Despite linkage to chromosome 16q in 1996, the mutation causing spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, remained unknown. Here, using long-read single-strand whole-genome sequencing (LR-GS), we identified a heterozygous GGC-repeat expansion in a large Utah pedigree encoding polyglycine (polyG) in zinc finger homeobox protein 3 (ZFHX3), also known as AT-binding transcription factor 1 (ATBF1). We queried 6,495 genome sequencing datasets and identified the repeat expansion in seven additional pedigrees. Ultrarare DNA variants near the repeat expansion indicate a common distant founder event in Sweden. Intranuclear ZFHX3–p62–ubiquitin aggregates were abundant in SCA4 basis pontis neurons. In fibroblasts and induced pluripotent stem cells, the GGC expansion led to increased ZFHX3 protein levels and abnormal autophagy, which were normalized with small interfering RNA-mediated ZFHX3 knockdown in both cell types. Improving autophagy points to a therapeutic avenue for this novel polyG disease. The coding GGC-repeat expansion in an extremely G+C-rich region was not detectable by short-read whole-exome sequencing, which demonstrates the power of LR-GS for variant discovery.

尽管 1996 年与染色体 16q 连锁，但导致脊髓小脑共济失调 4 型 (SCA4)（一种迟发性感觉和小脑共济失调）的突变仍然未知。在这里，使用长读长单链全基因组测序（LR-GS），我们在犹他州的一个大谱系中鉴定了锌指同源盒蛋白 3（ZFHX3）中编码多聚甘氨酸（polyG）的杂合 GGC 重复序列扩展。 AT 结合转录因子 1 (ATBF1)。我们查询了 6,495 个基因组测序数据集，并在另外 7 个谱系中发现了重复扩展。重复扩增附近极其罕见的 DNA 变异表明瑞典存在一个常见的遥远的创始人事件。核内 ZFHX3-p62-泛素聚集体在 SCA4 基底桥脑神经元中丰富。在成纤维细胞和诱导多能干细胞中，GGC 扩增导致 ZFHX3 蛋白水平增加和异常自噬，而这两种细胞类型中的小干扰 RNA 介导的ZFHX3敲低可使其正常化。改善自噬为这种新型多聚G疾病提供了一条治疗途径。短读长全外显子组测序无法检测到 G+C 极其丰富区域中的编码 GGC 重复序列扩展，这证明了 LR-GS 在变异发现方面的强大功能。