Renal Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania.
J Am Soc Nephrol. 2023 Jul 1;34(7):1279-1291. doi: 10.1681/ASN.0000000000000141. Epub 2023 Apr 5.
Although gene expression changes have been characterized in human diabetic kidney disease (DKD), unbiased tissue proteomics information for this condition is lacking. The authors conducted an unbiased aptamer-based proteomic analysis of samples from patients with DKD and healthy controls, identifying proteins with levels that associate with kidney function (eGFR) or fibrosis, after adjusting for key covariates. Overall, tissue gene expression only modestly correlated with tissue protein levels. Kidney protein and RNA levels of matrix metalloproteinase 7 (MMP7) strongly correlated with fibrosis and with eGFR. Single-cell RNA sequencing indicated that kidney tubule cells are an important source of MMP7. Furthermore, plasma MMP7 levels predicted future kidney function decline. These findings identify kidney tissue MMP7 as a biomarker of fibrosis and blood MMP7 as a biomarker for future kidney function decline.
Diabetic kidney disease (DKD) is responsible for close to half of all ESKD cases. Although unbiased gene expression changes have been extensively characterized in human kidney tissue samples, unbiased protein-level information is not available.
We collected human kidney samples from 23 individuals with DKD and ten healthy controls, gathered associated clinical and demographics information, and implemented histologic analysis. We performed unbiased proteomics using the SomaScan platform and quantified the level of 1305 proteins and analyzed gene expression levels by bulk RNA and single-cell RNA sequencing (scRNA-seq). We validated protein levels in a separate cohort of kidney tissue samples as well as in 11,030 blood samples.
Globally, human kidney transcript and protein levels showed only modest correlation. Our analysis identified 14 proteins with kidney tissue levels that correlated with eGFR and found that the levels of 152 proteins correlated with interstitial fibrosis. Of the identified proteins, matrix metalloprotease 7 (MMP7) showed the strongest association with both fibrosis and eGFR. The correlation between tissue MMP7 protein expression and kidney function was validated in external datasets. The levels of MMP7 RNA correlated with fibrosis in the primary and validation datasets. Findings from scRNA-seq pointed to proximal tubules, connecting tubules, and principal cells as likely cellular sources of increased tissue MMP7 expression. Furthermore, plasma MMP7 levels correlated not only with kidney function but also associated with prospective kidney function decline.
Our findings, which underscore the value of human kidney tissue proteomics analysis, identify kidney tissue MMP7 as a diagnostic marker of kidney fibrosis and blood MMP7 as a biomarker for future kidney function decline.
意义陈述：尽管已经在人类糖尿病肾病（DKD）中描述了基因表达的变化，但这种疾病缺乏基于无偏倚的组织蛋白质组学信息。作者对 DKD 患者和健康对照者的样本进行了基于无偏倚适配子的蛋白质组学分析，在调整了关键协变量后，鉴定了与肾功能（eGFR）或纤维化相关的蛋白水平。总体而言，组织基因表达仅与组织蛋白水平中度相关。肾脏蛋白质和 RNA 水平的基质金属蛋白酶 7（MMP7）与纤维化和 eGFR 强烈相关。单细胞 RNA 测序表明，肾脏肾小管细胞是 MMP7 的重要来源。此外，血浆 MMP7 水平可预测未来肾功能下降。这些发现确定了肾脏组织 MMP7 作为纤维化的生物标志物和血液 MMP7 作为未来肾功能下降的生物标志物。
背景：糖尿病肾病（DKD）导致近一半的终末期肾病（ESKD）病例。尽管已经广泛描述了人类肾脏组织样本中的无偏倚基因表达变化，但没有无偏倚的蛋白质水平信息。
方法：我们收集了 23 名 DKD 患者和 10 名健康对照者的肾脏样本，收集了相关的临床和人口统计学信息，并进行了组织学分析。我们使用 SomaScan 平台进行了无偏蛋白质组学分析，定量了 1305 种蛋白质的水平，并通过批量 RNA 和单细胞 RNA 测序（scRNA-seq）分析了基因表达水平。我们在另一批肾脏组织样本以及 11030 个血液样本中验证了蛋白质水平。
结果：总体而言，人类肾脏的转录物和蛋白质水平仅显示出适度的相关性。我们的分析确定了 14 种与 eGFR 相关的肾脏组织水平的蛋白质，发现 152 种蛋白质的水平与间质纤维化相关。在鉴定出的蛋白质中，基质金属蛋白酶 7（MMP7）与纤维化和 eGFR 的相关性最强。组织 MMP7 蛋白表达与肾脏功能的相关性在外部数据集中得到了验证。MMP7 RNA 的水平与原发性和验证性数据集的纤维化相关。scRNA-seq 的结果表明，近端小管、连接小管和主细胞可能是组织中 MMP7 表达增加的潜在细胞来源。此外，血浆 MMP7 水平不仅与肾功能相关，还与未来的肾功能下降相关。
结论：我们的研究结果强调了人类肾脏组织蛋白质组学分析的价值，确定了肾脏组织 MMP7 作为肾脏纤维化的诊断标志物和血液 MMP7 作为未来肾功能下降的生物标志物。
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