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Yin Y, Zhang H, Sun L, Han Q, Zheng M, Chen H, Fei S, Tan R, Ju X, Wang Z, Gu M. Association between fibrosis-related gene polymorphism and long-term allograft outcome in renal transplant recipients. BMC Med Genomics 2023; 16:255. [PMID: 37867197 PMCID: PMC10591404 DOI: 10.1186/s12920-023-01686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Renal allograft fibrosis is one of characteristic causes of long-term renal function loss. The purpose of our study is to investigate the association between fibrosis-related genes single nucleotide polymorphism (SNPs) and kidney function in 5 years after kidney transplantation. METHODS A total of 143 recipients were eligible for screening with 5-year follow-up information and SNP sequencing information from blood samples were included in this study. Minor Allele Frequency (MAF) and Hardy-Weinberg Equilibrium (HWE) analysis was conducted to identify tagger single-nucleotide polymorphisms (SNPs) and haplotypes. SNPs associated with the fifth year chronic kidney disease (CKD) staging were screened by SPSS and the "SNPassoc" package in RStudio and used for subsequent prediction model construction. RESULTS A total of 275 renal transplant-related SNPs identified after target sequencing analysis. 64 Tagger SNPs were selected, and two SNPs (rs13969 and rs243849) were statistically significant for stage of CKD in 5 years. Finally, a model based on Gender, Age, rs1396, and rs243849 was constructed by multivariate linear regression analysis. Additionally, this model has a good performance in predicting uremia five years after kidney transplantation. CONCLUSION Two SNPs (rs13969 and rs243849) were identified to be significantly associated with long-term renal allograft function. Based on this, a prediction model for long-term allograft function was established containing Gender, Age, rs1396, and rs243849. However, an independent cohort should be enrolled to validate the predicting performance.
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Affiliation(s)
- Yu Yin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Han Zhang
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianguang Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Zheng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Min Gu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Auwul MR, Zhang C, Rahman MR, Shahjaman M, Alyami SA, Moni MA. Network-based transcriptomic analysis identifies the genetic effect of COVID-19 to chronic kidney disease patients: A bioinformatics approach. Saudi J Biol Sci 2021; 28:5647-5656. [PMID: 34127904 PMCID: PMC8190333 DOI: 10.1016/j.sjbs.2021.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 has emerged as global health threats. Chronic kidney disease (CKD) patients are immune-compromised and may have a high risk of infection by the SARS-CoV-2. We aimed to detect common transcriptomic signatures and pathways between COVID-19 and CKD by systems biology analysis. We analyzed transcriptomic data obtained from peripheral blood mononuclear cells (PBMC) infected with SARS-CoV-2 and PBMC of CKD patients. We identified 49 differentially expressed genes (DEGs) which were common between COVID-19 and CKD. The gene ontology and pathways analysis showed the DEGs were associated with "platelet degranulation", "regulation of wound healing", "platelet activation", "focal adhesion", "regulation of actin cytoskeleton" and "PI3K-Akt signalling pathway". The protein-protein interaction (PPI) network encoded by the common DEGs showed ten hub proteins (EPHB2, PRKAR2B, CAV1, ARHGEF12, HSP90B1, ITGA2B, BCL2L1, E2F1, TUBB1, and C3). Besides, we identified significant transcription factors and microRNAs that may regulate the common DEGs. We investigated protein-drug interaction analysis and identified potential drugs namely, aspirin, estradiol, rapamycin, and nebivolol. The identified common gene signature and pathways between COVID-19 and CKD may be therapeutic targets in COVID-19 patients with CKD comorbidity.
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Affiliation(s)
- Md. Rabiul Auwul
- School of Economics and Statistics, Guangzhou University, Guangzhou 510006, China
| | - Chongqi Zhang
- School of Economics and Statistics, Guangzhou University, Guangzhou 510006, China
| | - Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Enayetpur, Sirajganj 6751, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur 5400, Bangladesh
| | - Salem A. Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Saudi Arabia
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
- The Garvan Institute of Medical Research, Healthy Ageing Theme, Darlinghurst, NSW 2010, Australia
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Caveolin-1 in Kidney Chronic Antibody-Mediated Rejection: An Integrated Immunohistochemical and Transcriptomic Analysis Based on the Banff Human Organ Transplant (B-HOT) Gene Panel. Biomedicines 2021; 9:biomedicines9101318. [PMID: 34680435 PMCID: PMC8533527 DOI: 10.3390/biomedicines9101318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Caveolin-1 overexpression has previously been reported as a marker of endothelial injury in kidney chronic antibody-mediated rejection (c-ABMR), but conclusive evidence supporting its use for daily diagnostic practice is missing. This study aims to evaluate if Caveolin-1 can be considered an immunohistochemical surrogate marker of c-ABMR. Caveolin-1 expression was analyzed in a selected series of 22 c-ABMR samples and 11 controls. Caveolin-1 immunohistochemistry proved positive in peritubular and glomerular capillaries of c-ABMR specimens, irrespective of C4d status whereas all controls were negative. Multiplex gene expression profiling in c-ABMR cases confirmed Caveolin-1 overexpression and identified additional genes (n = 220) and pathways, including MHC Class II antigen presentation and Type II interferon signaling. No differences in terms of gene expression (including Caveolin-1 gene) were observed according to C4d status. Conversely, immune cell signatures showed a NK-cell prevalence in C4d-negative samples compared with a B-cell predominance in C4d-positive cases, a finding confirmed by immunohistochemical assessment. Finally, differentially expressed genes were observed between c-ABMR and controls in pathways associated with Caveolin-1 functions (angiogenesis, cell metabolism and cell–ECM interaction). Based on our findings, Caveolin-1 resulted as a key player in c-ABMR, supporting its role as a marker of this condition irrespective of C4d status.
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Hwang E. Polymorphisms in the 5’-UTR region of IL-10RA gene are associated with chronic kidney disease. EUR J INFLAMM 2020. [DOI: 10.1177/2058739220959911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chronic kidney disease (CKD), characterized by the progressive, irreversible loss of kidney function, has been a significant socioeconomic burden. Thus, identifying potential treatment targets and incipient biological risk indicators for CKD prediction is crucial. Recently several studies revealed that IL-10, IL-10RA, and IL-10RB genes were involved in the development of vascular complications in hypertension and stroke. The purpose of this study was to evaluate the association between CKD and IL-10, IL-10RA, and IL-10RB gene polymorphisms in the Korean population. Ninety-two CKD patients and 312 control subjects participated in the study. Blood samples were drawn for biochemical measurements and genetic polymorphism analysis. To analyze the genotypes of each single nucleotide polymorphism (SNP), PCR products were sequenced by a DNA analyzer. The four SNPs of the IL-10RA gene showed significant associations between CKD and the control group in the codominant1 (rs2228054, rs2228055, and rs9610, OR = 0.48, 95% CI = 0.28–0.82, p = 0.007; rs2256111, OR = 0.49, 95% CI = 0.29–0.83, p = 0.008, respectively), dominant (rs2228054, rs2228055, and rs9610, OR = 0.59, 95% CI = 0.36–0.95, p = 0.028; rs2256111, OR = 0.60, 95% CI = 0.38–0.97, p = 0.037, respectively), and over-dominant model (rs2228054 and rs2228055, OR = 0.47, 95% CI = 0.28–0.79, p = 0.0034; rs9610, OR = 0.48, 95% CI = 0.29–0.80, p = 0.0037; rs2256111, OR = 0.49, 95% CI = 0.29–0.80, p = 0.0039). The four SNPs of IL-10 showed significant associations with the estimated glomerular filtration rate (eGFR) and C-reactive protein (CRP), with the minor homozygote genotype of each SNP associated with lower eGFRs and decreased CRP levels ( p < 0.05, p = 0.001, respectively). The two SNPs of IL-10RA showed significant associations with the CRP levels ( p < 0.05). The two SNPs of IL-10RB were significantly associated with the eGFR, with the minor homozygote genotype of each SNP associated with lower eGFRs ( p < 0.01). Our results show that IL-10RA gene variants are associated with CKD development. Additionally, this study suggests that SNPs of IL-10RA were associated with CRP levels in CKD.
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Affiliation(s)
- Eunah Hwang
- Keimyung University Kidney Institute, Daegu, Korea
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Caveolin-1 rs4730751 single-nucleotide polymorphism may not influence kidney transplant allograft survival. Sci Rep 2019; 9:15541. [PMID: 31664124 PMCID: PMC6820546 DOI: 10.1038/s41598-019-52079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/11/2019] [Indexed: 11/27/2022] Open
Abstract
Caveolin-1 is a protein (encoded by the CAV1 gene) supposedly harboring a protective effect against fibrosis. CAV1 rs4730751 single nucleotide polymorphism (SNP) AA genotype was initially associated with lower graft survival compared to non-AA. However, subsequent studies could not find the same effect. CAV1 rs4730751 SNP was investigated on 918 kidney donors. Multivariate Cox-model analyses were performed to evaluate risk factors for graft loss. Longitudinal changes on long-term estimated glomerular filtration rate (eGFRs) were evaluated with a linear mixed model. Histopathological findings from protocolled biopsies after 3 months post transplantation were also analyzed. Donor CAV1 rs4730751 genotyping proportions were 7.1% for AA, 41.6% for AC and 51.3% for CC. The AA genotype, compared to non-AA, was not associated with lower graft survival censored or not for death (multivariate analysis: HR = 1.23 [0.74–2.05] and HR = 1.27 [0.84–1.92]). Linear mixed model on long-term eGFRs revealed also no significant difference according to the genotype, yet we observed a trend. AA genotype was also not associated with a higher degree of fibrosis index on protocolled kidney biopsies at 3 months. To conclude, donor CAV1 rs4730751 SNP may impact on kidney transplantation outcomes, but this study could not confirm this hypothesis.
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Gui Z, Li W, Fei S, Guo M, Chen H, Sun L, Han Z, Tao J, Ju X, Yang H, Wei JF, Tan R, Gu M. Single Nucleotide Polymorphisms of Ubiquitin-Related Genes were Associated with Allograft Fibrosis of Renal Transplant Fibrosis. Ann Transplant 2019; 24:553-568. [PMID: 31582715 PMCID: PMC6792502 DOI: 10.12659/aot.917767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interstitial fibrosis and tubular atrophy (IF/TA) have been recognized as crucial factors contributing to graft loss resulting from chronic renal allograft injuries. Recent studies have indicated a significant association between the progression of organ fibrosis and single nucleotide polymorphisms (SNPs) found on certain genes. Our research sought to understand these potential associations and detect the potential impact of SNPs on ubiquitin-related genes related to allograft fibrosis in kidney transplant recipients. MATERIAL AND METHODS There were 200 patients enrolled in this study, from which samples were extracted for total DNA. Targeted next-generation sequencing was used to detect SNPs on 9 genes (FBXL21, PIAS1/2, SUMO1/2/3/4, UBE2D1, and UBE2I). Minor allele frequency (MAF) and Hardy-Weinberg equilibrium (HWE) tests were used and followed by linkage disequilibrium analysis. General linear models (GLM) were used to identify significant confounding factors. Finally, multiple inheritance models and haplotype analyses were conducted to explore associations between SNPs and the degree of the severity of renal allograft fibrosis. RESULTS In total, 144 SNPs were identified in targeted sequencing. After filtering based on results from MAF and HWE tests, 15 tagger SNPs were selected for further analyses of associations. GLMs indicated that the administration of sirolimus significantly contributed to the degree of severity of allograft fibrosis (P=0.011). After adjusting for confounding factors and applying a Bonferroni correction, multiple inheritance model analyses indicated that the recessive model of rs644731 of the PIAS2 gene was significantly correlated with the occurrence of IF/TA (P=0.01). Furthermore, single-locus based analysis of rs644731 did not indicate that it had a positive influence on IF/TA in a degree-dependent manner. Finally, linkage disequilibrium analysis revealed 3 haplotypes all lacking significant correlation with respect to the IF/TA experimental cohort. CONCLUSIONS We are the first to reveal that mutations of rs644731 in the PIAS2 gene were significantly correlated with the progression of IF/TA in kidney transplant recipients.
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Affiliation(s)
- Zeping Gui
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Wencheng Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical Iniversity, Nanjing, Jiangsu, China (mainland)
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Miao Guo
- Research Division of Clinical Pharmacology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Li Sun
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Xiaobin Ju
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
| | - Min Gu
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China (mainland)
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Sago CD, Lokugamage MP, Lando GN, Djeddar N, Shah NN, Syed C, Bryksin AV, Dahlman JE. Modifying a Commonly Expressed Endocytic Receptor Retargets Nanoparticles in Vivo. NANO LETTERS 2018; 18:7590-7600. [PMID: 30216729 PMCID: PMC6426696 DOI: 10.1021/acs.nanolett.8b03149] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanoparticles are often targeted to receptors expressed on specific cells, but few receptors are (i) highly expressed on one cell type and (ii) involved in endocytosis. One unexplored alternative is manipulating an endocytic gene expressed on multiple cell types; an ideal gene would inhibit delivery to cell type A more than cell type B, promoting delivery to cell type B. This would require a commonly expressed endocytic gene to alter nanoparticle delivery in a cell type-dependent manner in vivo; whether this can occur is unknown. Based on its microenvironmental regulation, we hypothesized Caveolin 1 (Cav1) would exert cell type-specific effects on nanoparticle delivery. Fluorescence was not sensitive enough to investigate this question, and as a result, we designed a platform named QUANT to study nanoparticle biodistribution. QUANT is 108× more sensitive than fluorescence and can be multiplexed. By measuring how 226 lipid nanoparticles (LNPs) delivered nucleic acids to multiple cell types in vivo in wild-type and Cav1 knockout mice, we found Cav1 altered delivery in a cell-type specific manner. Cav1 knockout did not alter LNP delivery to lung and kidney macrophages but substantially reduced LNP delivery to Kupffer cells, which are liver-resident macrophages. These data suggest caveolin-mediated endocytosis of nanomedicines by macrophages varies with tissue type. These results suggest manipulating receptors expressed on multiple cell types can tune drug delivery.
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Słuczanowska-Głąbowska S, Malinowski D, Safranow K, Domański L, Czerewaty M, Ustianowski P, Laszczyńska M, Pawlik A. Caveolin-1 rs4730751 gene polymorphism in kidney allograft recipients. J Appl Biomed 2018. [DOI: 10.1016/j.jab.2017.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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