Supplementary Material for: Proteomics to metabolomics: A new insight into the pathogenesis of hypertensive nephropathy

Abstract
Background: Hypertensive nephropathy (HN) is a high burden disorder and a leading cause of end-stage renal disorder. In spite of huge investigations, the underlying mechanisms are yet largely unknown. Systems biology is a promising approach to provide a comprehensive insight towards this complex disorder.
Methods: Protein expression profiles of kidney tubule and cortex sub-compartments were retrieved from the PRIDE database and the quality of the datasets were assessed using principal component analysis (PCA) and hierarchical clustering. Differentially expressed proteins (DEPs) were detected and their attributed metabolites were enriched and their interactions were assessed in multi-layer networks. Moreover, considering the DEPs and the predicted metabolites, key biomedical phenomena with a leading role in HN pathogenesis were proposed.
Results: Amino acid and purine metabolisms are the most prominent alteration in kidney cortex whereas dysregulation of energy hemostasis is a key pathogenic mechanism in tubule. Besides, actin cytoskeleton disorganization is an enriched pathway in both anatomical areas.
Conclusion: The proteomics profiles of kidney sub-compartments were analyzed using a top-down approach to infer the main pathogenic processes. The constructed holistic map of HN can be exploited to propose novel therapeutic strategies.
Keywords: Hypertensive nephropathy, Proteomics, Metabolomics, Systems biology

摘要
背景：高血压肾病（Hypertensive Nephropathy, HN）是一类负担沉重的疾病，亦是终末期肾病的首要致病原因。尽管已有大量研究投入，其潜在发病机制仍未被充分阐明。系统生物学作为极具前景的研究方法，可为解析这一复杂疾病提供全面的认知视角。
方法：本研究从PRIDE数据库获取肾脏肾小管与皮质亚分区的蛋白质表达谱，通过主成分分析（Principal Component Analysis, PCA）与层次聚类对数据集质量进行评估；筛选得到差异表达蛋白（Differentially Expressed Proteins, DEPs），对其关联代谢物开展富集分析，并通过多层网络解析二者的相互作用关系。此外，结合差异表达蛋白与预测代谢物，本研究提出了在高血压肾病发病机制中发挥核心作用的关键生物医学现象。
结果：肾皮质的显著代谢异常主要集中于氨基酸代谢与嘌呤代谢通路，而肾小管的关键致病机制则为能量稳态失调；此外，肌动蛋白细胞骨架紊乱在两个解剖区域中均为富集通路。
结论：本研究采用自上而下的分析策略，对肾脏亚分区的蛋白质组学图谱进行解析，以推断高血压肾病的主要致病过程。本研究构建的高血压肾病整体调控图谱，可为新型治疗策略的提出提供参考依据。
关键词：高血压肾病（Hypertensive Nephropathy）、蛋白质组学、代谢组学、系统生物学