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Quantitative Analysis of Protein Crotonylation Identifies Its Association with Immunoglobulin a Nephropathy

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Quantitative Analysis of Protein Crotonylation Identifies Its Association with Immunoglobulin a Nephropathy 1242 MOLECULAR MEDICINE REPORTS 21: 1242-1250, 2020 Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy HUA LIN1, DONGE TANG2, YONG XU2, RUOHAN ZHANG1, MINGLIN OU1, FENGPING ZHENG2, JIEJING CHEN1, YUE ZHANG1, GUIMIAN ZOU1, WEN XUE1, YAOSHUANG ZOU1, WEIER DAI3, WEIGUO SUI1 and YONG DAI1,2 1Nephrology Department of 924th Hospital, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin Key Laboratory of Kidney Diseases Research, Guilin, Guangxi 541002; 2Clinical Medical Research Center of The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China; 3College of Natural Science, University of Texas at Austin, Austin, TX 78712, USA Received June 9, 2019; Accepted November 19, 2019 DOI: 10.3892/mmr.2020.10931 Abstract. Posttranslational modifications (PTMs) to histones Introduction such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes Posttranslational modifications (PTMs) have important roles and occurs in active promoters, directly accelerating tran- in numerous biological processes, including organismal devel- scription. The present study performed a proteomics analysis opment and cell differentiation, thus constituting a primary of crotonylation between healthy controls and patients with pathway in epigenetic regulation (1). PTMs of proteins have immunoglobulin A (IgA) nephropathy using tandem mass been discovered using various technologies, including mass spectrometry and high‑resolution liquid chromatography. The spectrometry (MS) (2). PTMs present at low levels are present results identified 353 crotonylated proteins and 770 enriched at the peptide level in MS detection (3,4). Using modification sites, including 155 upregulated and 198 down- MS‑based proteomics, the present study may have identi- regulated crotonylated proteins. In total, seven conserved motifs fied novel histone PTMs, such as crotonylation and different were identified in the present study. The present bioinformatics non‑acetyl lysine acylation events. Lysine crotonylation analysis results suggested a number of the crotonylated proteins regulates the transcription of active genes in the murine male exhibited various subcellular localization patterns, such as in germ cell and human cell genomes (5). Furthermore, lysine the cytoplasm. Protein domains, including thioredoxin, moesin crotonylation may play an important role in modulating gene tail and myosin like IQ motif domains were markedly enriched expression in male haploid cells (6). Lysine crotonylation is in crotonylated proteins. Kyoto Encyclopedia of Genes and principally related to active transcription (7). The histone Genomes and functional enrichment analyses suggested signifi- acetyltransferase p300/CREB‑binding protein catalyzes cant enrichment of crotonylated proteins in complement and histone crotonylation and directly participates in transcrip- coagulation cascades, and antigen processing and presentation tional activation in vivo (8). Moreover, the abundance of pathways displaying important relationships with IgA nephrop- crotonyl‑coenzyme A may affect levels of crotonylation (9). athy. The present results suggested that crotonylation occurred Therefore, lysine crotonylation sites in proteins must be identi- in numerous proteins and may play key regulatory roles in IgA fied to provide improved understanding of the physiological nephropathy. functions of crotonylation. PTMs have been identified in subjects with chronic renal disease (10). Crotonylation has been identified in renal tissues and is a key contributor to the epigenetic regulation of gene expression (5). A useful in vivo effect over preclinical kidney injury has been showed for drugs that interfere with histone Correspondence to: Professor Yong Dai or Mr. Weiguo Sui, modification readers such as inhibition of extra‑terminal Nephrology Department of 924th Hospital, Guangxi Key Laboratory proteins and bromodomain, or increase histone crotonyl- of Metabolic Diseases Research, Guilin Key Laboratory of Kidney ation (11). Histone crotonylation protects against nephrotoxic Diseases Research, 1 Xinqiaoyuan Road, Xiangshan, Guilin, Guangxi 541002, P.R. China acute kidney injury; however, research is inconsistent on DNA E‑mail: [email protected] methylation inhibitors for preclinical acute kidney injury (12). E‑mail: [email protected] Immunoglobulin A nephropathy (IgAN), a common glomerular disease that results in chronic or end‑stage kidney Key words: posttranslational modifications, lysine crotonylation, disease (13), is caused by an accumulation of IgA in the tandem mass spectrometry, proteome, immunoglobulin A nephropathy glomerular mesangium (14). Differences in IgAN have been observed between ethnicities, with a higher incidence disease reported in Asian populations (15). A high concentration of LIN et al: QuantitativE analysis of protein crotonylation in IGAN 1243 IgA in the blood increases the risk of IgAN (16). Patients Inc.) and stored at ‑80˚C. Samples were sonicated 3 min at 4˚C are diagnosed with IgAN or other glomerulonephritides by a three times on ice using a high intensity ultrasonic processor kidney biopsy, which is an invasive method (17). Therefore, (Ningbo Scientz Biotechnology Co., Ltd.) in lysis buffer non‑invasive diagnostic markers of IgAN would aid current containing 8 M urea (Sigma‑Aldrich; Merck KGaA) and 1% laboratory and clinical methods. In total, ~30% of patients protease inhibitor cocktail (Merck KGaA). The remaining with IgAN progress to end‑stage renal disease, with the debris was centrifugated at 12,000 x g for 10 min at 4˚C. The remainder having low‑grade proteinuria or hematuria (18). The supernatant was obtained and the protein concentration in all pathogenic mechanisms of IgAN are complex. IgA immune six IgAN samples was determined using a BCA kit. complexes, including the IgA1 subtype, accumulate in the glomerulus, and cause inflammation and renal injury (19). Trypsin digestion. The protein solution was reduced with A previous study revealed a new function for microRNAs 5 mM dithiothreitol for 30 min at 56˚C and alkylated with (miRs) in nephropathy with IgA1 (20). Abnormal miR‑148b 11 mM iodoacetamide for 15 min at room temperature in the expression results in high levels of galactose‑deficient IgA1 in dark. The protein sample was then diluted with 100 mM trieth- peripheral blood mononuclear cells (PBMCs) in patients with ylammonium bicarbonate (TEAB) buffer (Sigma‑Aldrich; IgAN (21). Additional factors such as CD89‑IgA complexes Merck KGaA) to obtain a urea concentration <2 M. Trypsin and low‑molecular‑weight proteins in the blood are related to was added at a 1:50 trypsin‑to‑protein mass ratio for the first hematuria, proteinuria and organic lesions (22,23). However, digestion overnight at 37˚C and a 1:100 trypsin‑to‑protein no previous studies have translated into clinical assessment, mass ratio for a second 4‑h digestion at 37˚C. thus the specificity of the findings for IgAN must be evaluated. Currently, genetic and serological methods for differentiating Tandem mass tag (TMT) labelling. Peptides were desalted IgAN from other renal diseases are unavailable. Therefore, the using a Strata X C18 SPE column (Phenomenex) and then pathogenesis of glomerular disease must be investigated. vacuum‑dried. The peptides were reconstituted in 0.5 M The present study performed liquid‑chromatography TEAB and processed with a TMT Mass Tagging kits and fractionation and MS to investigate differences in crotonyl- reagents (Thermo Fisher Scientific, Inc.). One unit of TMT ated peptides and proteins between healthy negative controls reagent was thawed and reconstituted in acetonitrile (100%). (NC) and patients with IgAN. Subsequently, bioinformatics The peptide mixtures were incubated with the mixture for 2 h analysis was conducted to investigate the functions of mark- at room temperature, pooled, desalted and dried by vacuum edly enriched proteins. Crotonylation was identified in a centrifugation at 1,400 x g for 2 h at 30˚C. proteomics analysis of samples from patients with IgAN. The aim of the present study was to understand the function of High‑performance liquid chromatography (HPLC) fraction‑ lysine crotonylation in patients with IgAN. PTMs may repre- ation. No internal standards were used. The flow rate was sent a potentially novel biomarker and factor contributing to 1 ml/min. Column temperature box was 35˚C during the the pathogenesis of IgAN. classification. Mobile phase A: 98% water and 2% acetonitrile, Mobile phase B: 2% water and 98% acetonitrile. Tryptic Materials and methods peptides were fractionated using high pH reverse‑phase HPLC (Agilent 1260; Agilent Technologies GmbH) with a Thermo Controls and patients. Peripheral blood was collected from Betasil C18 column (Thermo Fisher Scientific, Inc.; particle 6 patients at 924nd Hospital between March 2017 and April size, 5 µm; ID, 10 mm; length, 250 mm). The peptides (200 µg) 2018 (age, 25‑41, 33±8; male to female ratio of 4:2) with IgAN were first separated into 60 fractions using a gradient of 8‑32% and 25 control subjects (age 30‑50, 38±4.5; male to female acetonitrile (pH 9.0) over 60 min, combined into crotonylated ratio of 16:9). The diagnosis of IgAN in all patients was fractions and dried via centrifugation under a vacuum at confirmed via histology. IgAN was diagnosed based on the 1,400 x g for 5 h at 30˚C. presence of dominant IgA deposits in proliferating
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