An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation

Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type - amino acid (AA) substitutions - despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate the first comprehensive atlas of diverse variant effects for a disease protein, amyloid beta (Aß) that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD variants and many mutations beyond substitutions that accelerate Aß aggregation. Truncations, substitutions, insertions, single- and multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are strongly enriched in the polar N-terminus of Aß. This first comparative atlas for any disease gene highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.变异效应多重检测（Multiplexed Assays of Variant Effects, MAVEs）可指导临床变异解读并揭示疾病致病机制。迄今为止，尽管引发疾病的编码变异类型繁多，但MAVEs的研究始终局限于单一突变类型——氨基酸（amino acid, AA）替换。本研究借助深度插入缺失诱变（Deep Indel Mutagenesis, DIM）技术，针对阿尔茨海默病（Alzheimer’s disease, AD）中发生聚集、且在家族性阿尔茨海默病（familial AD, fAD）中存在致病突变的疾病蛋白β淀粉样蛋白（amyloid beta, Aß），构建了首个覆盖多类型变异效应的综合图谱。该图谱不仅鉴定出已知的fAD致病变异，还发现了大量非替换型突变可加速Aß聚集。截短突变、氨基酸替换、插入突变以及单氨基酸或多氨基酸缺失突变，在增强或削弱蛋白聚集的倾向性上存在显著差异，但所有突变类别中的疑似致病变异均在Aß的极性N端区域显著富集。这一针对任一疾病基因的首个比较性研究图谱，强调了在MAVEs研究中纳入多样化突变类型的重要性，并为淀粉样蛋白成核机制提供了关键的机理性见解。