Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy

Abstract Background Idiopathic membranous nephropathy (IMN) is a cause of nephrotic syndrome that is increasing in incidence but has unclear pathogenesis. Urinary peptidomics is a promising technology for elucidating molecular mechanisms underlying diseases. Dysregulation of the proteolytic system is implicated in various diseases. Here, we aimed to conduct urinary peptidomics to identify IMN-related proteases. Results Peptide fingerprints indicated differences in naturally produced urinary peptide components among 20 healthy individuals, 22 patients with IMN, and 15 patients with other kidney diseases. In total, 1,080 peptide-matched proteins were identified, 279 proteins differentially expressed in the urine of IMN patients were screened, and 32 proteases were predicted; 55 of the matched proteins were also differentially expressed in the kidney tissues of IMN patients, and these were mainly involved in the regulation of proteasome-, lysosome-, and actin cytoskeleton-related signaling pathways. The 32 predicted proteases showed abnormal expression in the glomeruli of IMN patients based on Gene Expression Omnibus databases. Western blot revealed abnormal expression of calpain, matrix metalloproteinase 14, and cathepsin S in kidney tissues of patients with IMN. Conclusions This work shown the calpain/matrix metalloproteinase/cathepsin axis might be dysregulated in IMN. Our study is the first to systematically explore the role of proteases in IMN by urinary peptidomics, which are expected to facilitate discovery of better biomarkers for IMN.

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Phospholipase A2 Receptor Antibody IgG4 Subclass Improves Sensitivity and Specificity in the Diagnosis of Idiopathic Membranous Nephropathy

Kidney & Blood Pressure Research ◽

10.1159/000500456 ◽

2019 ◽

Vol 44 (4) ◽

pp. 848-857 ◽

Cited By ~ 3

Author(s):

Biao Huang ◽

Yi Zhang ◽

Liang Wang ◽

Wenwei Xu ◽

Jue Zhang ◽

...

Keyword(s):

Phospholipase A2 ◽

Sensitivity And Specificity ◽

Membranous Nephropathy ◽

Kidney Diseases ◽

Measurement Range ◽

Idiopathic Membranous Nephropathy ◽

Time Resolved ◽

Specificity And Sensitivity ◽

Phospholipase A2 Receptor ◽

Highly Sensitive

Aims: The aim of this study was to develop a new method for detecting anti-phospholipase A2 receptor-IgG4 to improve the sensitivity and specificity in the diagnosis of idiopathic membranous nephropathy (IMN). Methods: A highly sensitive quantitative assay was developed for the detection of serum anti-phospholipase A2 receptor-IgG4 with europium chelation by time-resolved fluoroimmunoassay (TRFIA), and a mouse anti-human IgG4 tracer was prepared using europium chelation for detection. The specificity and sensitivity of anti-phospholipase A2 receptor-IgG4 in the diagnosis of IMN were further assessed in patients with different kidney diseases. Results: The detection limit of anti-PLA2R-IgG4 was 0.69 ng/mL. The measurement range of anti-PLA2R-IgG4 TRFIA was 0.69–2,500 ng/mL. Mean serum anti-PLA2R-IgG4 was 21.27 ± 15.15 ng/mL in 45 healthy volunteers, 31.08 ± 18.17 ng/mL in 29 IgA nephropathy patients, 49.10 ± 34.32 ng/mL in 8 lupus nephropathy patients, and 10,324.11 ± 17,030.40 ng/mL in 30 IMN patients. The anti-PLA2R-IgG4 cutoff concentration was >161.2 ng/mL with the sensitivity of 90.0% and specificity of 100% in the diagnosis of IMN. However, the cutoff for other kidney diseases was lower than 161.2 ng/mL. Conclusion: The serum anti-phospholipase A2 receptor IgG4 detected with the method developed in this study has higher sensitivity and higher specificity than total IgG in the diagnosis of IMN.

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Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease

Parkinson s Disease ◽

10.1155/2019/6078251 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

Lu-Mei Chi ◽

Li-Ping Wang ◽

Dan Jiao

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Noncoding Rnas ◽

Gene Expression Omnibus ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Similar Treatment ◽

Blood Samples

Objectives. This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. We selected 72 samples comprising 22 healthy control blood samples and 50 PD blood samples for further analysis. Later, we used Limma to screen DEGs and differentially expressed lncRNAs (DElncRNAs) and estimated their functions by the Gene Ontology (GO). Besides, the competing endogenous RNA (ceRNA) network, including microRNAs, lncRNAs, and mRNAs, was constructed to elucidate the regulatory mechanism. Furthermore, we performed the KEGG pathway enrichment with mRNAs in the ceRNA regulatory network and constructed a final network, including pathways, mRNAs, microRNAs, and lncRNAs. Results. Overall, we obtained 394 DEGs, including 207 upregulated DEGs and 187 downregulated DEGs, and 7 DElncRNAs, including 2 upregulated DElncRNAs and 5 downregulated DElncRNAs. Insulin-like growth factor-1 receptor (IGF1R) was considerably enriched in the endocytosis pathway. In the ceRNA regulation network, IGF1R was the target of hsa-miR-133b and lncRNAs of XIST, and PART1 could also be the target of hsa-miR-133b. While the upregulated DEGs were enriched in the GO terms of the cytoskeleton, cytoskeletal part, and microtubule cytoskeleton, the downregulated DEGs were enriched in the immune response. PRKACA was markedly enriched in numerous pathways, including the MAPK and insulin signaling pathways. Conclusions. IGF1R, PRKACA, and lncRNA-XIST could be potentially involved in PD, and these diverse molecular mechanisms could support the development of the similar treatment for PD.

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Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

BioMed Research International ◽

10.1155/2019/2767512 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Siying He ◽

Hui Sun ◽

Yifang Huang ◽

Shiqi Dong ◽

Chen Qiao ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

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Integrative analysis of miRNA–mRNA network in idiopathic membranous nephropathy by bioinformatics analysis

PeerJ ◽

10.7717/peerj.12271 ◽

2021 ◽

Vol 9 ◽

pp. e12271

Author(s):

Wenfang He ◽

Jinshi Zhang ◽

Shizhu Yuan ◽

Mingzhu Liang ◽

Weidong Chen ◽

...

Keyword(s):

Membranous Nephropathy ◽

Regulatory Networks ◽

Target Genes ◽

Therapeutic Targets ◽

Differentially Expressed ◽

Idiopathic Membranous Nephropathy ◽

Validation Dataset ◽

Epidermal Growth ◽

Specific Antigens

Background Currently, several specific antigens, M-type receptor for secretory phospholipase A2(PLA2R1), thrombospondin type-1 domain-containing 7A(THSD7A), and neural epidermal growth factor-like 1 protein (NELL-1), are discovered associated with the onset of idiopathic membranous nephropathy (IMN). But the pathomechanisms of IMN still need to be further claried. Understanding the mechanisms of IMN is required to improve its diagnosis and treatment. Methods In this study, we constructed miRNA regulatory networks to investigate IMN development. Moreover, miRNAs and mRNAs that were differentially expressed between Idiopathic Membranous Nephropathy (IMN) patients and normal controls were examined using the GSE115857 dataset and our previous sequence study. DE miRNA target genes were determined based on the FUNRICH software, starBase, miRDB, and miRWalk, and an miRNA-mRNA network was designed using DE-mRNAs that were negatively correlated with DE-miRNAs. The miRNA-mRNA network contained 228 miRNA-mRNA pairs. Thereafter, we conducted KEGG pathway, GO functional annotation, immune-related gene screening, protein interaction networks, and potential hub gene analyses. Furthermore, 10 miRNAs and 10 genes were determined and preliminarily validated using the validation dataset from GEO. Finally, we identified which pair may offer more accurate diagnosis and therapeutic targets for IMN. Results Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes. These findings may offer more accurate diagnoses and therapeutic targets for IMN.

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Screening and evaluation of key genes in contributing to pathogenesis of hepatic fibrosis based on microarray data

European Journal of Medical Research ◽

10.1186/s40001-020-00443-0 ◽

2020 ◽

Vol 25 (1) ◽

Author(s):

Furong Wu ◽

Lijuan Ning ◽

Ran Zhou ◽

Aizong Shen

Keyword(s):

Hepatic Fibrosis ◽

Molecular Mechanisms ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Receptor Interaction ◽

Protein Protein Interaction ◽

Functional Studies ◽

Oxidation Reduction ◽

Crucial Information ◽

Underlying Mechanisms

Abstract Background Hepatic fibrosis (HF), which is characterized by the excessive accumulation of extracellular matrix (ECM) in the liver, usually progresses to liver cirrhosis and then death. To screen differentially expressed (DE) long non-coding RNAs (lncRNAs) and mRNAs, explore their potential functions to elucidate the underlying mechanisms of HF. Methods The microarray of GSE80601 was downloaded from the Gene Expression Omnibus database, which is based on the GPL1355 platform. Screening for the differentially expressed LncRNAs and mRNAs was conducted between the control and model groups. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to analyze the biological functions and pathways of the DE mRNAs. Additionally, the protein–protein interaction (PPI) network was delineated. In addition, utilizing the Weighted Gene Co-expression Network Analysis (WGCNA) package and Cytoscape software, we constructed lncRNA-mRNA weighted co-expression networks. Results A total of 254 significantly differentially expressed lncRNAs and 472 mRNAs were identified. GO and KEGG analyses revealed that DE mRNAs regulated HF by participating in the GO terms of metabolic process, inflammatory response, response to wounding and oxidation–reduction. DE mRNAs were also significantly enriched in the pathways of ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion (FA), retinol metabolism and metabolic pathways. Moreover, 24 lncRNAs associated with 40 differentially expressed genes were observed in the modules of lncRNA-mRNA weighted co-expression network. Conclusions This study revealed crucial information on the molecular mechanisms of HF and laid a foundation for subsequent genes validation and functional studies, which could contribute to the development of novel diagnostic markers and provide new therapeutic targets for the clinical treatment of HF.

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Identification of key biomarkers for thyroid cancer by integrative gene expression profiles

Experimental Biology and Medicine ◽

10.1177/15353702211008809 ◽

2021 ◽

pp. 153537022110088

Author(s):

Jinyi Tian ◽

Yizhou Bai ◽

Anyang Liu ◽

Bin Luo

Keyword(s):

Gene Expression ◽

Thyroid Cancer ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Thyroid Tissue ◽

Gene Signature ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Tissue Samples

Thyroid cancer is a frequently diagnosed malignancy and the incidence has been increased rapidly in recent years. Despite the favorable prognosis of most thyroid cancer patients, advanced patients with metastasis and recurrence still have poor prognosis. Therefore, the molecular mechanisms of progression and targeted biomarkers were investigated for developing effective targets for treating thyroid cancer. Eight chip datasets from the gene expression omnibus database were selected and the inSilicoDb and inSilicoMerging R/Bioconductor packages were used to integrate and normalize them across platforms. After merging the eight gene expression omnibus datasets, we obtained one dataset that contained the expression profiles of 319 samples (188 tumor samples plus 131 normal thyroid tissue samples). After screening, we identified 594 significantly differentially expressed genes (277 up-regulated genes plus 317 down-regulated genes) between the tumor and normal tissue samples. The differentially expressed genes exhibited enrichment in multiple signaling pathways, such as p53 signaling. By building a protein–protein interaction network and module analysis, we confirmed seven hub genes, and they were all differentially expressed at all the clinical stages of thyroid cancer. A diagnostic seven-gene signature was established using a logistic regression model with the area under the receiver operating characteristic curve (AUC) of 0.967. Seven robust candidate biomarkers predictive of thyroid cancer were identified, and the obtained seven-gene signature may serve as a useful marker for thyroid cancer diagnosis and prognosis.

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Urinary Matrix Metalloproteinase-9 and Nephrin in Idiopathic Membranous Nephropathy: A Cross-Sectional Study

Disease Markers ◽

10.1155/2021/1620545 ◽

2021 ◽

Vol 2021 ◽

pp. 1-6

Author(s):

Akankwasa Gilbert ◽

An Changjuan ◽

Cheng Guixue ◽

Liu Jianhua ◽

Qin Xiaosong

Keyword(s):

Matrix Metalloproteinase ◽

Membranous Nephropathy ◽

Healthy Subjects ◽

Kidney Injury ◽

Matrix Metalloproteinase 9 ◽

Idiopathic Membranous Nephropathy ◽

Enzyme Linked Immunosorbent Assay ◽

Cross Sectional ◽

Glomerular Diseases ◽

Metalloproteinase 9

Aim. Idiopathic membranous nephropathy (IMN) has a varied clinical course that requires accurate prediction as a prerequisite for treatment administration. Currently, its prognosis relies on proteinuria, a clinical parameter whose onset lags behind kidney injury. Increased urinary excretion of matrix metalloproteinase-9 (MMP-9) and nephrin has been reported in a number of IMN-like glomerular diseases in which they reflected disease severity. However, little or nothing is known of the importance of these biomarkers in IMN, a major cause of adult nephrotic syndrome. To highlight their potential, we measured both biomarkers and assessed their relationships with key parameters of renal function in IMN. Methods. We quantified urinary MMP-9 and nephrin in 107 biopsy-proven IMN patients and 70 healthy subjects by enzyme-linked immunosorbent assay (ELISA). We then compared biomarker levels between patients and healthy subjects and among patients with different clinical features. We also determined the relationship of each biomarker with proteinuria and the estimated glomerular filtration rate (eGFR). Results. Urinary MMP-9 and nephrin were significantly higher in IMN compared to healthy controls. Unlike nephrin, MMP-9 correlated significantly with proteinuria and was significantly higher among patients with nephrotic range proteinuria. Both biomarkers were correlated with eGFR, but only MMP-9 was significantly higher in patients with eGFR less than 90 ml/min/1.73 m2. Conclusion. Our findings suggest that urinary MMP-9 holds a greater potential than urinary nephrin in monitoring the severity of IMN.

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Analysis of pathways and networks influencing the differential expression of genes in coronary artery disease

Archives of Biological Sciences ◽

10.2298/abs1403983l ◽

2014 ◽

Vol 66 (3) ◽

pp. 983-988 ◽

Cited By ~ 1

Author(s):

Hui Li ◽

Xiaolan Zhong ◽

Chaomin Li ◽

Lijing Peng ◽

Wei Liu ◽

...

Keyword(s):

Gene Expression ◽

Coronary Artery Disease ◽

Coronary Artery ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Hub Genes ◽

Network Analyses ◽

Artery Disease

Coronary artery disease (CAD) is the leading cause of death worldwide. Microarray analysis is a practical approach to study gene transcription changes that may reflect signatures that underlie the pathogenesis of CAD. Using gene expression profile data from the Gene Expression Omnibus database, we identified differentially expressed genes that can contribute to the pathology of CAD. Further pathway and network analyses were also implemented to identify pathways and hub genes related to the disease. We observed 466 downregulated and 560 upregulated genes. The ribosome pathway was the most significantly over-represented pathway with differentially expressed genes. Over 35% of the genes in this pathway were downregulated. Hub genes in the network, such as IL7R, FYN, CALM1 ESR1 and PLCG1, may play crucial roles in the pathogenesis of CAD. Our results facilitate the identification of molecular mechanisms that underlie CAD.

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Differential Expression of Urinary Exosomal Small RNAs in Idiopathic Membranous Nephropathy

BioMed Research International ◽

10.1155/2020/3170927 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Jinshi Zhang ◽

Yifan Zhu ◽

Ruyi Cai ◽

Juan Jin ◽

Qiang He

Keyword(s):

Membranous Nephropathy ◽

High Throughput Sequencing ◽

Expression Profiles ◽

Repetitive Sequences ◽

Differentially Expressed ◽

Idiopathic Membranous Nephropathy ◽

Healthy Controls ◽

Differentially Expressed Mirnas ◽

Urinary Exosomes ◽

Noninvasive Biomarkers

Background. Idiopathic membranous nephropathy (IMN) is a major cause of adult nephrotic syndromes, and reliable noninvasive biomarkers for diagnosis and monitoring are urgently needed. In this study, we performed small RNA (sRNA) sequencing to explore sRNA profiles of urinary exosomes derived from IMN patients and healthy controls (CON) to provide clues for identifying novel noninvasive sRNA biomarkers for IMN. Methods. Urine samples were collected from five healthy controls and six patients with IMN. High-throughput sequencing was used to screen sRNA expression profiles of urinary exosomes from patients with IMN in two independent cohorts. Results. Urinary exosomes were successfully isolated and used to obtain exosomal sRNAs. We screened 131 differentially expressed miRNAs, including 28 specifically expressed miRNAs, then explored the top 10 specifically expressed miRNAs in all IMN individuals. The specifically expressed miRNAs and differentially expressed miRNAs provide potential biomarkers for IMN. Additionally, we discovered numerous sRNAs derived from genomic repetitive sequences, which could represent an exciting new area of research. Conclusion. Herein, we revealed significant differences in expression profiles of urinary exosomal miRNAs and repetitive region-derived sRNAs between patients with IMN and healthy controls. The findings could facilitate the development of potential molecular targets for membranous nephropathy.

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Detection of urinary podocytes by flow cytometry in idiopathic membranous nephropathy

Scientific Reports ◽

10.1038/s41598-020-73335-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Alberto Mella ◽

Ilaria Deambrosis ◽

Silvia Mingozzi ◽

Loredana Colla ◽

Manuel Burdese ◽

...

Keyword(s):

Flow Cytometry ◽

Linear Correlation ◽

Membranous Nephropathy ◽

Kidney Diseases ◽

Continuous Variable ◽

Idiopathic Membranous Nephropathy ◽

Non Linear ◽

Prognostic Utility ◽

Circulating Autoantibodies ◽

Antibody Levels

AbstractIdiopathic membranous nephropathy (iMN) is considered an immune-mediated disease where circulating autoantibodies against podocyte targets (mainly the PLA2R) cause the deposition of in-situ subepithelial immune-complexes. The consequent podocyte damage may cause cell detachment in urine (Podocyturia-PdoU). PdoU has been assessed in different kidney diseases, but limited data are available in iMN. In this study all patients with a diagnosis of iMN between 15/12/1999–16/07/2014 were tested for PLA2R antibodies (Ab anti-PLA2R, ELISA kit) and PdoU by flow cytometry with anti-podocalyxin antibody. A semi-quantitative PdoU score was defined according to the percentage of podocalyxin positive cells normalized to the total volume of sample and set relative to the urine creatinine measured in the supernatant. PdoU was positive in 17/27 patients (63%; 1+ score in 6/27—22.2%, 2+ in 4/27—14.8%, 3+ in 2/27—7.4%, 4+ in 5/27—18.5%). Only 2/7 patients with complete remission showed a positive PdoU (1+) while all six patients without remission have significant PdoU. PdoU+ was statistically correlated with the absence of remission and Ab anti-PLA2R + (p < 0.05) but PdoU, analysed as a continuous variable, showed a non-linear correlation with proteinuria or PLA2R antibody levels also in the cohort of patients with two available PdoU tests. In conclusion, PdoU could be detected in iMN and seems to be associated with commonly considered markers of disease activity (proteinuria and Ab anti-PLA2R) with a non-linear correlation. Despite data should be confirmed in large and prospective cohorts, according to the podocyte depletion hypothesis PdoU may represent an early marker of immunological activation with potential prognostic utility.

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