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Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy.

ABSTRACT: Posttranslational modifications (PTMs) to histones such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes and occurs in active promoters, directly accelerating transcription. The present study performed a proteomics analysis of crotonylation between healthy controls and patients with immunoglobulin A (IgA) nephropathy using tandem mass spectrometry and high‑resolution liquid chromatography. The present results identified 353 crotonylated proteins and 770 modification sites, including 155 upregulated and 198 downregulated crotonylated proteins. In total, seven conserved motifs were identified in the present study. The present bioinformatics analysis results suggested a number of the crotonylated proteins exhibited various subcellular localization patterns, such as in the cytoplasm. Protein domains, including thioredoxin, moesin tail and myosin like IQ motif domains were markedly enriched in crotonylated proteins. Kyoto Encyclopedia of Genes and Genomes and functional enrichment analyses suggested significant enrichment of crotonylated proteins in complement and coagulation cascades, and antigen processing and presentation pathways displaying important relationships with IgA nephropathy. The present results suggested that crotonylation occurred in numerous proteins and may play key regulatory roles in IgA nephropathy.

SUBMITTER: Lin H

PROVIDER: S-EPMC7002971 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy.

Lin Hua H Tang Donge D Xu Yong Y Zhang Ruohan R Ou Minglin M Zheng Fengping F Chen Jiejing J Zhang Yue Y Zou Guimian G Xue Wen W Zou Yaoshuang Y Dai Weier W Sui Weiguo W Dai Yong Y

Molecular medicine reports 20200113 3

Posttranslational modifications (PTMs) to histones such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes and occurs in active promoters, directly accelerating transcription. The present study performed a proteomics analysis of crotonylation between healthy controls and patients with immunoglobulin A (IgA) nephropathy using tandem mass spectrometry and high‑resolution liquid chromatography. The present results identified ...[more]

PMID: 32016442

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Project description:There is considerable evidence that human genetic variation influences gene expression. Genome-wide studies have revealed that mRNA levels are associated with genetic variation in or close to the gene coding for those mRNA transcripts - cis effects, and elsewhere in the genome - trans effects. The role of genetic variation in determining protein levels has not been systematically assessed. Using a genome-wide association approach we show that common genetic variation influences levels of clinically relevant proteins in human serum and plasma. We evaluated the role of 496,032 polymorphisms on levels of 42 proteins measured in 1200 fasting individuals from the population based InCHIANTI study. Proteins included insulin, several interleukins, adipokines, chemokines, and liver function markers that are implicated in many common diseases including metabolic, inflammatory, and infectious conditions. We identified eight Cis effects, including variants in or near the IL6R (p = 1.8x10(-57)), CCL4L1 (p = 3.9x10(-21)), IL18 (p = 6.8x10(-13)), LPA (p = 4.4x10(-10)), GGT1 (p = 1.5x10(-7)), SHBG (p = 3.1x10(-7)), CRP (p = 6.4x10(-6)) and IL1RN (p = 7.3x10(-6)) genes, all associated with their respective protein products with effect sizes ranging from 0.19 to 0.69 standard deviations per allele. Mechanisms implicated include altered rates of cleavage of bound to unbound soluble receptor (IL6R), altered secretion rates of different sized proteins (LPA), variation in gene copy number (CCL4L1) and altered transcription (GGT1). We identified one novel trans effect that was an association between ABO blood group and tumour necrosis factor alpha (TNF-alpha) levels (p = 6.8x10(-40)), but this finding was not present when TNF-alpha was measured using a different assay , or in a second study, suggesting an assay-specific association. Our results show that protein levels share some of the features of the genetics of gene expression. These include the presence of strong genetic effects in cis locations. The identification of protein quantitative trait loci (pQTLs) may be a powerful complementary method of improving our understanding of disease pathways.

Project description:ImportanceImmunoglobulin A nephropathy is a major cause of end-stage renal disease worldwide; previous methods of medical management, including use of renin-angiotensin system inhibitors and corticosteroids, remain unproven in clinical trials.ObjectiveTo investigate the possible association between tonsillectomy and outcomes in patients with IgA nephropathy.Design, setting, and participantsThis cohort study included 1065 patients with IgA nephropathy enrolled between 2002 and 2004 and divided into 2 groups, those who underwent tonsillectomy and those who did not. Initial treatments (renin-angiotensin system inhibitors or corticosteroids) within 1 year after renal biopsy were also evaluated. A 1:1 propensity score matching was performed to account for between-group differences and 153 matched pairs were obtained. Follow-up concluded January 31, 2014. Analysis was conducted between September 11, 2017, and July 31, 2018.ExposureTonsillectomy.Main outcomes and measuresThe primary outcome was the first occurrence of a 1.5-fold increase in serum creatinine level from baseline or dialysis initiation. Secondary outcomes included additional therapy with renin-angiotensin system inhibitors or corticosteroids initiated 1 year after renal biopsy and adverse events.ResultsIn 1065 patients (49.8% women; median [interquartile range] age, 35 [25-52] years), the mean (SD) estimated glomerular filtration rate was 76.6 (28.9) mL/min/1.73 m2 and the median (interquartile range) proteinuria was 0.68 (0.29-1.30) g per day. In all, 252 patients (23.7%) underwent tonsillectomy within 1 year after renal biopsy and 813 patients (76.3%) did not undergo tonsillectomy. The primary outcome was reached by 129 patients (12.1%) during a median (interquartile range) follow-up of 5.8 (1.9-8.5) years. In matching analysis, tonsillectomy was associated with primary outcome reduction (hazard ratio, 0.34; 95% CI, 0.13-0.77; P = .009). In subgroup analyses, benefit associated with tonsillectomy was not modified by baseline characteristic differences. Those undergoing tonsillectomy required fewer additional therapies 1 year following renal biopsy (adjusted hazard ratio, 0.37; 95% CI, 0.20-0.63; P < .001) without increased risks for adverse events, except transient tonsillectomy-related complications.Conclusions and relevanceThis study found that tonsillectomy was associated with a lower risk of renal outcomes in patients with IgA nephropathy. The potential role of tonsillectomy should be considered for preventing end-stage renal disease in patients with IgA nephropathy.

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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.

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