Proteomic View of Basement Membranes from Human Retinal Blood Vessels, Inner Limiting Membranes, and Lens Capsules

Basement membranes (BMs) are extracellular matrix sheets comprising the laminins, type-IV collagens, nidogens, and the heparan sulfate proteoglycans, perlecan, collagen XVIII, and agrin. In intact BMs, BM proteins are physiologically insoluble and partially resistant to proteolytic digestion, making BMs a challenge to study. Here three types of BMs from adult human eyes, the inner limiting membrane (ILM), the retinal vascular BMs, and the lens capsule, were isolated for analysis by 1D-SDS-PAGE and LC–MS/MS. Peptide and protein identifications were done using MaxQuant. 1129 proteins were identified with a 1% false discovery rate. Data showed that BMs are composed of multiple laminins, collagen IVs, nidogens, and proteoglycans. The dominant laminin family member in all BMs was laminin α5β2γ1. The dominant collagen IV trimer in lens capsule (LC) and blood vessel (BV) BMs had a chain composition of α1­(IV)2, α2 (IV), whereas the dominant collagen IV in the ILM had the α3­(IV), α4­(IV), α5­(IV) chain composition. The data also showed that the ratio of laminin and collagen IVs varied among different BM types: the ratio of collagen IV to the other BM proteins is highest in LC, followed by BV and lowest for the ILM. The data have been deposited to the ProteomeXchange with identifier PXD001025.

基底膜（Basement membranes, BMs）是一类细胞外基质薄层，由层粘连蛋白、Ⅳ型胶原蛋白、巢蛋白以及硫酸乙酰肝素蛋白聚糖（包括串珠蛋白聚糖（perlecan）、胶原蛋白XVIII（collagen XVIII）与聚集蛋白聚糖（agrin））构成。在完整的基底膜中，BM蛋白生理状态下不溶于水，且对蛋白水解消化具有部分抗性，这为基底膜的研究带来了挑战。本研究分离得到成人眼部的三种基底膜：内界膜（Inner limiting membrane, ILM）、视网膜血管基底膜与晶状体囊膜（Lens capsule, LC），并通过一维十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（1D-SDS-PAGE）与液相色谱-串联质谱（LC–MS/MS）开展分析。肽段与蛋白质的鉴定采用MaxQuant软件完成，最终以1%的错误发现率（false discovery rate, FDR）鉴定得到1129种蛋白质。分析数据显示，基底膜由多种层粘连蛋白、Ⅳ型胶原蛋白、巢蛋白及蛋白聚糖组成。三类基底膜中占主导的层粘连蛋白家族成员均为层粘连蛋白α5β2γ1。晶状体囊膜与血管（Blood vessel, BV）基底膜中占主导的Ⅳ型胶原蛋白三聚体的链组成为α1(IV)₂、α2(IV)，而内界膜中占主导的Ⅳ型胶原蛋白则为α3(IV)、α4(IV)、α5(IV)链组成。数据还表明，不同类型基底膜中层粘连蛋白与Ⅳ型胶原蛋白的比例存在差异：Ⅳ型胶原蛋白相较于其他基底膜蛋白的占比在晶状体囊膜中最高，其次为血管基底膜，内界膜的占比最低。本数据集已通过标识符PXD001025提交至ProteomeXchange数据库。