Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells

The double membrane nuclear envelope (NE), which is contiguous with the ER, contains nuclear pore complexes (NPCs) – the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) – a scaffold for NE and chromatin organization. Since numerous human diseases linked to NE proteins occur in mesenchyme-derived cells, we used proteomics to characterize NE and other subcellular fractions isolated from mesenchymal stem cells and from adipocytes and myocytes. Based on spectral abundance, we calculated enrichment scores for proteins in the NE fractions. We demonstrated by quantitative immunofluorescence microscopy that five little-characterized proteins with high enrichment scores are substantially concentrated at the NE, with Itprip exposed at the outer nuclear membrane, Smpd4 enriched at the NPC, and Mfsd10, Tmx4, and Arl6ip6 likely residing in the inner nuclear membrane. These proteins provide new focal points for studying the functions of the NE. Moreover, our datasets provide a resource for evaluating additional potential NE proteins.

双层核膜（nuclear envelope, NE）与内质网（endoplasmic reticulum, ER）相连，其包含核孔复合体（nuclear pore complexes, NPCs）——介导核质运输的通道——以及核纤层（nuclear lamina, NL）——核膜与染色质组织的支架结构。鉴于诸多与核膜蛋白相关的人类疾病均发生于间充质来源的细胞中，本研究通过蛋白质组学技术对间充质干细胞、脂肪细胞及肌细胞中分离得到的核膜组分与其他亚细胞组分进行了表征。研究基于光谱丰度计算了核膜组分中蛋白质的富集得分。本研究通过定量免疫荧光显微镜实验证实，5种富集得分较高且研究较少的蛋白质显著富集于核膜：其中Itprip暴露于外核膜，Smpd4富集于核孔复合体，而Mfsd10、Tmx4及Arl6ip6则可能定位于内核膜。上述蛋白质为核膜功能的研究提供了新的聚焦点。此外，本研究构建的数据集可为后续评估潜在核膜蛋白提供宝贵的资源库。