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Zhang H, Zhou Y, Jiang C, Jian N, Wang J. Crosstalk of ubiquitin system and non-coding RNA in fibrosis. Int J Biol Sci 2024; 20:3802-3822. [PMID: 39113708 PMCID: PMC11302871 DOI: 10.7150/ijbs.93644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/14/2024] [Indexed: 08/10/2024] Open
Abstract
Chronic tissue injury triggers changes in the cell type and microenvironment at the site of injury and eventually fibrosis develops. Current research suggests that fibrosis is a highly dynamic and reversible process, which means that human intervention after fibrosis has occurred has the potential to slow down or cure fibrosis. The ubiquitin system regulates the biological functions of specific proteins involved in the development of fibrosis, and researchers have designed small molecule drugs to treat fibrotic diseases on this basis, but their therapeutic effects are still limited. With the development of molecular biology technology, researchers have found that non-coding RNA (ncRNA) can interact with the ubiquitin system to jointly regulate the development of fibrosis. More in-depth explorations of the interaction between ncRNA and ubiquitin system will provide new ideas for the clinical treatment of fibrotic diseases.
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Affiliation(s)
- Huamin Zhang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Yutong Zhou
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Ni Jian
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Jie Wang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
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2
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Li X, Ma TK, Wang P, Shi H, Hai S, Qin Y, Zou Y, Zhu WT, Li HM, Li YN, Yin L, Xu YY, Yang Q, Zhang S, Ding H. HOXD10 attenuates renal fibrosis by inhibiting NOX4-induced ferroptosis. Cell Death Dis 2024; 15:398. [PMID: 38844470 PMCID: PMC11156659 DOI: 10.1038/s41419-024-06780-w] [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: 10/13/2023] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
In chronic kidney disease (CKD), renal fibrosis is an unavoidable result of various manifestations. However, its pathogenesis is not yet fully understood. Here, we revealed the novel role of Homeobox D10 (HOXD10) in CKD-related fibrosis. HOXD10 expression was downregulated in CKD-related in vitro and in vivo fibrosis models. UUO model mice were administered adeno-associated virus (AAV) containing HOXD10, and HOXD10 overexpression plasmids were introduced into human proximal tubular epithelial cells induced by TGF-β1. The levels of iron, reactive oxygen species (ROS), lipid ROS, the oxidized glutathione/total glutathione (GSSG/GSH) ratio, malonaldehyde (MDA), and superoxide dismutase (SOD) were determined using respective assay kits. Treatment with AAV-HOXD10 significantly attenuated fibrosis and renal dysfunction in UUO model mice by inhibiting NOX4 transcription, ferroptosis pathway activation, and oxidative stress. High levels of NOX4 transcription, ferroptosis pathway activation and profibrotic gene expression induced by TGF-β1/erastin (a ferroptosis agonist) were abrogated by HOXD10 overexpression in HK-2 cells. Moreover, bisulfite sequencing PCR result determined that HOXD10 showed a hypermethylated level in TGF-β1-treated HK-2 cells. The binding of HOXD10 to the NOX4 promoter was confirmed by chromatin immunoprecipitation (ChIP) analysis and dual-luciferase reporter assays. Targeting HOXD10 may represent an innovative therapeutic strategy for fibrosis treatment in CKD.
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Affiliation(s)
- Xin Li
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Tian-Kui Ma
- Biological Therapy Department, First Hospital of China Medical University, Shenyang, China
| | - Pu Wang
- General Practice Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Hang Shi
- Intensive Care Unit Department, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Sang Hai
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Yu Qin
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Yun Zou
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Wan-Ting Zhu
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Hui-Min Li
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Yan-Nong Li
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Li Yin
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Yan-Yan Xu
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Qi Yang
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Shuang Zhang
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China
| | - Hong Ding
- Nephrology Department, Fourth Hospital of China Medical University, Shenyang, China.
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3
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Xu L, Wang J, Yu H, Mei H, He P, Wang M, Liu Y, Fan Q, Chen Y, Li Y, Liu F. GLIS1 alleviates cell senescence and renal fibrosis through PGC1-α mediated mitochondrial quality control in kidney aging. Free Radic Biol Med 2023; 209:171-184. [PMID: 37852548 DOI: 10.1016/j.freeradbiomed.2023.09.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
Mitochondrial dysfunction is implied as a crucial factor in age-related chronic kidney disease. It is confirmed that Gli-like transcription factor 1 (GLIS1) is involved in age-related renal fibrosis, however, the correlation between mitochondrial disturbances and GLIS1-driven kidney aging are not clearly clarified. Thus, we investigated the regulatory mechanism of GLIS1 in the homeostasis of mitochondrial quality control both in vivo and in vitro. The lower expression of GLIS1 was identified in natural and accelerated kidney aged models, accompanied by the dysfunctions of mitochondrial quality control, including enhanced mitochondrial fission, reduced mitochondrial biogenesis and mitophagy, whereas, GLIS1 could maintain mitochondrial stability by interacting with peroxisome proliferator-activated receptor γ coactivator-1α (PGC1-α). Additionally, the over-expressed GLIS1 inhibited extracellular matrix accumulation and alleviated renal fibrosis while siGLIS1 inhibited PGC1-α transcription, as well as affecting its mitochondria-protective functions. Collectively, we demonstrated that GLIS1 mediated mitochondrial quality control through targeting PGC1-α in kidney aging, which might be a promising therapeutic target for attenuating cell senescence and age-related renal fibrosis.
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Affiliation(s)
- Li Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524003, China
| | - Jiao Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Hongyuan Yu
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Hang Mei
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Ping He
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Min Wang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yue Liu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Qiuling Fan
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200086, China
| | - Ying Chen
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China.
| | - Yanqiu Li
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, 110001, China.
| | - Fan Liu
- Department of Orthodontics, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, 110002, China.
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4
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Distefano R, Ilieva M, Madsen JH, Ishii H, Aikawa M, Rennie S, Uchida S. T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes. Noncoding RNA 2023; 9:30. [PMID: 37218990 PMCID: PMC10204529 DOI: 10.3390/ncrna9030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.
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Affiliation(s)
- Rebecca Distefano
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan;
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Excellence in Vascular Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
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5
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Qi C, Liang T, Lin J, Xie J, Cao D, Wang H, Li Q, Li S, Li J, Zhang Y, Wang Y, Li S, Chen Z, Yau H, Lin S, Zhang S, Liu S, Liang X, Zhang L, Wang W. Linc279227 contributes to mitochondrial dysfunction in high glucose-treated mouse renal tubular epithelial cells. Biochem Biophys Res Commun 2023; 644:95-104. [PMID: 36640668 DOI: 10.1016/j.bbrc.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND The aberrant expression of long noncoding RNAs (lncRNAs) has been associated with diabetic nephropathy (DN), a major complication of diabetes mellitus (DM). This study investigated the differential expression of lncRNAs in DM without renal damage and DM with renal damage, known as DN, and elucidated the functions of a pathogenic lncRNA. METHODS High-throughput sequencing was performed on the kidneys of male db/db mice with kidney injury, db/db mice without kidney involvement and db/m control littermates. Linc279227 expression was confirmed by RT‒qPCR and fluorescence in situ hybridization. The effects of linc279227 on high glucose (HG)-treated renal tubular epithelial cells (RTECs) were evaluated by autophagy flux monitoring, Western blot determination and mitochondrial morphological detection. RESULTS With high-throughput sequencing, we identified a 1024 nt long intergenic noncoding RNA, TCONS_00279227 (linc279227), whose expression was markedly increased in the kidneys of db/db mice with kidney injury compared to db/db mice without kidney injury and db/m control littermates. Fluorescence in situ hybridization confirmed that linc279227 was mainly located in the renal tubules of mice with DN. In vitro, linc279227 expression was found to be significantly increased in RTECs treated with high glucose (HG) for 48 h. Silencing linc279227 markedly restored the levels of autophagy-/mitophagy-associated proteins in HG-stimulated RTECs. Furthermore, silencing linc279227 reduced phosphorylated Drp1 expression and increased Mfn2 expression in RTECs exposed to HG. CONCLUSION Our data suggest that linc279227 plays an important role in mitochondrial dysfunction in HG-treated RTECs and that silencing linc279227 rescues RTECs exposed to HG.
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Affiliation(s)
- Chunfang Qi
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Tiantian Liang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Jinxin Lin
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Jianteng Xie
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Dan Cao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Huizhen Wang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Qiuling Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shenheng Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Jing Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yifan Zhang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yanhui Wang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Sheng Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zujiao Chen
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Hokhim Yau
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shaochun Lin
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shaogui Zhang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shuangxin Liu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Xinling Liang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Liang Zhang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| | - Wenjian Wang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
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6
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Lin X, Xiang QY, Li S, Song WL, Wang YJ, Ni YQ, Zhao Y, Li C, Wang Y, Li HH, Liang Z, Zhan JK, Liu YS. BMF-AS1/BMF Promotes Diabetic Vascular Calcification and Aging both In Vitro and In Vivo. Aging Dis 2023; 14:170-183. [PMID: 36818559 PMCID: PMC9937703 DOI: 10.14336/ad.2022.0427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Vascular calcification and aging often increase morbidity and mortality in patients with diabetes mellitus (DM); however, the underlying mechanisms are still unknown. In the present study, we found that Bcl-2 modifying factor (BMF) and BMF antisense RNA 1 (BMF-AS1) were significantly increased in high glucose-induced calcified and senescent vascular smooth muscle cells (VSMCs) as well as artery tissues from diabetic mice. Inhibition of BMF-AS1 and BMF reduced the calcification and senescence of VSMCs, whereas overexpression of BMF-AS1 and BMF generates the opposite results. Mechanistic analysis showed that BMF-AS1 interacted with BMF directly and up-regulated BMF at both mRNA and protein levels, but BMF did not affect the expression of BMF-AS1. Moreover, knocking down BMF-AS1 and BMF suppressed the calcification and senescence of VSMCs, and BMF knockout (BMF-/-) diabetic mice presented less vascular calcification and aging compared with wild type diabetic mice. In addition, higher coronary artery calcification scores (CACs) and increased plasma BMF concentration were found in patients with DM, and there was a positive correlation between CACs and plasma BMF concentration. Thus, BMF-AS1/BMF plays a key role in promoting high glucose-induced vascular calcification and aging both in vitro and in vivo. BMF-AS1 and BMF represent potential therapeutic targets in diabetic vascular calcification and aging.
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Affiliation(s)
- Xiao Lin
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Department of Radiology, the Second Xiangya Hospital of Central South University, Hunan, China.
| | - Qun-Yan Xiang
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Shuang Li
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Wan-Ling Song
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Yan-Jiao Wang
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Yu-Qing Ni
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Yan Zhao
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Chen Li
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Yi Wang
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.
| | - Hua-Hua Li
- Department of Geriatrics, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Hunan, China.
| | - Zhen Liang
- Department of Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Guangdong, China
| | - Jun-Kun Zhan
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.,Correspondence should be addressed to: Dr. You-Shuo Liu (E-mail: ) and Jun-Kun Zhan (E-mail: ). the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - You-Shuo Liu
- Department of Geriatrics, the Second Xiangya Hospital of Central South University, Hunan, China.,Institute of Aging and Age-related Disease Research, Central South University, Hunan, China.,Correspondence should be addressed to: Dr. You-Shuo Liu (E-mail: ) and Jun-Kun Zhan (E-mail: ). the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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7
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Li X, Ma TK, Wang M, Zhang XD, Liu TY, Liu Y, Huang ZH, Zhu YH, Zhang S, Yin L, Xu YY, Ding H, Liu C, Shi H, Fan QL. YY1-induced upregulation of LncRNA-ARAP1-AS2 and ARAP1 promotes diabetic kidney fibrosis via aberrant glycolysis associated with EGFR/PKM2/HIF-1α pathway. Front Pharmacol 2023; 14:1069348. [PMID: 36874012 PMCID: PMC9974832 DOI: 10.3389/fphar.2023.1069348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Objectives: Dimeric pyruvate kinase (PK) M2 (PKM2) plays an important role in promoting the accumulation of hypoxia-inducible factor (HIF)-1α, mediating aberrant glycolysis and inducing fibrosis in diabetic kidney disease (DKD). The aim of this work was to dissect a novel regulatory mechanism of Yin and Yang 1 (YY1) on lncRNA-ARAP1-AS2/ARAP1 to regulate EGFR/PKM2/HIF-1α pathway and glycolysis in DKD. Materials and methods: We used adeno-associated virus (AAV)-ARAP1 shRNA to knocked down ARAP1 in diabetic mice and overexpressed or knocked down YY1, ARAP1-AS2 and ARAP1 expression in human glomerular mesangial cells. Gene levels were assessed by Western blotting, RT-qPCR, immunofluorescence staining and immunohistochemistry. Molecular interactions were determined by RNA pull-down, co-immunoprecipitation, ubiquitination assay and dual-luciferase reporter analysis. Results: YY1, ARAP1-AS2, ARAP1, HIF-1α, glycolysis and fibrosis genes expressions were upregulated and ARAP1 knockdown could inhibit dimeric PKM2 expression and partly restore tetrameric PKM2 formation, while downregulate HIF-1α accumulation and aberrant glycolysis and fibrosis in in-vivo and in-vitro DKD models. ARAP1 knockdown attenuates renal injury and renal dysfunction in diabetic mice. ARAP1 maintains EGFR overactivation in-vivo and in-vitro DKD models. Mechanistically, YY1 transcriptionally upregulates ARAP1-AS2 and indirectly regulates ARAP1 and subsequently promotes EGFR activation, HIF-1α accumulation and aberrant glycolysis and fibrosis. Conclusion: Our results first highlight the role of the novel regulatory mechanism of YY1 on ARAP1-AS2 and ARAP1 in promoting aberrant glycolysis and fibrosis by EGFR/PKM2/HIF-1α pathway in DKD and provide potential therapeutic strategies for DKD treatments.
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Affiliation(s)
- Xin Li
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China.,Department of Nephrology, Fourth Hospital of China Medical University, Shenyang, China
| | - Tian-Kui Ma
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Min Wang
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Xiao-Dan Zhang
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Tian-Yan Liu
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Yue Liu
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Zhao-Hui Huang
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Yong-Hong Zhu
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China
| | - Shuang Zhang
- Department of Nephrology, Fourth Hospital of China Medical University, Shenyang, China
| | - Li Yin
- Department of Nephrology, Fourth Hospital of China Medical University, Shenyang, China
| | - Yan-Yan Xu
- Department of Nephrology, Fourth Hospital of China Medical University, Shenyang, China
| | - Hong Ding
- Department of Nephrology, Fourth Hospital of China Medical University, Shenyang, China
| | - Cong Liu
- Department of General Surgery, First Hospital of Harbin Medical University, Harbin, China
| | - Hang Shi
- Department of Intensive Care Unit, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiu-Ling Fan
- Department of Nephrology, First Hospital of China Medical University, Shenyang, China.,Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Niu R, Zhao F, Dong Z, Li Z, Li S. A stratification system of ferroptosis and iron-metabolism related LncRNAs guides the prediction of the survival of patients with esophageal squamous cell carcinoma. Front Oncol 2022; 12:1010074. [PMID: 36185246 PMCID: PMC9520776 DOI: 10.3389/fonc.2022.1010074] [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: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Ferroptosis and iron-metabolism have been widely reported to play an important role in cancer. Long non-coding RNAs (lncRNAs) are increasingly recognized as the crucial mediators in the regulation of ferroptosis and iron metabolism. A systematic understanding of ferroptosis and iron-metabolism related lncRNAs (FIRLs) in esophageal squamous cell carcinoma (ESCC) is essential for prognosis prediction. Herein, Pearson’s correlation analysis was carried out between ferroptosis and iron-metabolism-related genes (FIRGs) and all lncRNAs to derive the FIRLs. Based on weighted gene co-expression network exploration (WCGNA), least absolute shrinkage and selection operator (LASSO) regression and Cox regression analysis, a risk stratification system, including 3 FIRLs (LINC01068, TMEM92-AS1, AC243967.2), was established. According to Kaplan-Meier analysis, receiver operating characteristic (ROC) curve analysis, and univariate and multivariate Cox regression analyses, the risk stratification system had excellent predictive ability and clinical relevance. The validity of the established prognostic signature was further examined in TCGA (training set) and GEO (validation set) cohorts. A nomogram with enhanced precision for forecasting OS was set up on basis of the independent prognostic elements. Functional enrichment analysis revealed that three FIRLs took part in various cellular functions and signaling pathways, and the immune status was varied in the high-risk and low-risk groups. In the end, the oncogenic effects of LINC01068 was explored using in vitro researches. Overall, a risk stratification system of three FIRLs was found to have significant prognostic value for ESCC and may serve as a ferroptosis-associated therapeutic target in the clinic.
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Affiliation(s)
- Ren Niu
- Department of Oncology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zefang Dong
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhirong Li
- Clinical Laboratory Center, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Zhirong Li, ; Shujun Li,
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Zhirong Li, ; Shujun Li,
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9
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miR-181a-5p Inhibits Pyroptosis in Sepsis-Induced Acute Kidney Injury through Downregulation of NEK7. J Immunol Res 2022; 2022:1825490. [PMID: 35991122 PMCID: PMC9385359 DOI: 10.1155/2022/1825490] [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: 05/12/2022] [Revised: 06/27/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by the uncontrolled inflammation, easily affecting the kidney. Sepsis-induced acute kidney injury (S-AKI) has high morbidity and mortality, of which the pathophysiological mechanisms have not been completely illuminated, leading to nonspecific therapies. Specific microRNAs were related with the pathogenesis of AKI. However, only limited studies focused on the pyroptosis in the context of S-AKI. The in vitro LPS-induced HK-2 cell model and in vivo CLP-induced mouse model were established. qRT-PCR, Western blot, ELISA, and RNA pulldown were used for expression examination. Multiple biological databases were used for miRNA screening. H&E staining and IHC staining were performed. The LPS-induced HK-2 cells showed significantly increased (P < 0.01) fluorescence intensity of N-GSDMD and ASC compared with the HK-2 cells. The expression of NLRP3, NEK7, ASC, active caspase-1, and N-GSDMD was significantly enhanced (P < 0.05) and the inflammatory factors including IL-18, IL-1β, and THF-α were all increased in LPS-induced HK-2 cells and CLP-induced mice. Renal edema, serum Cr and BUN, and expression of KIM-1 and NGAL were significantly higher (P < 0.05) in CLP-induced S-AKI mice than the sham group. miR-101-3p, miR-144-3p, miR-181a-5p, miR-4262, and miR-513b-5p could inhibit NEK7. NEK7 is an interacting protein of miRNA-181a-5p. miR-181a-5p inhibits pyroptosis of the LPS-induced HK-2 cells through downregulation of NEK7. Pyroptosis of HK-2 cells promotes inflammation. miR-181a-5p inhibits pyroptosis through downregulation of NEK7 in LPS-induced HK-2 cells and CLP-induced mice. Our study indicated miR-181a-5p as a new potential therapeutic target for S-AKI therapy.
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Ma T, Li X, Zhu Y, Yu S, Liu T, Zhang X, Chen D, Du S, Chen T, Chen S, Xu Y, Fan Q. Excessive Activation of Notch Signaling in Macrophages Promote Kidney Inflammation, Fibrosis, and Necroptosis. Front Immunol 2022; 13:835879. [PMID: 35280997 PMCID: PMC8913942 DOI: 10.3389/fimmu.2022.835879] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 12/24/2022] Open
Abstract
Diabetic nephropathy (DN) is one of the main causes of end-stage renal disease (ESRD). Existing treatments cannot control the progression of diabetic nephropathy very well. In diabetic nephropathy, Many monocytes and macrophages infiltrate kidney tissue. However, the role of these cells in the pathogenesis of diabetic nephropathy has not been fully elucidated. In this study, we analyzed patient kidney biopsy specimens, diabetic nephropathy model animals. Meanwhile, we cocultured cells and found that in diabetic nephropathy, damaged intrinsic renal cells (glomerular mesangial cells and renal tubular epithelial cells) recruited monocytes/macrophages to the area of tissue damage to defend against and clear cell damage. This process often involved the activation of different types of macrophages. Interestingly, the infiltrating macrophages were mainly M1 (CD68+iNOS+) macrophages. In diabetic nephropathy, crosstalk between the Notch pathway and NF-κB signaling in macrophages contributed to the polarization of macrophages. Hyperpolarized macrophages secreted large amounts of inflammatory cytokines and exacerbated the inflammatory response, extracellular matrix secretion, fibrosis, and necroptosis of intrinsic kidney cells. Additionally, macrophage depletion therapy with clodronate liposomes and inhibition of the Notch pathway in macrophages alleviated the pathological changes in kidney cells. This study provides new information regarding diabetic nephropathy-related renal inflammation, the causes of macrophage polarization, and therapeutic targets for diabetic nephropathy.
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Affiliation(s)
- Tiankui Ma
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Xin Li
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China.,Department of Nephrology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yonghong Zhu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Shufan Yu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Tianyan Liu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Xiaodan Zhang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Dong Chen
- Department of Centre Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Shuyan Du
- Department of Centre Laboratory, The First Hospital of China Medical University, Shenyang, China
| | - Tong Chen
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Shuo Chen
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
| | - Yanyan Xu
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China.,Department of Nephrology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Qiuling Fan
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, China
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Xing X, Xia Q, Gong B, Shen Z, Zhang Y. Identification of Tissue-Specific Expressed Hub Genes and Potential Drugs in Rheumatoid Arthritis Using Bioinformatics Analysis. Front Genet 2022; 13:855557. [PMID: 35368701 PMCID: PMC8971206 DOI: 10.3389/fgene.2022.855557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/18/2022] [Indexed: 12/29/2022] Open
Abstract
Background: Rheumatoid arthritis (RA) is a common autoimmune disease characterized by progressive, destructive polyarthritis. However, the cause and underlying molecular events of RA are not clear. Here, we applied integrated bioinformatics to identify tissue-specific expressed hub genes involved in RA and reveal potential targeted drugs. Methods: Three expression profiles of human microarray datasets involving fibroblast-like synoviocytes (FLS) were downloaded from the Gene Expression Omnibus (GEO) database, the differentially expressed mRNAs (DEGs), miRNAs (DEMs), and lncRNAs (DELs) between normal and RA synovial samples were screened using GEO2R tool. BioGPS was used to identified tissue-specific expressed genes. Functional and pathway enrichment analyses were performed for common DEGs using the DAVID database, and the protein-protein interaction (PPI) network of common DEGs was constructed to recognize hub genes by the STRING database. Based on receiver operating characteristic (ROC) curve, we further investigated the prognostic values of tissue-specific expressed hub genes in RA patients. Connectivity Map (CMap) was run to identify novel anti-RA potential drugs. The DEM–DEG pairs and ceRNA network containing key DEMs were established by Cytoscape. Results: We obtain a total of 418 DEGs, 23 DEMs and 49 DELs. 64 DEGs were verified as tissue-specific expressed genes, most derive from the hematologic/immune system (20/64, 31.25%). GO term and KEGG pathway enrichment analysis showed that DEGs focused primarily on immune-related biological process and NF-κB pathway. 10 hub genes were generated via using MCODE plugin. Among them, SPAG5, CUX2, and THEMIS2 were identified as tissue-specific expressed hub genes, these 3 tissue-specific expressed hub genes have superior diagnostic value in the RA samples compared with osteoarthritis (OA) samples. 5 compounds (troleandomycin, levodopa, trichostatin A, LY-294002, and levamisole) rank among the top five in connectivity score. In addition, 5 miRNAs were identified to be key DEMs, the lncRNA–miRNA–mRNA network with five key DEMs was formed. The networks containing tissue-specific expressed hub genes are as follows: ARAP1-AS2/miR-20b-3p/TRIM3, ARAP1-AS2/miR-30c-3p/FRZB. Conclusion: This study indicates that screening for identify tissue-specific expressed hub genes and ceRNA network in RA using integrated bioinformatics analyses could help us understand the mechanism of development of RA. Besides, SPAG5 and THEMIS2 might be candidate biomarkers for diagnosis of RA. LY-294002, trichostatin A, and troleandomycin may be potential drugs for RA.
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Affiliation(s)
- Xuewu Xing
- Department of Orthopaedics, Tianjin First Central Hospital, Tianjin, China
- School of Medicine, Nankai University, Tianjin, China
| | - Qun Xia
- Department of Orthopaedics, Tianjin First Central Hospital, Tianjin, China
| | - Baoqi Gong
- Department of Rheumatology, Tianjin First Central Hospital, Tianjin, China
| | - Zhongyang Shen
- Department of Transplant Surgery, Tianjin First Central Hospital, Tianjin, China
| | - Yingze Zhang
- School of Medicine, Nankai University, Tianjin, China
- Department of Orthopaedic Surgery of Hebei Province, Third Hospital of Hebei Medical University, Shijiazhuang, China
- Chinese Academy of Engineering, Beijing, China
- *Correspondence: Yingze Zhang,
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Abstract
With the development of precision medicine, the efficiency of tumor treatment has been significantly improved. More attention has been paid to targeted therapy and immunotherapy as the key to precision treatment of cancer. Targeting epidermal growth factor receptor (EGFR) has become one of the most important targeted treatments for various cancers. Comparing with traditional chemotherapy drugs, targeting EGFR is highly selective in killing tumor cells with better safety, tolerability and less side effect. In addition, tumor immunotherapy has become the fourth largest tumor therapy after surgery, radiotherapy and chemotherapy, especially immune checkpoint inhibitors. However, these treatments still produce a certain degree of drug resistance. Non-coding RNAs (ncRNAs) were found to play a key role in carcinogenesis, treatment and regulation of the efficacy of anticancer drugs in the past few years. Therefore, in this review, we aim to summarize the targeted treatment of cancers and the functions of ncRNAs in cancer treatment.
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Cui XY, Zhan JK, Liu YS. Roles and functions of antisense lncRNA in vascular aging. Ageing Res Rev 2021; 72:101480. [PMID: 34601136 DOI: 10.1016/j.arr.2021.101480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/08/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022]
Abstract
Vascular aging is a major cause of morbidity and mortality in the elderly population. Endothelial cells (ECs) and vascular smooth muscle cells (VSMCs), forming the intima and media layers of the vessel wall respectively, are closely associated with the process of vascular aging and vascular aging-related diseases. Numerous studies have revealed the pathophysiologic mechanism through which lncRNA contributes to vascular aging, hence more attention is now paid to the role played by antisense long non-coding RNA (AS-lncRNA) in the pathogenesis of vascular aging. Nonetheless, only a small number of studies focus on the specific mechanism through which AS-lncRNA mediates vascular aging. In this review, we summarize the roles and functions of AS-lncRNA with regards to the development of vascular aging and vascular aging-related disease. We also aim to deepen our understanding of this process and provide alternative therapeutic modalities for vascular aging-related diseases.
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Affiliation(s)
- Xing-Yu Cui
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Aging and Age-related Disease Research, Central South University, Changsha, Hunan 410011, China
| | - Jun-Kun Zhan
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Aging and Age-related Disease Research, Central South University, Changsha, Hunan 410011, China.
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Institute of Aging and Age-related Disease Research, Central South University, Changsha, Hunan 410011, China.
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Construction and Comprehensive Analysis of a Stratification System Based on AGTRAP in Patients with Hepatocellular Carcinoma. DISEASE MARKERS 2021; 2021:6144476. [PMID: 34840632 PMCID: PMC8612796 DOI: 10.1155/2021/6144476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/15/2021] [Indexed: 01/10/2023]
Abstract
Background With the development of sequencing technology, several signatures have been reported for the prediction of prognosis in patients with hepatocellular carcinoma (HCC). However, the above signatures are characterized by cumbersome application. Therefore, the study is aimed at screening out a robust stratification system based on only one gene to guide treatment. Methods Firstly, we used the limma package for performing differential expression analysis on 374 HCC samples, followed by Cox regression analysis on overall survival (OS) and disease-free interval (PFI). Subsequently, hub prognostic genes were found at the intersection of the above three groups. In addition, the topological degree inside the PPI network was used to screen for a unique hub gene. The rms package was used to construct two visual stratification systems for OS and PFI, and Kaplan-Meier analysis was utilized to investigate survival differences in clinical subgroups. The ssGSEA algorithm was then used to reveal the relationship between the hub gene and immune cells, immunological function, and checkpoints. In addition, we also used function annotation to explore into putative biological functions. Finally, for preliminary validation, the hub gene was knocked down in the HCC cell line. Results We discovered 6 prognostic genes (SKA1, CDC20, AGTRAP, BIRC5, NEIL3, and CDC25C) for constructing a PPI network after investigating survival and differential expression genes. According to the topological degree, AGTRAP was chosen as the basis for the stratification system, and it was revealed to be a risk factor with an independent prognostic value in Kaplan-Meier analysis and Cox regression analysis (P < 0.05). In addition, we constructed two visualized nomograms based on AGTRAP. The novel stratification system had a robust predictive value for PFI and OS in ROC analysis and calibration curve (P < 0.05). Meanwhile, AGTRAP upregulation was associated with T staging, N staging, M staging, pathological stage, grade, and vascular invasion (P < 0.05). Notably, AGTRAP was overexpressed in tumor tissues in all pancancers with paired samples (P < 0.05). Furthermore, AGTRAP was associated with immune response and may change immune microenvironment in HCC (P < 0.05). Next, gene enrichment analysis suggested that AGTRAP may be involved in the biological process, such as cotranslational protein targeting to the membrane. Finally, we identified the oncogenic effect of AGTRAP by qRT-PCR, colony formation, western blot, and CCK-8 assay (P < 0.05). Conclusion We provided robust evidences that a stratification system based on AGTRAP can guide survival prediction for HCC patients.
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