortosa Estrella, Pastor Pau, Ortega-Cubero Sara, Pastor Maria A, Graff Caroline, Thonberg Håkan, Benussi Luisa, Ghidoni Roberta, Binetti Giuliano, de Mendonça Alexandre, Martins Madalena, Borroni Barbara, Padovani Alessandro, Almeida Maria Rosário, Santana Isabel, Diehl-Schmid Janine, Alexopoulos Panagiotis, Clarimon Jordi, Lleó Alberto, Fortea Juan, Tsolaki Magda, Koutroumani Maria, Matěj Radoslav, Rohan Zdenek, De Deyn Peter, Engelborghs Sebastiaan, Cras Patrick, Van Broeckhoven Christine, Sleegers Kristel
Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
Acta Neuropathol. 2017 Sep;134(3):475-487. doi: 10.1007/s00401-017-1714-x. Epub 2017 Apr 27.
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A亚家族第7成员基因（ABCA7）中的过早终止密码子（PTC）突变最近被确定为晚发性阿尔茨海默病（LOAD）的中高外显率风险因素。然而，在ABCA7下游的mRNA和蛋白质表达、疾病外显率和发病年龄方面观察到高度变异性，这表明存在未知的修饰因素。在此，我们在一个大型早发性AD（EOAD）-对照队列中研究了ABCA7 PTC突变的患病率和疾病外显率，并通过全面的第三代长读长测序检查了对转录水平的影响。我们用下一代测序对928例EOAD患者和980例匹配的对照个体的ABCA7编码序列进行了特征分析。通过MetaSKAT罕见变异关联分析，我们观察到EOAD患者（3%）的PTC突变相对于对照（0.6%）有五倍的富集（p = 0.0004）。仅在患者中观察到10种新的PTC突变，并且PTC突变携带者总体上有增加的家族性AD负荷。此外，我们观察到三种常见编码变异有降低风险的名义趋势。使用牛津纳米孔MinION平台上的靶向长读长cDNA测序对7种PTC突变进行了进一步分析。在不同比例（占总读数的5 - 41%）下观察到每个研究的PTC突变的含PTC转录本，这意味着无义介导的mRNA衰变（NMD）不完全。此外，我们区分并分阶段确定了几个以前未知的可变剪接事件（高达转录本的30%）。与PTC突变一起，这些新的ABCA7异构体中的几种有可能挽救有害的PTC效应。总之，ABCA7 PTC突变在EOAD中起重要作用，值得对基因未明的患者进行ABCA7基因筛查。长读长cDNA测序揭示了不同程度的NMD和转录本修饰事件，这可能影响ABCA7的剂量、疾病严重程度，并可能为AD的治疗干预创造机会。
