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Zhang H, Lu H, Zhan B, Shi H, Shui B. Comprehensive Analysis of ceRNA Network and Immune Cell Infiltration Pattern of Autophagy-Related Genes in IgA Nephropathy. Kidney Blood Press Res 2024; 49:528-547. [PMID: 38824914 DOI: 10.1159/000539571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/26/2024] [Indexed: 06/04/2024] Open
Abstract
INTRODUCTION IgA nephropathy (IgAN) is a prevalent worldwide glomerular disease with a complex pathophysiology that has significant economic implications. Despite the lack of successful research, this study aims to discover the potential competing endogenous RNA (ceRNA) network of autophagy-associated genes in IgAN and examine their correlation with immune cell infiltration. METHODS Autophagy-related hub genes were discovered by assessing the GSE116626 dataset and constructing a protein-protein interaction network. Nephroseq v5 analysis engine was used to analyze correlations between hub genes and proteinuria, glomerular filtration rate (GFR), and serum creatinine levels. Then, a ceRNA network construction and the CIBERSORT tool for immune cell infiltration analysis were also performed. Additionally, the differentially expressed autophagy-related genes were used to predict potential targeted medications for IgAN. RESULTS Overall, 1,396 differentially expressed genes were identified in IgAN along with 25 autophagy-related differentially expressed messenger RNAs. Enrichment analysis revealed significant involvement of autophagy and apoptosis in biological processes. Next, we evaluated the top hub nodes based on their highest degrees. The ability of IgAN discrimination was confirmed in the GSE35487 and GSE37460 datasets by validating the five hub genes: SIRT1, FOS, CCL2, CDKN1A, and MYC. In the Nephroseq v5 analysis engine, the clinical correlation of the five hub genes was confirmed. Furthermore, the ceRNA network identified 18 circular RNAs and 2 microRNAs associated with hub autophagy-related genes in IgAN. Our investigation identified hsa-miR-32-3p and hsa-let-7i-5p as having elevated expression levels and substantial diagnostic value. Finally, four distinctively infiltrated immune cells were found to be associated with the hub autophagy-related genes, and 67 drugs were identified as potential therapeutic options for IgAN. CONCLUSION This study sheds light on a novel ceRNA regulatory network mechanism associated with autophagy in IgAN development.
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Affiliation(s)
- Huaying Zhang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Huiai Lu
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Bicui Zhan
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - He Shi
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Bingjie Shui
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
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Noncoding RNAs associated with IgA nephropathy. J Nephrol 2022; 36:911-923. [PMID: 36495425 DOI: 10.1007/s40620-022-01498-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
IgA nephropathy (IgAN) is one of the most common glomerulonephritides. The disease is characterized by haematuria, proteinuria, deposition of galactose-deficient IgA1 in the glomerular mesangium and mesangial hypercellularity, further leading to extracellular matrix expansion. Kidney biopsy is the gold standard for IgAN diagnosis. Due to the invasiveness of renal biopsy, there is an unmet need for noninvasive biomarkers to diagnose and estimate the severity of IgAN. Understanding the role of RNA molecules as genetic markers to target diseases may allow developing therapeutic and diagnostic markers. In this review we have focused on intrarenal, extrarenal and extracellular noncoding RNAs involved in the progression of IgAN. This narrative review summarizes the pathogenesis of IgAN along with the correlation of noncoding RNA molecules such as microRNAs, small interfering RNAs, circular RNAs and long non-coding RNAs that play an important role in regulating gene expression, and that represent another type of regulation affecting the expression of specific glycosyltranferases, a key element contributing to the development of IgAN.
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Jianping W, Wei X, Li J, Zhang R, Han Q, Yang Q. Identifying DUSP-1 and FOSB as hub genes in immunoglobulin A nephropathy by WGCNA and DEG screening and validation. PeerJ 2022; 10:e13725. [PMID: 35910761 PMCID: PMC9332322 DOI: 10.7717/peerj.13725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/22/2022] [Indexed: 01/17/2023] Open
Abstract
Background The mechanism of immunoglobulin A nephropathy (IgAN) is still unknown. A bioinformatics analysis is a powerful method to identify the biomarkers and possible therapeutic targets of a certain disease from related datasets. Methods The GSE93973 dataset, obtained from the Gene Expression Omnibus (GEO) database, was used to construct a weighted gene co-expression network (WGCNA) and filter differentially expressed genes (DEGs). The biological process (BP) enrichment among all the genes in the key modules was analyzed through a Gene Ontology (GO) enrichment analysis. We selected the overlap of hub genes in the WGCNA and Protein-Protein Interaction (PPI) network as the final hub genes in IgAN. We verified the final hub genes in two other datasets and in clinical kidney tissue specimens. A receiver operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of hub genes for IgAN. Results The turquoise module, which contained 1,806 genes, was the module with the highest correlation coefficient with IgAN in the GSE93973 dataset. The GO enrichment analysis showed that these 1,806 genes were mainly enriched in inflammation and immune responses. There were five hub genes identified by WGCNA and 34 hub genes identified in a DEG analysis in the GSE93973 dataset. DUSP1 and FOSB were identified as the final hub genes in IgAN. The validation results of the final hub genes in two other databases and clinical kidney tissue specimens validated the result that, compared to the control group, FOSB and DUSP1 were expressed at lower levels in the glomerulus of IgAN patients. The ROC curve indicated that DUSP1 and FOSB were good diagnostic indicators for IgAN. Conclusions Our analysis identified two hub genes that might be potential targets for the intervention and treatment of IgAN.
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Ahmad SM, Bhat B, Manzoor Z, Dar MA, Taban Q, Ibeagha-Awemu EM, Shabir N, Hussain MI, Shah RA, Ganai NA. Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis. PeerJ 2022; 10:e13029. [PMID: 35251787 PMCID: PMC8896013 DOI: 10.7717/peerj.13029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/08/2022] [Indexed: 01/11/2023] Open
Abstract
Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms. A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lactation. In the present study, genome wide identification and expression of the circRNAs in mammary epithelial cells of two distinct cattle breeds viz Jersey and Kashmiri at peak lactation was conducted. We reported 1554 and 1286 circRNA in Jersey and Kashmiri cattle, respectively, with 21 circRNAs being differentially expressed in the two breeds. The developmental genes of the established differentially expressed circRNAs were found to be largely enriched in antioxidant activity, progesterone, estradiol, lipid, growth hormone, and drug response. Certain pathways like MAPK, IP3K and immune response pathways were found significantly enriched in KEGG analysis. These results add to our understanding of the controlling mechanisms connected with the lactation process, as well as the function of circRNAs in bovine milk synthesis. Additionally, the comparative analysis of differentially expressed circRNAs showed significant conservation across different species.
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Affiliation(s)
- Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
| | - Zainab Manzoor
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India,Department of Clinical Biochemistry, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Qamar Taban
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
| | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Canada
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
| | - Mohd Isfaqul Hussain
- Division of Veterinary Microbiology, SKUAST-Kashmir, Srinagar, Jammu and Kashmir, India
| | - Riaz A. Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
| | - Nazir A. Ganai
- Division of Animal Biotechnology, Faculty of Veterinary Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India, Srinagar, Jammu and Kashmir, India
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Yu J, Xie D, Huang N, Zhou Q. Circular RNAs as Novel Diagnostic Biomarkers and Therapeutic Targets in Kidney Disease. Front Med (Lausanne) 2021; 8:714958. [PMID: 34604256 PMCID: PMC8481637 DOI: 10.3389/fmed.2021.714958] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel type of non-coding RNAs that have aroused growing attention in this decade. They are widely expressed in eukaryotes and generally have high stability owing to their special closed-loop structure. Many circRNAs are abundant, evolutionarily conserved, and exhibit cell-type-specific and tissue-specific expression patterns. Mounting evidence suggests that circRNAs have regulatory potency for gene expression by acting as microRNA sponges, interacting with proteins, regulating transcription, or directly undergoing translation. Dysregulated expression of circRNAs were found in many pathological conditions and contribute to the pathogenesis and progression of various disorders, including renal diseases. Recent studies have revealed that circRNAs may serve as novel reliable biomarkers for the diagnosis and prognosis prediction of multiple kidney diseases, such as renal cell carcinoma (RCC), acute kidney injury (AKI), diabetic kidney disease (DKD), and other glomerular diseases. Furthermore, circRNAs expressed by intrinsic kidney cells are shown to play a substantial role in kidney injury, mostly reported in DKD and RCC. Herein, we review the biogenesis and biological functions of circRNAs, and summarize their roles as promising biomarkers and therapeutic targets in common kidney diseases.
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Affiliation(s)
- Jianwen Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danli Xie
- Department of Nephrology, Shishi General Hospital, Quanzhou, China
| | - Naya Huang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qin Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Ohyama Y, Renfrow MB, Novak J, Takahashi K. Aberrantly Glycosylated IgA1 in IgA Nephropathy: What We Know and What We Don't Know. J Clin Med 2021; 10:jcm10163467. [PMID: 34441764 PMCID: PMC8396900 DOI: 10.3390/jcm10163467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
IgA nephropathy (IgAN), the most common primary glomerular disease worldwide, is characterized by glomerular deposition of IgA1-containing immune complexes. The IgA1 hinge region (HR) has up to six clustered O-glycans consisting of Ser/Thr-linked N-acetylgalactosamine usually with β1,3-linked galactose and variable sialylation. Circulating levels of IgA1 with abnormally O-glycosylated HR, termed galactose-deficient IgA1 (Gd-IgA1), are increased in patients with IgAN. Current evidence suggests that IgAN is induced by multiple sequential pathogenic steps, and production of aberrantly glycosylated IgA1 is considered the initial step. Thus, the mechanisms of biosynthesis of aberrantly glycosylated IgA1 and the involvement of aberrant glycoforms of IgA1 in disease development have been studied. Furthermore, Gd-IgA1 represents an attractive biomarker for IgAN, and its clinical significance is still being evaluated. To elucidate the pathogenesis of IgAN, it is important to deconvolute the biosynthetic origins of Gd-IgA1 and characterize the pathogenic IgA1 HR O-glycoform(s), including the glycan structures and their sites of attachment. These efforts will likely lead to development of new biomarkers. Here, we review the IgA1 HR O-glycosylation in general and the role of aberrantly glycosylated IgA1 in the pathogenesis of IgAN in particular.
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Affiliation(s)
- Yukako Ohyama
- Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan;
| | - Matthew B. Renfrow
- Departments of Biochemistry and Molecular Genetics and Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.B.R.); (J.N.)
| | - Jan Novak
- Departments of Biochemistry and Molecular Genetics and Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.B.R.); (J.N.)
| | - Kazuo Takahashi
- Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan;
- Correspondence: ; Tel.: +81-(562)-93-2430; Fax: +81-(562)-93-1830
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Harnessing the Physiological Functions of Cellular Prion Protein in the Kidneys: Applications for Treating Renal Diseases. Biomolecules 2021; 11:biom11060784. [PMID: 34067472 PMCID: PMC8224798 DOI: 10.3390/biom11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
A cellular prion protein (PrPC) is a ubiquitous cell surface glycoprotein, and its physiological functions have been receiving increased attention. Endogenous PrPC is present in various kidney tissues and undergoes glomerular filtration. In prion diseases, abnormal prion proteins are found to accumulate in renal tissues and filtered into urine. Urinary prion protein could serve as a diagnostic biomarker. PrPC plays a role in cellular signaling pathways, reno-protective effects, and kidney iron uptake. PrPC signaling affects mitochondrial function via the ERK pathway and is affected by the regulatory influence of microRNAs, small molecules, and signaling proteins. Targeting PrPC in acute and chronic kidney disease could help improve iron homeostasis, ameliorate damage from ischemia/reperfusion injury, and enhance the efficacy of mesenchymal stem/stromal cell or extracellular vesicle-based therapeutic strategies. PrPC may also be under the influence of BMP/Smad signaling and affect the progression of TGF-β-related renal fibrosis. PrPC conveys TNF-α resistance in some renal cancers, and therefore, the coadministration of anti-PrPC antibodies improves chemotherapy. PrPC can be used to design antibody-drug conjugates, aptamer-drug conjugates, and customized tissue inhibitors of metalloproteinases to suppress cancer. With preclinical studies demonstrating promising results, further research on PrPC in the kidney may lead to innovative PrPC-based therapeutic strategies for renal disease.
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