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Identification of key candidate genes for IgA nephropathy using machine learning and statistics based bioinformatics models. Sci Rep 2022; 12:13963. [PMID: 35978028 PMCID: PMC9385868 DOI: 10.1038/s41598-022-18273-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Immunoglobulin-A-nephropathy (IgAN) is a kidney disease caused by the accumulation of IgAN deposits in the kidneys, which causes inflammation and damage to the kidney tissues. Various bioinformatics analysis-based approaches are widely used to predict novel candidate genes and pathways associated with IgAN. However, there is still some scope to clearly explore the molecular mechanisms and causes of IgAN development and progression. Therefore, the present study aimed to identify key candidate genes for IgAN using machine learning (ML) and statistics-based bioinformatics models. First, differentially expressed genes (DEGs) were identified using limma, and then enrichment analysis was performed on DEGs using DAVID. Protein-protein interaction (PPI) was constructed using STRING and Cytoscape was used to determine hub genes based on connectivity and hub modules based on MCODE scores and their associated genes from DEGs. Furthermore, ML-based algorithms, namely support vector machine (SVM), least absolute shrinkage and selection operator (LASSO), and partial least square discriminant analysis (PLS-DA) were applied to identify the discriminative genes of IgAN from DEGs. Finally, the key candidate genes (FOS, JUN, EGR1, FOSB, and DUSP1) were identified as overlapping genes among the selected hub genes, hub module genes, and discriminative genes from SVM, LASSO, and PLS-DA, respectively which can be used for the diagnosis and treatment of IgAN.
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Cox SN, Chiurlia S, Divella C, Rossini M, Serino G, Bonomini M, Sirolli V, Aiello FB, Zaza G, Squarzoni I, Gangemi C, Stangou M, Papagianni A, Haas M, Schena FP. Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy. Sci Rep 2020; 10:15164. [PMID: 32938960 PMCID: PMC7494931 DOI: 10.1038/s41598-020-72026-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Primary IgA nephropathy (IgAN) diagnosis is based on IgA-dominant glomerular deposits and histological scoring is done on formalin-fixed paraffin embedded tissue (FFPE) sections using the Oxford classification. Our aim was to use this underexploited resource to extract RNA and identify genes that characterize active (endocapillary–extracapillary proliferations) and chronic (tubulo-interstitial) renal lesions in total renal cortex. RNA was extracted from archival FFPE renal biopsies of 52 IgAN patients, 22 non-IgAN and normal renal tissue of 7 kidney living donors (KLD) as controls. Genome-wide gene expression profiles were obtained and biomarker identification was carried out comparing gene expression signatures a subset of IgAN patients with active (N = 8), and chronic (N = 12) renal lesions versus non-IgAN and KLD. Bioinformatic analysis identified transcripts for active (DEFA4,TNFAIP6,FAR2) and chronic (LTB,CXCL6, ITGAX) renal lesions that were validated by RT-PCR and IHC. Finally, two of them (TNFAIP6 for active and CXCL6 for chronic) were confirmed in the urine of an independent cohort of IgAN patients compared with non-IgAN patients and controls. We have integrated transcriptomics with histomorphological scores, identified specific gene expression changes using the invaluable repository of archival renal biopsies and discovered two urinary biomarkers that may be used for specific clinical decision making.
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Affiliation(s)
- Sharon Natasha Cox
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
| | - Samantha Chiurlia
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy
| | - Chiara Divella
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Michele Rossini
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, 70013, Castellana Grotte, Bari, Italy
| | - Mario Bonomini
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Vittorio Sirolli
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Francesca B Aiello
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Isabella Squarzoni
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Concetta Gangemi
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Maria Stangou
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aikaterini Papagianni
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mark Haas
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesco Paolo Schena
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
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Schena FP, Serino G, Sallustio F, Falchi M, Cox SN. Omics studies for comprehensive understanding of immunoglobulin A nephropathy: state-of-the-art and future directions. Nephrol Dial Transplant 2019; 33:2101-2112. [PMID: 29905852 DOI: 10.1093/ndt/gfy130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics. First, the identification of molecular biomarkers, including mapping of the full spectrum of common and rare IgAN risk alleles, could permit a more precise stratification of IgAN patients. Second, the analysis of transcriptomic patterns and their modulation by epigenetic factors like microRNAs has the potential to increase our understanding in the pathogenic mechanisms of the disease. Third, the specificity of urinary proteomic and metabolomic signatures and the understanding of their functional relevance may contribute to the development of new non-invasive biomarkers for a better molecular characterization of the renal damage and its follow-up. All these approaches can give information for targeted therapeutic decisions and will support novel clinical decision making. In conclusion, we offer a framework of omic studies and outline barriers and potential solutions that should be used for improving the diagnosis and treatment of the disease. The ongoing decade is exploiting novel high-throughput molecular technologies and computational analyses for improving the diagnosis (precision nephrology) and treatment (personalized therapy) of the IgAN subtypes.
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Affiliation(s)
- Francesco Paolo Schena
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology 'S. de Bellis', Research Hospital, Castellana Grotte, Bari, Italy
| | - Fabio Sallustio
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sharon N Cox
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
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Mulder S, Hamidi H, Kretzler M, Ju W. An integrative systems biology approach for precision medicine in diabetic kidney disease. Diabetes Obes Metab 2018; 20 Suppl 3:6-13. [PMID: 30294956 PMCID: PMC6541014 DOI: 10.1111/dom.13416] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022]
Abstract
Current therapeutic approaches are ineffective in many patients with established diabetic kidney disease (DKD), an epidemic affecting one in three patients with diabetes. Early identification of patients at high risk for progression and individualizing therapies have the potential to mitigate kidney complications due to diabetes. To achieve this, a better understanding of the complex pathophysiology of DKD is needed. A system biology approach integrating large-scale omic data is well suited to unravel the molecular mechanisms driving DKD and may offer new perspectives how to personalize therapy. Recent studies indeed show that integrating genome scale data sets generated from prospectively designed clinical cohort studies with model systems using innovative bioinformatics analysis revealed critical molecular pathways in DKD and led to the development of candidate prognostic molecular biomarkers. This review seeks to provide an overview of the recent progress in the application of the integrative systems biology approaches specifically in the field of molecular biomarkers for DKD. We will mainly focus the discussion on how to use integrative system biology approach to first identify patients at high risk of progression, and second to identify patients who may or may not respond to treatment. Challenges and opportunities in applying precision medicine in DKD will also be discussed.
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Affiliation(s)
- Skander Mulder
- University Medical Center Groningen, Groningen, Netherlands
| | - Habib Hamidi
- University of Michigan, Ann Arbor, MI, United States
| | | | - Wenjun Ju
- University of Michigan, Ann Arbor, MI, United States
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Schena FP, Nistor I, Curci C. Transcriptomics in kidney biopsy is an untapped resource for precision therapy in nephrology: a systematic review. Nephrol Dial Transplant 2017; 33:1094-1102. [DOI: 10.1093/ndt/gfx211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Ionut Nistor
- Nephrology Department, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
- Methods Support Team ERBP, Ghent University, Ghent, Belgium
| | - Claudia Curci
- University of Bari, Bari, Italy
- Schena Foundation, Valenzano, Italy
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Gao J, Wei L, Fu R, Wei J, Niu D, Wang L, Ge H, Yu Q, Wang M, Liu X, Zhang W. Association of Interleukin-10 Polymorphisms (rs1800872, rs1800871, and rs1800896) with Predisposition to IgA Nephropathy in a Chinese Han Population: A Case-Control Study. Kidney Blood Press Res 2017; 42:89-98. [PMID: 28359052 DOI: 10.1159/000471899] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/21/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS IgA nephropathy (IgAN) is a common form of primary glomerulonephritis worldwide. Previous studies indicated that IL-10 single nucleotide polymorphisms (SNP) play an important role in IgAN pathogenesis, but the results were controversy. This study aimed to investigate the association between IL-10 SNPs (rs1800872, rs1800871, and rs1800896) with IgAN in a Chinese Han population. METHODS We conducted a case-control study that included 351 patients with IgAN and 310 age-, gender- and ethnicity-matched healthy controls. Three promoter SNPs (rs1800872, rs1800871, and rs1800896) of IL-10 were genotyped by Sequenom MassARRAY. Odds ratios (ORs) with 95% confidence intervals (CI) were used to assess the relationship with IgAN. RESULTS We found that the rs1800896 did not correlate with IgAN risk, whereas rs1800872 and rs1800871 were significantly associated with increased IgAN risk in all genetic models. The haplotype analysis indicated that the CCA haplotype was associated with increased IgAN risk (OR = 1.36; 95% CI = 1.05-1.75). Moreover, there were no associations between these SNPs and blood pressure or gender, whereas the rs1800896 variant was correlated with higher 24-hour urine protein in patients with IgAN. CONCLUSION Taken together, these results suggest that IL-10 is a susceptibility gene in patients with IgAN.
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Affiliation(s)
- Jie Gao
- Department of Nephrology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Linting Wei
- Department of Nephrology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rongguo Fu
- Department of Nephrology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiali Wei
- Department of Nephrology, Hainan general hospital, Haikou, China
| | - Dan Niu
- Department of Nephrology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Wang
- Department of Nephrology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Heng Ge
- Department of Nephrology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | | | - Meng Wang
- Department of Oncology, Xi'an, China
| | | | - Wanggang Zhang
- Department of Hematology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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MiR-100-3p and miR-877-3p regulate overproduction of IL-8 and IL-1β in mesangial cells activated by secretory IgA from IgA nephropathy patients. Exp Cell Res 2016; 347:312-21. [DOI: 10.1016/j.yexcr.2016.08.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 01/27/2023]
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