Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue.

IF 2.1 4区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

PROTEOMICS – Clinical Applications Pub Date : 2024-11-01 Epub Date: 2024-06-24 DOI:10.1002/prca.202400018

Stefanie K Schwab, Peter S Harris, Cole Michel, Courtney D McGinnis, Rooban B Nahomi, Mohammed A Assiri, Richard Reisdorph, Kammi Henriksen, David J Orlicky, Moshe Levi, Avi Rosenberg, Ram H Nagaraj, Kristofer S Fritz

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引用次数: 0

Abstract

Purpose: Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end-stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post-translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.

Experimental design: A novel extraction and LC-MS/MS approach was adapted to quantify sites of lysine acetylation from formalin-fixed paraffin-embedded (FFPE) kidney tissue and from patients with DKD and non-diabetic donors (n = 5 and n = 7, respectively).

Results: Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.

Conclusions and clinical relevance: A quantitative acetylomics platform was developed for protein biomarker discovery in formalin-fixed and paraffin-embedded biopsies of kidney transplant patients suffering from DKD.

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从福尔马林固定的石蜡包埋组织中量化糖尿病肾病的蛋白质乙酰化。

目的：糖尿病肾病（DKD）是糖尿病的一种严重并发症，也是导致慢性肾病和终末期肾病的主要原因。导致肾病的细胞功能障碍的潜在机制之一是蛋白质翻译后修饰异常。赖氨酸乙酰化与细胞代谢通量有关，被认为是糖尿病患者和肾脏代谢功能障碍患者体内赖氨酸乙酰化的改变：实验设计：采用一种新颖的提取和LC-MS/MS方法，对福尔马林固定石蜡包埋（FFPE）肾组织中的赖氨酸乙酰化位点进行量化，这些位点分别来自DKD患者和非糖尿病供体（n = 5和n = 7）：对 FFPE 组织的分析确定了 840 种总蛋白质，其中 225 种在 DKD 患者中发生了显著变化。乙酰化组学分析定量分析了289个乙酰化肽，其中69个有明显变化。DKD患者受影响的途径包括许多代谢途径，特别是线粒体功能、氧化磷酸化和sirtuin信号转导。DKD患者蛋白质乙酰化的差异影响了sirtuin信号转导、缬氨酸、亮氨酸和异亮氨酸降解、乳酸代谢、氧化磷酸化和酮生成：该研究开发了一个定量乙酰组学平台，用于发现DKD肾移植患者福尔马林固定和石蜡包埋活检组织中的蛋白质生物标记物。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

PROTEOMICS – Clinical Applications 医学-生化研究方法

CiteScore

5.20

自引率

5.00%

发文量

审稿时长

1 months

期刊介绍： PROTEOMICS - Clinical Applications has developed into a key source of information in the field of applying proteomics to the study of human disease and translation to the clinic. With 12 issues per year, the journal will publish papers in all relevant areas including: -basic proteomic research designed to further understand the molecular mechanisms underlying dysfunction in human disease -the results of proteomic studies dedicated to the discovery and validation of diagnostic and prognostic disease biomarkers -the use of proteomics for the discovery of novel drug targets -the application of proteomics in the drug development pipeline -the use of proteomics as a component of clinical trials.