背景:肌萎缩侧索硬化症(ALS)是一种神经退行性疾病,影响全球300,000多人。它的特点是神经系统的进行性衰退,导致影响身体功能的肌肉减弱。大约,15%的被诊断患有ALS的个体具有导致其疾病的已知遗传变异。随着减缓或预防症状的疗法继续发展,如反义寡核苷酸,重要的是发现可能成为治疗靶点的新基因。此外,随着队列的持续增长,在ALS亚型中进行分析,如原发性侧索硬化症(PLS),由于功率的增加而成为可能。这些分析可以突出疾病表现中的新途径。
方法:在我们以前的发现基础上,使用罕见的变异关联分析,我们对6,970名ALS患者的更大的多种族队列进行了罕见的变异负担测试,166名PLS患者,和22,524个控件。我们使用基于子区域残余变异不容忍评分(subRVIS)的不耐受域百分位数,先前已将其与基于基因的折叠方法结合进行负荷测试,以鉴定与ALS和PLS相关的基因。
结果:基于基因的塌陷模型显示出与SOD1,TARDBP,TBK1(OR=19.18,p=3.67×10-39;OR=4.73,p=2×10-10;OR=2.3,p=7.49×10-9)。这些基因以前与ALS有关。此外,一个重要的新的控制富集基因,ALKBH3(p=4.88×10-7),在这个模型中对ALS有保护作用。基于不耐受域的塌陷模型在识别TARDBP中与ALS相关的区域方面显示出显着改善(OR=10.08,p=3.62×10-16)。我们的PLS蛋白截短变体塌陷分析表明ANTXR2中的显着病例富集(p=8.38×10-6)。
结论:在一个由6,970名ALS患者组成的大型多种族队列中,折叠分析验证了已知的ALS基因,并确定了一种新的潜在保护性基因,ALKBH3.对166例PLS患者进行的首次分析发现与ANTXR2功能丧失突变相关。
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 300,000 people worldwide. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms continue to develop, such as antisense oligonucleotides, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation.
METHODS: Building on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger multi-ethnic cohort of 6,970 ALS patients, 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS.
RESULTS: A gene based collapsing model showed significant associations with SOD1, TARDBP, and TBK1 (OR = 19.18, p = 3.67 × 10-39; OR = 4.73, p = 2 × 10-10; OR = 2.3, p = 7.49 × 10-9, respectively). These genes have been previously associated with ALS. Additionally, a significant novel control enriched gene, ALKBH3 (p = 4.88 × 10-7), was protective for ALS in this model. An intolerant domain-based collapsing model showed a significant improvement in identifying regions in TARDBP that associated with ALS (OR = 10.08, p = 3.62 × 10-16). Our PLS protein truncating variant collapsing analysis demonstrated significant case enrichment in ANTXR2 (p = 8.38 × 10-6).
CONCLUSIONS: In a large multi-ethnic cohort of 6,970 ALS patients, collapsing analyses validated known ALS genes and identified a novel potentially protective gene, ALKBH3. A first-ever analysis in 166 patients with PLS found a candidate association with loss-of-function mutations in ANTXR2.