ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia.
Int J Mol Sci. 2023 Feb 1;24(3):2827. doi: 10.3390/ijms24032827.
Precise characterization of a tissue's extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules' activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome.
精确描述组织的细胞外基质（ECM）蛋白组成（基质组）对于生物医学至关重要。然而，需要器官特异性优化的 ECM 蛋白提取仍然是基质组研究的主要限制因素。特别是，尽管小鼠模型对于肾脏研究至关重要，但小鼠肾脏的基质组仍未得到充分研究。在这里，我们使用两种 ECM 提取方法结合液相色谱串联质谱（LC-MS/MS）、使用 MaxQuant 的蛋白质鉴定和无标记定量（LFQ），全面描述了健康 C57BL/6 小鼠肾脏的基质组。我们鉴定了 113 种基质组蛋白，其中 22 种蛋白以前未被列入基质组数据库。根据提取方法的不同，核心基质组（结构蛋白）占肾脏 ECM 蛋白的 45%或 73%，主要由糖蛋白组成，其次是胶原蛋白和蛋白聚糖。在基质组相关蛋白中，ECM 调节剂的 LFQ 强度最高，其次是 ECM 相关蛋白和分泌因子。鉴定出的肾脏 ECM 蛋白主要参与细胞、发育和代谢过程，以及分子结合和催化及结构分子活性的调节。我们还根据公开数据对人类和小鼠肾脏基质组组成进行了计算机比较分析。这些结果为小鼠肾脏基质组提供了第一个参考数据库。
