Proteomic Investigation of Differential Interactomes of Glypican 1 and a Putative Disease-Modifying Variant of Ataxia

In a currently 13-year-old girl of consanguineous Turkish parents, who developed unsteady gait and polyneuropathy at the ages of 3 and 6 years, respectively, we performed whole genome sequencing and identified a biallelic missense variant c.424C>T, p.R142W in glypican 1 (GPC1) as a putative disease-associated variant. Up to date, GPC1 has not been associated with a neuromuscular disorder, and we hypothesized that this variant, predicted as deleterious, may be causative for the disease. Using mass spectrometry-based proteomics, we investigated the interactome of GPC1 WT and the missense variant. We identified 198 proteins interacting with GPC1, of which 16 were altered for the missense variant. This included CANX as well as vacuolar ATPase (V-ATPase) and the mammalian target of rapamycin complex 1 (mTORC1) complex members, whose dysregulation could have a potential impact on disease severity in the patient. Importantly, these proteins are novel interaction partners of GPC1. At 10.5 years, the patient developed dilated cardiomyopathy and kyphoscoliosis, and Friedreich’s ataxia (FRDA) was suspected. Given the unusually severe phenotype in a patient with FRDA carrying only 104 biallelic GAA repeat expansions in FXN, we currently speculate that disturbed GPC1 function may have exacerbated the disease phenotype. LC–MS/MS data are accessible in the ProteomeXchange Consortium (PXD040023).本研究对象为一名现年13岁的土耳其籍女孩，其父母为近亲婚配。该患儿分别于3岁和6岁时出现步态不稳与多发性神经病。我们对其实施全基因组测序，鉴定出磷脂酰肌醇蛋白聚糖1（glypican 1, GPC1）基因存在双等位错义变异c.424C>T、p.R142W，该变异为疑似疾病相关致病变异。截至目前，GPC1尚未被证实与神经肌肉疾病存在关联，我们推测这一经预测具有有害效应的变异可能是该疾病的致病根源。我们采用基于质谱的蛋白质组学技术，分析了野生型GPC1与该错义变异体的蛋白质相互作用组。共鉴定出198种与GPC1存在互作的蛋白质，其中16种在该错义变异体中出现表达量异常。上述异常蛋白包括钙连蛋白（CANX）、液泡型ATP酶（vacuolar ATPase, V-ATPase）以及雷帕霉素靶蛋白复合物1（mammalian target of rapamycin complex 1, mTORC1）的复合物亚基，这些蛋白的失调可能对患者的疾病严重程度产生潜在影响。值得关注的是，上述蛋白均为GPC1此前未被报道的互作伴侣。该患儿在10.5岁时并发扩张型心肌病与脊柱侧后凸畸形，临床曾怀疑为弗里德赖希共济失调（Friedreich’s ataxia, FRDA）。该FRDA患者仅携带FXN基因104个双等位GAA重复扩增，却表现出异常严重的临床表型，我们据此推测GPC1功能异常可能加剧了其疾病表型。本研究产生的液相色谱-串联质谱（LC–MS/MS）数据可通过ProteomeXchange联盟（登录号PXD040023）获取。