Ziliotto Nicole, Marchetti Giovanna, Scapoli Chiara, Bovolenta Matteo, Meneghetti Silvia, Benazzo Andrea, Lunghi Barbara, Balestra Dario, Laino Lorenza Anna, Bozzini Nicolò, Guidi Irene, Salvi Fabrizio, Straudi Sofia, Gemmati Donato, Menegatti Erica, Zamboni Paolo, Bernardi Francesco
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy.
Front Genet. 2019 Jun 26;10:573. doi: 10.3389/fgene.2019.00573. eCollection 2019.
In light of the complex nature of multiple sclerosis (MS) and the recently estimated contribution of low-frequency variants into disease, decoding its genetic risk components requires novel variant prioritization strategies. We selected, by reviewing MS Genome Wide Association Studies (GWAS), 107 candidate loci marked by intragenic single nucleotide polymorphisms (SNPs) with a remarkable association (-value ≤ 5 × 10). A whole exome sequencing (WES)-based pilot study of SNPs with minor allele frequency (MAF) ≤ 0.04, conducted in three Italian families, revealed 15 exonic low-frequency SNPs with affected parent-child transmission. These variants were detected in 65/120 Italian unrelated MS patients, also in combination (22 patients). Compared with databases (controls gnomAD, dbSNP150, ExAC, Tuscany-1000 Genome), the allelic frequencies of rs16870005 and rs12722600 were significantly higher (i.e., controls gnomAD, = 9.89 × 10 and < 1 × 10). rs61744960 and rs138943371 frequencies were also significantly higher, except in Tuscany-1000 Genome. Interestingly, the association of rs16870005 (Ala431Thr) with MS did not depend on its linkage disequilibrium with the locus. Sequencing in the MS cohort of the 3' region revealed 14 rare mutations (10 not previously reported). Four variants were null, and significantly more frequent than in the databases. Further, the rare variants were observed in combinations, both intra-locus and with other low-frequency SNPs. The Ser389Xfr was found homozygous in a patient with early onset of the MS. Taking into account the potentially functional impact of the identified exonic variants, their expression in combination at the protein level could provide functional insights in the heterogeneous pathogenetic mechanisms contributing to MS.
鉴于多发性硬化症（MS）的复杂性质以及最近估计低频变异对疾病的影响，解码其遗传风险成分需要新颖的变异优先级策略。通过回顾MS全基因组关联研究（GWAS），我们选择了107个由基因内单核苷酸多态性（SNP）标记的候选基因座，这些基因座具有显著关联（-值≤5×10）。在三个意大利家庭中进行的一项基于全外显子测序（WES）的试点研究，针对次要等位基因频率（MAF）≤0.04的SNP，发现了15个外显子低频SNP存在亲子传递受影响的情况。这些变异在65/120名意大利非相关MS患者中被检测到，也存在组合情况（22名患者）。与数据库（对照gnomAD、dbSNP150、ExAC、托斯卡纳1000基因组）相比，rs16870005和rs12722600的等位基因频率显著更高（即对照gnomAD，=9.89×10且<1×10）。rs61744960和rs138943371的频率也显著更高，但在托斯卡纳1000基因组中除外。有趣的是，rs16870005（Ala431Thr）与MS的关联并不依赖于其与该基因座的连锁不平衡。在MS队列中对3'区域进行测序发现了14个罕见突变（10个此前未报道）。四个变异为无效变异，且比在数据库中更为频繁。此外，这些罕见变异在基因座内以及与其他低频SNP组合中均有观察到。Ser389Xfr在一名MS早发患者中被发现为纯合子。考虑到已鉴定的外显子变异的潜在功能影响，它们在蛋白质水平的组合表达可为导致MS的异质性致病机制提供功能见解。
