White matter hyperintensities (WMH) are among the most common radiological abnormalities in the ageing population and an established risk factor for stroke and dementia. While common variant association studies have revealed multiple genetic loci with an influence on their volume, the contribution of rare variants to the WMH burden in the general population remains largely unexplored. We conducted a comprehensive analysis of this burden in the UK Biobank using publicly available whole-exome sequencing data (n up to 17 830) and found a splice-site variant in GBE1, encoding 1,4-alpha-glucan branching enzyme 1, to be associated with lower white matter burden on an exome-wide level [c.691+2T>C, β = −0.74, standard error (SE) = 0.13, P = 9.7 × 10−9]. Applying whole-exome gene-based burden tests, we found damaging missense and loss-of-function variants in HTRA1 (frequency of 1 in 275 in the UK Biobank population) to associate with an increased WMH volume (P = 5.5 × 10−6, false discovery rate = 0.04). HTRA1 encodes a secreted serine protease implicated in familial forms of small vessel disease. Domain-specific burden tests revealed that the association with WMH volume was restricted to rare variants in the protease domain (amino acids 204–364; β = 0.79, SE = 0.14, P = 9.4 × 10−8). The frequency of such variants in the UK Biobank population was 1 in 450. The WMH volume was brought forward by ∼11 years in carriers of a rare protease domain variant. A comparison with the effect size of established risk factors for WMH burden revealed that the presence of a rare variant in the HTRA1 protease domain corresponded to a larger effect than meeting the criteria for hypertension (β = 0.26, SE = 0.02, P = 2.9 × 10−59) or being in the upper 99.8% percentile of the distribution of a polygenic risk score based on common genetic variants (β = 0.44, SE = 0.14, P = 0.002). In biochemical experiments, most (6/9) of the identified protease domain variants resulted in markedly reduced protease activity. We further found EGFL8, which showed suggestive evidence for association with WMH volume (P = 1.5 × 10−4, false discovery rate = 0.22) in gene burden tests, to be a direct substrate of HTRA1 and to be preferentially expressed in cerebral arterioles and arteries. In a phenome-wide association study mapping ICD-10 diagnoses to 741 standardized Phecodes, rare variants in the HTRA1 protease domain were associated with multiple neurological and non-neurological conditions including migraine with aura (odds ratio = 12.24, 95%CI: 2.54–35.25; P = 8.3 × 10−5]. Collectively, these findings highlight an important role of rare genetic variation and the HTRA1 protease in determining WMH burden in the general population.

中文翻译：

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全外显子组测序揭示了 HTRA1 和 EGFL8 在脑白质高信号中的作用


白质高信号（WMH）是老龄化人群中最常见的放射学异常之一，也是中风和痴呆症的既定危险因素。虽然常见变异关联研究揭示了多个对其体积有影响的遗传位点，但罕见变异对普通人群 WMH 负担的贡献在很大程度上仍未得到探索。我们使用公开的全外显子组测序数据（n 高达 17 830）对英国生物银行的这一负担进行了全面分析，并发现 GBE1 中的剪接位点变体编码 1,4-α-葡聚糖分支酶 1，从而与全外显子组水平上较低的白质负担相关[c.691+2T>C，β = -0.74，标准误差（SE）= 0.13，P = 9.7 × 10−9]。应用基于全外显子组基因的负担测试，我们发现 HTRA1 中的破坏性错义和功能丧失变异（在英国生物库人群中，频率为 275 分之一）与 WMH 体积增加相关（P = 5.5 × 10−6 ，错误发现率 = 0.04)。 HTRA1 编码一种与家族性小血管疾病有关的分泌型丝氨酸蛋白酶。域特异性负荷测试表明，与 WMH 体积的关联仅限于蛋白酶域中的罕见变异（氨基酸 204-364；β = 0.79，SE = 0.14，P = 9.4 × 10−8）。英国生物银行群体中此类变异的频率为 450 分之一。在罕见蛋白酶结构域变异的携带者中，WMH 体积提前了约 11 年。与已确定的 WMH 负担危险因素的影响大小进行比较显示，HTRA1 蛋白酶结构域中罕见变异的存在对应于比满足高血压标准更大的影响（β = 0.26，SE = 0.02，P = 2.9 × 10−59) 或位于上 99 中。基于常见遗传变异的多基因风险评分分布的 8% 百分位（β = 0.44，SE = 0.14，P = 0.002）。在生化实验中，大多数（6/9）已识别的蛋白酶结构域变体导致蛋白酶活性显着降低。我们进一步发现 EGFL8，它在基因负荷测试中显示出与 WMH 体积相关的提示性证据（P = 1.5 × 10−4，错误发现率 = 0.22），是 HTRA1 的直接底物，并优先在脑小动脉和动脉。在一项将 ICD-10 诊断映射到 741 个标准化 Phecode 的全表组关联研究中，HTRA1 蛋白酶结构域中的罕见变异与多种神经系统和非神经系统疾病相关，包括先兆偏头痛（比值比 = 12.24，95%CI：2.54– 35.25；P = 8.3 × 10−5] 总的来说，这些发现强调了罕见遗传变异和 HTRA1 蛋白酶在决定普通人群 WMH 负担方面的重要作用。