The code used in the analyses.

<b>Background:</b> Focal segmental glomerulosclerosis (FSGS) is a clinicopathological syndrome manifesting glucocorticoid-resistant nephrosis, which requires new therapies targeting specific pathways. The Columbia classification stratifies FSGS into 5 variants: Collapsing, Tip, Cellular, Perihilar and NOS. Differences in their renal prognosis imply distinct underlying molecular mechanisms, which remain unclear.<b>Objective:</b> To investigate factors associated with the pathogenesis of FSGS and explore potential therapeutic targets.<b>Methods:</b> A total of 73 kidney biopsy tissues were analyzed by LC-MS/MS: FSGS (n=23), renal donors (n=14) as a healthy control group, and minimal change disease (n=15) and IgA nephropathy (n=21) as disease control groups. We validated the proteome data with immunohistochemistry and the Nephroseq microarray data.<b>Results:</b> Our proteomics platform identified a total of 4,168 proteins. A comparison between the FSGS with renal donor groups revealed 175 proteins increased in the FSGS group, which associated with the complement activation and immune responses. Together with comparisons against the disease control groups, complement factor D (CFD) emerged as a distinctive factor. Immunohistochemistry and the Nephroseq microarray analyses uncovered CFD production elevated primarily in glomeruli. Furthermore, the protein profiles demonstrated molecular differences underlying the Columbia variants. In the Cellular and Tip variants, factors involved in the complement pathway were enriched, while proteins associated with the ribosome, thermogenesis, and ferroptosis were predominant in the Collapsing variant.<b>Conclusion:</b> The elevated CFD and complement activation in glomeruli potentially contribute to the pathogenesis of FSGS. The molecular heterogeneity among the Columbia variants may enable to stratify treatment of FSGS as a new precision medicine approach.

背景：局灶节段性肾小球硬化症（Focal segmental glomerulosclerosis, FSGS）是一类表现为糖皮质激素抵抗性肾病的临床病理综合征，亟需开发靶向特定通路的新型治疗方案。哥伦比亚分型将FSGS分为5种亚型：塌陷型、顶端型、细胞型、门周型及非特指型（NOS）。不同亚型的肾脏预后存在差异，提示其潜在分子机制各不相同，但目前相关机制仍未阐明。目的：本研究旨在探讨与FSGS发病机制相关的影响因素，并探索潜在治疗靶点。方法：本研究通过液相色谱-串联质谱（LC-MS/MS）分析了73份肾脏活检组织样本：其中FSGS组23例，健康对照组为14例肾脏供体组织，疾病对照组包含15例微小病变肾病（minimal change disease）患者样本及21例IgA肾病患者样本。我们采用免疫组化技术及Nephroseq芯片数据集对蛋白质组学数据进行了验证。结果：本研究的蛋白质组学平台共鉴定出4168种蛋白质。对比FSGS组与肾脏供体对照组，发现FSGS组中共175种蛋白质表达上调，这些蛋白质与补体激活及免疫应答过程密切相关。结合与疾病对照组的对比分析，补体因子D（Complement Factor D, CFD）被鉴定为特异性差异分子。免疫组化及Nephroseq芯片分析结果显示，CFD主要在肾小球中表达上调。此外，蛋白质组谱分析揭示了哥伦比亚分型各亚型间的分子差异：细胞型与顶端型FSGS样本中补体通路相关因子富集显著，而塌陷型FSGS样本则以核糖体、产热及铁死亡相关蛋白质为主要特征。结论：肾小球内补体因子D表达上调及补体激活可能参与了FSGS的发病过程。哥伦比亚分型各亚型间存在的分子异质性，可为FSGS的分层治疗提供新型精准医学策略。