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Noda A. Morphogenesis-coupled DNA repair - in mammalian embryogenesis, morphogenesis and DNA double strand break (DSB) repair are carried out simultaneously to ensure normal development. JOURNAL OF RADIATION RESEARCH 2024; 65:416-419. [PMID: 38718394 PMCID: PMC11115463 DOI: 10.1093/jrr/rrae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/05/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Asao Noda
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama-Park, Minami-Ku, Hiroshima 732-0815, Japan
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2
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Jin J, Liu XM, Shao W, Meng XM. Nucleic acid and protein methylation modification in renal diseases. Acta Pharmacol Sin 2024; 45:661-673. [PMID: 38102221 PMCID: PMC10943093 DOI: 10.1038/s41401-023-01203-6] [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: 06/27/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Although great efforts have been made to elucidate the pathological mechanisms of renal diseases and potential prevention and treatment targets that would allow us to retard kidney disease progression, we still lack specific and effective management methods. Epigenetic mechanisms are able to alter gene expression without requiring DNA mutations. Accumulating evidence suggests the critical roles of epigenetic events and processes in a variety of renal diseases, involving functionally relevant alterations in DNA methylation, histone methylation, RNA methylation, and expression of various non-coding RNAs. In this review, we highlight recent advances in the impact of methylation events (especially RNA m6A methylation, DNA methylation, and histone methylation) on renal disease progression, and their impact on treatments of renal diseases. We believe that a better understanding of methylation modification changes in kidneys may contribute to the development of novel strategies for the prevention and management of renal diseases.
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Affiliation(s)
- Juan Jin
- School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
- Research Center for Translational Medicine, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Xue-Mei Liu
- School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei, 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei, 230032, China.
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3
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Liu Z, Liu J, Wang W, An X, Luo L, Yu D, Sun W. Epigenetic modification in diabetic kidney disease. Front Endocrinol (Lausanne) 2023; 14:1133970. [PMID: 37455912 PMCID: PMC10348754 DOI: 10.3389/fendo.2023.1133970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
Diabetic kidney disease (DKD) is a common microangiopathy in diabetic patients and the main cause of death in diabetic patients. The main manifestations of DKD are proteinuria and decreased renal filtration capacity. The glomerular filtration rate and urinary albumin level are two of the most important hallmarks of the progression of DKD. The classical treatment of DKD is controlling blood glucose and blood pressure. However, the commonly used clinical therapeutic strategies and the existing biomarkers only partially slow the progression of DKD and roughly predict disease progression. Therefore, novel therapeutic methods, targets and biomarkers are urgently needed to meet clinical requirements. In recent years, increasing attention has been given to the role of epigenetic modification in the pathogenesis of DKD. Epigenetic variation mainly includes DNA methylation, histone modification and changes in the noncoding RNA expression profile, which are deeply involved in DKD-related inflammation, oxidative stress, hemodynamics, and the activation of abnormal signaling pathways. Since DKD is reversible at certain disease stages, it is valuable to identify abnormal epigenetic modifications as early diagnosis and treatment targets to prevent the progression of end-stage renal disease (ESRD). Because the current understanding of the epigenetic mechanism of DKD is not comprehensive, the purpose of this review is to summarize the role of epigenetic modification in the occurrence and development of DKD and evaluate the value of epigenetic therapies in DKD.
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Affiliation(s)
- Zhe Liu
- Public Research Platform, First Hospital of Jilin University, Changchun, Jilin, China
- College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Jiahui Liu
- Public Research Platform, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wanning Wang
- Department of Nephrology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xingna An
- Public Research Platform, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ling Luo
- Public Research Platform, First Hospital of Jilin University, Changchun, Jilin, China
| | - Dehai Yu
- Public Research Platform, First Hospital of Jilin University, Changchun, Jilin, China
| | - Weixia Sun
- Department of Nephrology, First Hospital of Jilin University, Changchun, Jilin, China
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4
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Zhang F, Wei M, Chen H, Ji L, Nie Y, Kang J. The genomic stability regulator PTIP is required for proper chromosome segregation in mitosis. Cell Div 2022; 17:5. [PMID: 36153541 PMCID: PMC9509598 DOI: 10.1186/s13008-022-00081-4] [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: 02/11/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background The Pax transcription activation domain-interacting protein (PTIP) is a nuclear protein that is an essential component of H3K4 methylation for gene activation in vascular, kidney, B cell, and adipocyte development. Furthermore, it plays a key role in genomic stability in higher eukaryotic cells. It binds to 53BP1 and antagonizes inappropriate homologous recombination for a proper DNA damage response. Interestingly, an early study reported mitotic defects after PTIP inactivation, but it is not clear whether PTIP directly facilitates mitotic processes. Results Here, we showed that PTIP is essential for the mitotic integrity of HeLa cells. PTIP inactivation increases cell death during mitotic exit, which appears to result from direct mitotic defects. PTIP inactivation did not affect the G2M DNA damage checkpoint during interphase upon etoposide treatment. However, in mitosis, PTIP inactivation results in prolonged mitotic time, inefficient chromosome alignment, and increased cell death. Furthermore, PTIP localizes to the mitotic centrosome via BRCT domains at the C-terminus. Conclusion This study reveals a novel function of PTIP in maintaining the genomic stability of higher eukaryotes during mitosis. Therefore, its deregulation, which occurs in various tumors, may destabilize the genome by introducing an abnormal DNA damage response, as well as erroneous chromosome segregation. Supplementary Information The online version contains supplementary material available at 10.1186/s13008-022-00081-4.
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5
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Wang S, Zhang X, Wang Q, Wang R. Histone modification in podocyte injury of diabetic nephropathy. J Mol Med (Berl) 2022; 100:1373-1386. [PMID: 36040515 DOI: 10.1007/s00109-022-02247-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022]
Abstract
Diabetic nephropathy (DN), an important complication of diabetic microvascular disease, is one of the leading causes of end-stage renal disease (ESRD), which brings heavy burdens to the whole society. Podocytes are terminally differentiated glomerular cells, which act as a pivotal component of glomerular filtration barrier. When podocytes are injured, glomerular filtration barrier is damaged, and proteinuria would occur. Dysfunction of podocytes contributes to DN. And degrees of podocyte injury influence prognosis of DN. Growing evidences have shown that epigenetics does a lot in the evolvement of podocyte injury. Epigenetics includes DNA methylation, histone modification, and non-coding RNA. Among them, histone modification plays an indelible role. Histone modification includes histone methylation, histone acetylation, and other modifications such as histone phosphorylation, histone ubiquitination, histone ADP-ribosylation, histone crotonylation, and histone β-hydroxybutyrylation. It can affect chromatin structure and regulate gene transcription to exert its function. This review is to summarize documents about pathogenesis of podocyte injury, most importantly, histone modification of podocyte injury in DN recently to provide new ideas for further molecular research, diagnosis, and treatment.
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Affiliation(s)
- Simeng Wang
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Xinyu Zhang
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Qinglian Wang
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250012, Shandong, China. .,Department of Nephrology, Shandong Provincial Hospital, Shandong First Medical University, No. 324 Jingwu Street, Jinan, 250021, Shandong, China.
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250012, Shandong, China. .,Department of Nephrology, Shandong Provincial Hospital, Shandong First Medical University, No. 324 Jingwu Street, Jinan, 250021, Shandong, China.
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6
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Zhao YB, Wei W, Lin XX, Chai YF, Jin H. The Role of Histone H3 Methylation in Acute Kidney Injury. Drug Des Devel Ther 2022; 16:2453-2461. [PMID: 35941926 PMCID: PMC9356748 DOI: 10.2147/dddt.s376673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/27/2022] [Indexed: 12/28/2022] Open
Abstract
Acute kidney injury (AKI) is a clinical syndrome in which kidney function declines sharply due to various reasons. Although the morbidity and mortality of AKI are high, the mechanism of occurrence and development of AKI has not been fully elucidated, and precise prevention and treatment measures are lacking. Epigenetics is a branch of genetics that provides a new perspective to explore the pathophysiology of AKI and renal repair. A large amount of literature shows that the methylation mechanism of H3 in histones is closely related to the development of kidney diseases. The sorting out of histone H3 methylation mechanism in AKI and kidney repair can help understand the pathophysiological process of the disease more deeply. It may also provide new ideas for diagnosing and treating of the disease.
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Affiliation(s)
- Yi-Bo Zhao
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China
| | - Wei Wei
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China
| | - Xiao-Xi Lin
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China
| | - Yan-Fen Chai
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China
| | - Heng Jin
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China
- Correspondence: Heng Jin; Yan-Fen Chai, Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, 300000, People’s Republic of China, Email ;
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7
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Harris M, Schuh MP, McKinney D, Kaufman K, Erkan E. Whole Exome Sequencing in a Population With Severe Congenital Anomalies of Kidney and Urinary Tract. Front Pediatr 2022; 10:898773. [PMID: 35990004 PMCID: PMC9386178 DOI: 10.3389/fped.2022.898773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Fetal and neonatal interventions (e.g., amnioinfusions, amniotic shunting, and infant dialysis) have increased survival of infants with severe Congenital Anomalies of the Kidney and Urinary Tract (CAKUT), however, outcomes vary dramatically. Our aim was to perform Whole Exome Sequencing (WES) in a unique severe CAKUT population with the goal to identify new variants that will enhance prediction of postnatal outcomes. We performed trio WES on five infants with severe CAKUT (undergoing fetal interventions and/or those who initiated renal replacement therapy (RRT) within 1 month of life) and their parents as well as three singletons. We identified three potential candidate gene variants (NSUN7, MTMR3, CEP162) and validated two variants in known CAKUT genes (GATA3 and FRAS1) showing strong enrichment in this severe phenotype population. Based on our small pilot study of a unique severe CAKUT population, WES appears to be a potential tool to help predict the course of infants with severe CAKUT prenatally.
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Affiliation(s)
- Meredith Harris
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Nephrology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Meredith P Schuh
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David McKinney
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Kenneth Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Elif Erkan
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
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8
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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9
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Lepa C, Hoppe S, Stöber A, Skryabin BV, Sievers LK, Heitplatz B, Ciarimboli G, Neugebauer U, Lindenmeyer MT, Cohen CD, Drexler HC, Boor P, Weide T, Pavenstädt H, George B. TrkC Is Essential for Nephron Function and Trans-Activates Igf1R Signaling. J Am Soc Nephrol 2021; 32:357-374. [PMID: 33380522 PMCID: PMC8054883 DOI: 10.1681/asn.2020040424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/03/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Injury to kidney podocytes often results in chronic glomerular disease and consecutive nephron malfunction. For most glomerular diseases, targeted therapies are lacking. Thus, it is important to identify novel signaling pathways contributing to glomerular disease. Neurotrophic tyrosine kinase receptor 3 (TrkC) is expressed in podocytes and the protein transmits signals to the podocyte actin cytoskeleton. METHODS Nephron-specific TrkC knockout (TrkC-KO) and nephron-specific TrkC-overexpressing (TrkC-OE) mice were generated to dissect the role of TrkC in nephron development and maintenance. RESULTS Both TrkC-KO and TrkC-OE mice exhibited enlarged glomeruli, mesangial proliferation, basement membrane thickening, albuminuria, podocyte loss, and aspects of FSGS during aging. Igf1 receptor (Igf1R)-associated gene expression was dysregulated in TrkC-KO mouse glomeruli. Phosphoproteins associated with insulin, erb-b2 receptor tyrosine kinase (Erbb), and Toll-like receptor signaling were enriched in lysates of podocytes treated with the TrkC ligand neurotrophin-3 (Nt-3). Activation of TrkC by Nt-3 resulted in phosphorylation of the Igf1R on activating tyrosine residues in podocytes. Igf1R phosphorylation was increased in TrkC-OE mouse kidneys while it was decreased in TrkC-KO kidneys. Furthermore, TrkC expression was elevated in glomerular tissue of patients with diabetic kidney disease compared with control glomerular tissue. CONCLUSIONS Our results show that TrkC is essential for maintaining glomerular integrity. Furthermore, TrkC modulates Igf-related signaling in podocytes.
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Affiliation(s)
- Carolin Lepa
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Sascha Hoppe
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Antje Stöber
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Boris V. Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), Westfälische-Wilhelms-University, Münster, Germany
| | | | - Barbara Heitplatz
- Gerhard-Domagk Institute for Pathology, University Hospital Münster, Münster, Germany
| | | | - Ute Neugebauer
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | - Maja T. Lindenmeyer
- III. Medizinische Klinik und Poliklinik, University Hospital Hamburg-Eppendorf, Germany
| | - Clemens D. Cohen
- Klinik für Nieren-, Hochdruck- und Rheumaerkrankungen, München Klinik Harlaching, Germany
| | - Hannes C.A. Drexler
- Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Thomas Weide
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
| | | | - Britta George
- Medizinische Klinik D, University Hospital Münster, Münster, Germany
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10
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Targeting chromatin dysregulation in organ fibrosis. Cytokine Growth Factor Rev 2020; 57:64-72. [PMID: 32900600 DOI: 10.1016/j.cytogfr.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis leads to destruction of organ architecture accompanied by chronic inflammation and loss of function. Fibrosis affects nearly every organ in the body and accounts for ∼45% of total deaths worldwide. Over the past decade, tremendous progress has been made in understanding the basic mechanisms leading to organ fibrosis. However, we are limited with therapeutic options and there is a significant need to develop highly effective anti-fibrotic therapies. Recent advances in sequencing technologies have advanced the burgeoning field of epigenetics towards molecular understanding at a higher resolution. Here we provide a comprehensive review of the recent advances in chromatin regulatory processes, specifically DNA methylation, post-translational modification of histones, and chromatin remodeling complexes in kidney, liver and lung fibrosis. Although this research field is young, we discuss new strategies for potential therapeutic interventions for treating organ fibrosis.
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11
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Park K, Kim JA, Kim J. Transcriptional regulation by the KMT2 histone H3K4 methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194545. [DOI: 10.1016/j.bbagrm.2020.194545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/21/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
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12
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Lin CL, Hsu YC, Huang YT, Shih YH, Wang CJ, Chiang WC, Chang PJ. A KDM6A-KLF10 reinforcing feedback mechanism aggravates diabetic podocyte dysfunction. EMBO Mol Med 2020; 11:emmm.201809828. [PMID: 30948420 PMCID: PMC6505577 DOI: 10.15252/emmm.201809828] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diabetic nephropathy is the leading cause of end‐stage renal disease. Although dysfunction of podocytes, also termed glomerular visceral epithelial cells, is critically associated with diabetic nephropathy, the mechanism underlying podocyte dysfunction still remains obscure. Here, we identify that KDM6A, a histone lysine demethylase, reinforces diabetic podocyte dysfunction by creating a positive feedback loop through up‐regulation of its downstream target KLF10. Overexpression of KLF10 in podocytes not only represses multiple podocyte‐specific markers including nephrin, but also conversely increases KDM6A expression. We further show that KLF10 inhibits nephrin expression by directly binding to the gene promoter together with the recruitment of methyltransferase Dnmt1. Importantly, inactivation or knockout of either KDM6A or KLF10 in mice significantly suppresses diabetes‐induced proteinuria and kidney injury. Consistent with the notion, we also show that levels of both KDM6A and KLF10 proteins or mRNAs are substantially elevated in kidney tissues or in urinary exosomes of human diabetic nephropathy patients as compared with control subjects. Our findings therefore suggest that targeting the KDM6A–KLF10 feedback loop may be beneficial to attenuate diabetes‐induced kidney injury.
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Affiliation(s)
- Chun-Liang Lin
- Departments of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan.,Kidney Research Center, Chang Gung Memorial Hospital, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Kidney and Diabetic Complications Research Team (KDCRT), Chang Gung Memorial Hospital, Chiayi, Taiwan.,Center for Shockwave Medicine and Tissue Engineering, Department of Medical Research, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yung-Chien Hsu
- Departments of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan.,Kidney and Diabetic Complications Research Team (KDCRT), Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Ting Huang
- Departments of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan.,Kidney and Diabetic Complications Research Team (KDCRT), Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ya-Hsueh Shih
- Departments of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan.,Kidney and Diabetic Complications Research Team (KDCRT), Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ching-Jen Wang
- Center for Shockwave Medicine and Tissue Engineering, Department of Medical Research, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Department of Orthopedic Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Wen-Chih Chiang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pey-Jium Chang
- Departments of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan .,Kidney and Diabetic Complications Research Team (KDCRT), Chang Gung Memorial Hospital, Chiayi, Taiwan.,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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13
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Soofi A, Kutschat AP, Azam M, Laszczyk AM, Dressler GR. Regeneration after acute kidney injury requires PTIP-mediated epigenetic modifications. JCI Insight 2020; 5:130204. [PMID: 31917689 DOI: 10.1172/jci.insight.130204] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 01/03/2020] [Indexed: 01/25/2023] Open
Abstract
A terminally differentiated cellular phenotype is thought to be maintained, at least in part, by both active and repressive histone marks. However, it is unclear whether regenerating cells after injury need to replicate such epigenetic marks to recover. To test whether renal epithelial cell regeneration is dependent on histone H3K4 methylation, we generated a mouse model that deleted the Paxip1 gene in mature renal proximal tubules. Paxip1 encodes PTIP, an essential protein in the Mll3/4 histone H3K4 methyltransferase complex. Mice with PTIP deletions in the adult kidney proximal tubules were viable and fertile. Upon acute kidney injury, such mice failed to regenerate damaged tubules, leading to scarring and interstitial fibrosis. The inability to repair damage was likely due to a failure to reenter mitosis and reactivate regulatory genes such as Sox9. PTIP deletion reduced histone H3K4 methylation in uninjured adult kidneys but did not significantly affect function or the expression of epithelial specific markers. Strikingly, cell lineage tracing revealed that surviving PTIP mutant cells could alter their phenotype and lose epithelial markers. These data demonstrate that PTIP and associated MLL3/4-mediated histone methylation are needed for regenerating proximal tubules and to maintain or reestablish the cellular epithelial phenotype.
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14
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Yang YX, Shen HH, Cao F, Xie LY, Zhu GL, Sam NB, Wang DG, Pan HF. Therapeutic potential of enhancer of zeste homolog 2 in autoimmune diseases. Expert Opin Ther Targets 2019; 23:1015-1030. [PMID: 31747802 DOI: 10.1080/14728222.2019.1696309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Autoimmune diseases (ADs) are idiopathic and heterogeneous disorders with contentious pathophysiology. Great strides have been made in epigenetics and its involvement in ADs. Zeste homolog 2 (EZH2) has sparked extensive interest because of its pleiotropic roles in distinct pathologic contexts.Areas covered: This review summarizes the epigenetic functions and the biological significance of EZH2 in the etiology of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), inflammatory bowel disease (IBD), multiple sclerosis (MS), and systemic sclerosis (SSc). A brief recapitulation of the therapeutic potential of EZH2 targeting is provided.Expert opinion: There are questions marks and controversies surrounding the feasibility and safety of EZH2 targeting; it is recommended in RA and SLE, but queried in T1D, IBD, MS, and SSc. Future work should focus on contrast studies, systematic analyses and preclinical studies with optimizing methodologies. Selective research studies conducted in a stage-dependent manner are necessary because of the relapsing-remitting clinical paradigms.
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Affiliation(s)
- Yue-Xin Yang
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hui-Hui Shen
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Fan Cao
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Liang-Yu Xie
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Guang-Lin Zhu
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Napoleon Bellua Sam
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - De-Guang Wang
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
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15
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Majumder S, Hadden MJ, Thieme K, Batchu SN, Niveditha D, Chowdhury S, Yerra VG, Advani SL, Bowskill BB, Liu Y, Vakili H, Alghamdi TA, White KE, Geldenhuys L, Siddiqi FS, Advani A. Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease. Diabetologia 2019; 62:2129-2142. [PMID: 31399844 DOI: 10.1007/s00125-019-4967-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
AIMS/HYPOTHESIS Long non-coding RNAs (lncRNAs) are garnering increasing attention for their putative roles in the pathogenesis of chronic diseases, including diabetic kidney disease (DKD). However, much about in vivo lncRNA functionality in the adult organism remains unclear. To better understand lncRNA regulation and function in DKD, we explored the effects of the modular scaffold lncRNA HOTAIR (HOX antisense intergenic RNA), which approximates chromatin modifying complexes to their target sites on the genome. METHODS Experiments were performed in human kidney tissue, in mice with streptozotocin-induced diabetes, the db/db mouse model of type 2 diabetes, podocyte-specific Hotair knockout mice and conditionally immortalised mouse podocytes. RESULTS HOTAIR was observed to be expressed by several kidney cell-types, including glomerular podocytes, in both human and mouse kidneys. However, knockout of Hotair from podocytes had almost no effect on kidney structure, function or ultrastructure. Glomerular HOTAIR expression was found to be increased in human DKD, in the kidneys of mice with streptozotocin-induced diabetes and in the kidneys of db/db mice. Likewise, exposure of cultured mouse podocytes to high glucose caused upregulation of Hotair expression, which occurred in a p65-dependent manner. Although HOTAIR expression was upregulated in DKD and in high glucose-exposed podocytes, its knockout did not alter the development of kidney damage in diabetic mice. Rather, in a bioinformatic analysis of human kidney tissue, HOTAIR expression closely paralleled the expression of its genic neighbour, HOXC11, which is important to developmental patterning but which has an uncertain role in the adult kidney. CONCLUSIONS/INTERPRETATION Many lncRNAs have been found to bind to the same chromatin modifying complexes. Thus, there is likely to exist sufficient redundancy in the system that the biological effects of dysregulated lncRNAs in kidney disease may often be inconsequential. The example of the archetypal scaffold lncRNA, HOTAIR, illustrates how lncRNA dysregulation may be a bystander in DKD without necessarily contributing to the pathogenesis of the condition. In the absence of in vivo validation, caution should be taken before ascribing major functional roles to single lncRNAs in the pathogenesis of chronic diseases.
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Affiliation(s)
- Syamantak Majumder
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Mitchell J Hadden
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Karina Thieme
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sri N Batchu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Divya Niveditha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Shibasish Chowdhury
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Veera Ganesh Yerra
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Bridgit B Bowskill
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Youan Liu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Hana Vakili
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tamadher A Alghamdi
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada
| | - Kathryn E White
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, UK
| | | | - Ferhan S Siddiqi
- Department of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael's Hospital, 209 Victoria Street, Toronto, ON, M5C 1T8, Canada.
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16
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Li D, Zhao D, Zhang W, Ma Q, Liu D, Huang Q, Zheng Y, Bai X, Sun X, Chen X. Identification of proteins potentially associated with renal aging in rats. Aging (Albany NY) 2019; 10:1192-1205. [PMID: 29907735 PMCID: PMC6046247 DOI: 10.18632/aging.101460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/30/2018] [Indexed: 11/25/2022]
Abstract
We established a young (Y)-old (O) rat kidney transplantation model. With this model, we detected no age-related differences in renal structure between Y→Y and Y→O kidneys or O→O and O→Y kidneys. However, we did detect differences in levels of the senescence markers β-gal and p16 as well as the inflammatory cytokines TNF-α and IL-1β. Using proteomics analysis we detected 66 proteins associated with suppression of aging and 73 proteins associated with enhancement of aging. After construction of a protein-protein interaction network, a total of 73 nodes and 99 edges were analyzed using MCODE, and three significant modules were selected. GO and KEGG analyses showed that these proteins were mainly located in mitochondria and were largely related to oxidative stress. Among them, SOD1 expression was lower in Y→O than Y→Y kidneys and higher in O→Y than O→O kidneys. Acetylated (Ac)-NF-κB showed the opposite expression profile. In addition, SOD1 expression was higher in primary tubular epithelial cells from young rats than old rats, and SOD1 knockdown led to increased Ac-NF-κB expression. These findings suggest the local renal environment, particularly oxidative stress/mitochondrial function, affects renal aging.
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Affiliation(s)
- Diangeng Li
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Delong Zhao
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Weiguang Zhang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Qian Ma
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Dong Liu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Qi Huang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Ying Zheng
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Xueyuan Bai
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Xuefeng Sun
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing 100853, China
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17
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Felizardo RJF, de Almeida DC, Pereira RL, Watanabe IKM, Doimo NTS, Ribeiro WR, Cenedeze MA, Hiyane MI, Amano MT, Braga TT, Ferreira CM, Parmigiani RB, Andrade-Oliveira V, Volpini RA, Vinolo MAR, Mariño E, Robert R, Mackay CR, Camara NOS. Gut microbial metabolite butyrate protects against proteinuric kidney disease through epigenetic- and GPR109a-mediated mechanisms. FASEB J 2019; 33:11894-11908. [PMID: 31366236 DOI: 10.1096/fj.201901080r] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Butyrate is a short-chain fatty acid derived from the metabolism of indigestible carbohydrates by the gut microbiota. Butyrate contributes to gut homeostasis, but it may also control inflammatory responses and host physiology in other tissues. Butyrate inhibits histone deacetylases, thereby affecting gene transcription, and also signals through the metabolite-sensing G protein receptor (GPR)109a. We produced an mAb to mouse GPR109a and found high expression on podocytes in the kidney. Wild-type and Gpr109a-/- mice were induced to develop nephropathy by a single injection of Adriamycin and treated with sodium butyrate or high butyrate-releasing high-amylose maize starch diet. Butyrate improved proteinuria by preserving podocyte at glomerular basement membrane and attenuated glomerulosclerosis and tissue inflammation. This protective phenotype was associated with increased podocyte-related proteins and a normalized pattern of acetylation and methylation at promoter sites of genes essential for podocyte function. We found that GPR109a is expressed by podocytes, and the use of Gpr109a-/- mice showed that the protective effects of butyrate depended on GPR109a expression. A prebiotic diet that releases high amounts of butyrate also proved highly effective for protection against kidney disease. Butyrate and GPR109a play a role in the pathogenesis of kidney disease and provide one of the important molecular connections between diet, the gut microbiota, and kidney disease.-Felizardo, R. J. F., de Almeida, D. C., Pereira, R. L., Watanabe, I. K. M., Doimo, N. T. S., Ribeiro, W. R., Cenedeze, M. A., Hiyane, M. I., Amano, M. T., Braga, T. T., Ferreira, C. M., Parmigiani, R. B., Andrade-Oliveira, V., Volpini, R. A., Vinolo, M. A. R., Mariño, E., Robert, R., Mackay, C. R., Camara, N. O. S. Gut microbial metabolite butyrate protects against proteinuric kidney disease through epigenetic- and GPR109a-mediated mechanisms.
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Affiliation(s)
- Raphael J F Felizardo
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil.,Department of Biochemistry and Molecular Biology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
| | - Danilo C de Almeida
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael L Pereira
- Department of Physiology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ingrid K M Watanabe
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
| | - Nayara T S Doimo
- Center for Molecular Oncology, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Willian R Ribeiro
- Department of Pharmaceutics Sciences, Institute of Environmental Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, Brazil
| | - Marcos A Cenedeze
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Meire I Hiyane
- Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
| | - Mariane T Amano
- Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil.,Center for Molecular Oncology, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Tárcio T Braga
- Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
| | - Caroline M Ferreira
- Department of Pharmaceutics Sciences, Institute of Environmental Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, Diadema, Brazil
| | | | - Vinicius Andrade-Oliveira
- Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
| | - Rildo A Volpini
- Laboratório de Investigação Médica 12 (LIM12), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Marco Aurélio R Vinolo
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Eliana Mariño
- Department of Biochemistry and Molecular Biology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
| | - Remy Robert
- Department of Biochemistry and Molecular Biology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
| | - Charles R Mackay
- Department of Biochemistry and Molecular Biology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
| | - Niels O S Camara
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences IV, Universidade de São Paulo, São Paulo, Brazil
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18
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Epigenetic Modification Mechanisms Involved in Inflammation and Fibrosis in Renal Pathology. Mediators Inflamm 2018; 2018:2931049. [PMID: 30647531 PMCID: PMC6311799 DOI: 10.1155/2018/2931049] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 01/19/2023] Open
Abstract
The growing incidence of obesity, hypertension, and diabetes, coupled with the aging of the population, is increasing the prevalence of renal diseases in our society. Chronic kidney disease (CKD) is characterized by persistent inflammation, fibrosis, and loss of renal function leading to end-stage renal disease. Nowadays, CKD treatment has limited effectiveness underscoring the importance of the development of innovative therapeutic options. Recent studies have identified how epigenetic modifications participate in the susceptibility to CKD and have explained how the environment interacts with the renal cell epigenome to contribute to renal damage. Epigenetic mechanisms regulate critical processes involved in gene regulation and downstream cellular responses. The most relevant epigenetic modifications that play a critical role in renal damage include DNA methylation, histone modifications, and changes in miRNA levels. Importantly, these epigenetic modifications are reversible and, therefore, a source of potential therapeutic targets. Here, we will explain how epigenetic mechanisms may regulate essential processes involved in renal pathology and highlight some possible epigenetic therapeutic strategies for CKD treatment.
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19
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Hing B, Sathyaputri L, Potash JB. A comprehensive review of genetic and epigenetic mechanisms that regulate BDNF expression and function with relevance to major depressive disorder. Am J Med Genet B Neuropsychiatr Genet 2018; 177:143-167. [PMID: 29243873 DOI: 10.1002/ajmg.b.32616] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
Major depressive disorder (MDD) is a mood disorder that affects behavior and impairs cognition. A gene potentially important to this disorder is the brain derived neurotrophic factor (BDNF) as it is involved in processes controlling neuroplasticity. Various mechanisms exist to regulate BDNF's expression level, subcellular localization, and sorting to appropriate secretory pathways. Alterations to these processes by genetic factors and negative stressors can dysregulate its expression, with possible implications for MDD. Here, we review the mechanisms governing the regulation of BDNF expression, and discuss how disease-associated single nucleotide polymorphisms (SNPs) can alter these mechanisms, and influence MDD. As negative stressors increase the likelihood of MDD, we will also discuss the impact of these stressors on BDNF expression, the cellular effect of such a change, and its impact on behavior in animal models of stress. We will also describe epigenetic processes that mediate this change in BDNF expression. Similarities in BDNF expression between animal models of stress and those in MDD will be highlighted. We will also contrast epigenetic patterns at the BDNF locus between animal models of stress, and MDD patients, and address limitations to current clinical studies. Future work should focus on validating current genetic and epigenetic findings in tightly controlled clinical studies. Regions outside of BDNF promoters should also be explored, as should other epigenetic marks, to improve identification of biomarkers for MDD.
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Affiliation(s)
- Benjamin Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leela Sathyaputri
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - James B Potash
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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20
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Gromnitza S, Lepa C, Weide T, Schwab A, Pavenstädt H, George B. Tropomyosin-related kinase C (TrkC) enhances podocyte migration by ERK-mediated WAVE2 activation. FASEB J 2018; 32:1665-1676. [PMID: 29162704 DOI: 10.1096/fj.201700703r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Podocyte malfunction is central to glomerular diseases and is marked by defective podocyte intercellular junctions and actin cytoskeletal dynamics. Podocytes share many morphologic features with neurons, so that similar sets of proteins appear to regulate cell process formation. One such protein is the tropomyosin-related kinase C (TrkC). TrkC deficiency in mice leads to proteinuria as a surrogate of defective kidney filter function. Activation of endogenous TrkC by its ligand neurotrophin-3 resulted in increased podocyte migration-a surrogate of podocyte actin dynamics in vivo. Employing a mutagenesis approach, we found that the Src homologous and collagen-like (Shc) binding site Tyr516 within the TrkC cytoplasmic domain was necessary for TrkC-induced migration of podocytes. TrkC activation led to a mobility shift of Wiskott-Aldrich syndrome family verprolin-homologous protein (WAVE)-2 which is known to orchestrate Arp2/3 activation and actin polymerization. Chemical inactivation of Erk or mutagenesis of 2 of 4 known Erk target sites within WAVE2, Thr346 and Ser351, abolished the TrkC-induced WAVE2 mobility shift. Knockdown of WAVE2 by shRNA abolished TrkC-induced podocyte migration. In summary, TrkC signals to the podocyte actin cytoskeleton to induce migration by phosphorylating WAVE2 Erk dependently. This signaling mechanism may be important for TrkC-mediated cytoskeletal dynamics in podocyte disease.-Gromnitza, S., Lepa, C., Weide, T., Schwab, A., Pavenstädt, H., George, B. Tropomyosin-related kinase C (TrkC) enhances podocyte migration by ERK-mediated WAVE2 activation.
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Affiliation(s)
- Sascha Gromnitza
- Medizinische Klinik D, Universitätsklinikum Münster, Muenster, Germany
| | - Carolin Lepa
- Medizinische Klinik D, Universitätsklinikum Münster, Muenster, Germany
| | - Thomas Weide
- Medizinische Klinik D, Universitätsklinikum Münster, Muenster, Germany
| | - Albrecht Schwab
- Institut für Physiologie II, Westfälische-Wilhelms-Universität Münster, Muenster, Germany
| | | | - Britta George
- Medizinische Klinik D, Universitätsklinikum Münster, Muenster, Germany
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21
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Majumder S, Thieme K, Batchu SN, Alghamdi TA, Bowskill BB, Kabir MG, Liu Y, Advani SL, White KE, Geldenhuys L, Tennankore KK, Poyah P, Siddiqi FS, Advani A. Shifts in podocyte histone H3K27me3 regulate mouse and human glomerular disease. J Clin Invest 2017; 128:483-499. [PMID: 29227285 DOI: 10.1172/jci95946] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/31/2017] [Indexed: 01/09/2023] Open
Abstract
Histone protein modifications control fate determination during normal development and dedifferentiation during disease. Here, we set out to determine the extent to which dynamic changes to histones affect the differentiated phenotype of ordinarily quiescent adult glomerular podocytes. To do this, we examined the consequences of shifting the balance of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark in podocytes. Adriamycin nephrotoxicity and subtotal nephrectomy (SNx) studies indicated that deletion of the histone methylating enzyme EZH2 from podocytes decreased H3K27me3 levels and sensitized mice to glomerular disease. H3K27me3 was enriched at the promoter region of the Notch ligand Jag1 in podocytes, and derepression of Jag1 by EZH2 inhibition or knockdown facilitated podocyte dedifferentiation. Conversely, inhibition of the Jumonji C domain-containing demethylases Jmjd3 and UTX increased the H3K27me3 content of podocytes and attenuated glomerular disease in adriamycin nephrotoxicity, SNx, and diabetes. Podocytes in glomeruli from humans with focal segmental glomerulosclerosis or diabetic nephropathy exhibited diminished H3K27me3 and heightened UTX content. Analogous to human disease, inhibition of Jmjd3 and UTX abated nephropathy progression in mice with established glomerular injury and reduced H3K27me3 levels. Together, these findings indicate that ostensibly stable chromatin modifications can be dynamically regulated in quiescent cells and that epigenetic reprogramming can improve outcomes in glomerular disease by repressing the reactivation of developmental pathways.
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Affiliation(s)
- Syamantak Majumder
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Karina Thieme
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Sri N Batchu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tamadher A Alghamdi
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Bridgit B Bowskill
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - M Golam Kabir
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Youan Liu
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Kathryn E White
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Penelope Poyah
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ferhan S Siddiqi
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
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22
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Naudin C, Smith B, Bond DR, Dun MD, Scott RJ, Ashman LK, Weidenhofer J, Roselli S. Characterization of the early molecular changes in the glomeruli of Cd151 -/- mice highlights induction of mindin and MMP-10. Sci Rep 2017; 7:15987. [PMID: 29167507 PMCID: PMC5700190 DOI: 10.1038/s41598-017-15993-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/26/2017] [Indexed: 01/06/2023] Open
Abstract
In humans and FVB/N mice, loss of functional tetraspanin CD151 is associated with glomerular disease characterised by early onset proteinuria and ultrastructural thickening and splitting of the glomerular basement membrane (GBM). To gain insight into the molecular mechanisms associated with disease development, we characterised the glomerular gene expression profile at an early stage of disease progression in FVB/N Cd151 -/- mice compared to Cd151 +/+ controls. This study identified 72 up-regulated and 183 down-regulated genes in FVB/N Cd151 -/- compared to Cd151 +/+ glomeruli (p < 0.05). Further analysis highlighted induction of the matrix metalloprotease MMP-10 and the extracellular matrix protein mindin (encoded by Spon2) in the diseased FVB/N Cd151 -/- GBM that did not occur in the C57BL/6 diseased-resistant strain. Interestingly, mindin was also detected in urinary samples of FVB/N Cd151 -/- mice, underlining its potential value as a biomarker for glomerular diseases associated with GBM alterations. Gene set enrichment and pathway analysis of the microarray dataset showed enrichment in axon guidance and actin cytoskeleton signalling pathways as well as activation of inflammatory pathways. Given the known function of mindin, its early expression in the diseased GBM could represent a trigger of both further podocyte cytoskeletal changes and inflammation, thereby playing a key role in the mechanisms of disease progression.
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Affiliation(s)
- Crystal Naudin
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia.,Emory University, Atlanta, Georgia, USA
| | - Brian Smith
- School of Mathematics and Physical Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Danielle R Bond
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia.,Hunter Area Pathology Service, John Hunter Hospital, New Lambton, New South Wales, Australia
| | - Leonie K Ashman
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Judith Weidenhofer
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Séverine Roselli
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia. .,Hunter Medical Research Institute, New Lambton, New South Wales, Australia.
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23
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 674] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Leng S, Yang M, Zhao Y, Zhao J, Zeng Z, Yang Y, Yuan J, Lv B, Jun F, Wang B. PTIP promotes recurrence and metastasis of hepatocellular carcinoma by regulating epithelial-mesenchymal transition. Oncotarget 2017; 8:58184-58198. [PMID: 28938547 PMCID: PMC5601643 DOI: 10.18632/oncotarget.16436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/28/2017] [Indexed: 02/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal tumors worldwide, which is mainly due to the high recurrence and metastasis rate after hepatectomy. In this study, we found that PTIP expression was dramatically upregulated in human HCC tissues and cell lines. High expression of PTIP was shown to be associated with aggressive clinicopathological features, including liver cirrhosis, vascular invasion and advanced stage. In addition, PTIP overexpression was independently associated with shorter survival and increased HCC recurrence in patients. Knockdown of the PTIP expression significantly inhibited invasion and metastasis in vitro and in vivo, whereas ectopic expression of PTIP significantly promoted invasion and metastasis. Mechanistically, PTIP promotes HCC progress by facilitating epithelial-mesenchymal transition (EMT). Notably, we also found that PTIP might increase miR-374a expression to promote EMT and metastasis in HCC. In summary, our study identified PTIP as a new potential prognostic indicator and therapeutic target for HCC.
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Affiliation(s)
- Shusheng Leng
- General Surgery Department, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
| | - Mingyang Yang
- Intensive Care Unit, The First People's Hospital of Chengdu (Chengdu Combine Traditional Chinese and Western Medicine Hospital), Chengdu 610041, China
| | - Yanhua Zhao
- Department of Laboratory Medicine/Clinical Research Center of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jingfeng Zhao
- General Surgery Department, Chongqing Dazu District People's Hospital, Chongqing 402360, China
| | - Zhijun Zeng
- Department of Geratic Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yunpeng Yang
- Department of Pathology, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
| | - Jiatian Yuan
- General Surgery Department, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
| | - Bo Lv
- General Surgery Department, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
| | - Fan Jun
- General Surgery Department, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
| | - Bing Wang
- General Surgery Department, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu 610081, China
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Wanner N, Bechtel-Walz W. Epigenetics of kidney disease. Cell Tissue Res 2017; 369:75-92. [PMID: 28286899 DOI: 10.1007/s00441-017-2588-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation and histone modifications determine renal programming and the development and progression of renal disease. The identification of the way in which the renal cell epigenome is altered by environmental modifiers driving the onset and progression of renal diseases has extended our understanding of the pathophysiology of kidney disease progression. In this review, we focus on current knowledge concerning the implications of epigenetic modifications during renal disease from early development to chronic kidney disease progression including renal fibrosis, diabetic nephropathy and the translational potential of identifying new biomarkers and treatments for the prevention and therapy of chronic kidney disease and end-stage kidney disease.
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Affiliation(s)
- Nicola Wanner
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Center for Systems Biology (ZBSA), Albert-Ludwigs-University, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
| | - Wibke Bechtel-Walz
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
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Fujino T, Hasebe N. Alteration of histone H3K4 methylation in glomerular podocytes associated with proteinuria in patients with membranous nephropathy. BMC Nephrol 2016; 17:179. [PMID: 27855638 PMCID: PMC5114780 DOI: 10.1186/s12882-016-0390-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background Histone H3K4 trimethylation (H3K4 me3) is found in active euchromatic regions and plays an important role in podocyte function in which actin filaments are abundant in the foot processes. The pathogenesis of membranous nephropathy (MN), the most prevalent cause of primary nephrotic syndrome in the middle-aged and elderly, is podocyte dysfunction. Methods We investigated the role of H3K4 me3 in podocyte dysfunction in nephrotic syndrome using cultured podocytes and a mouse proteinuria model induced by LPS. We examined renal biopsy specimens from six patients with nephrotic syndrome caused by Phospholipase-A2-Receptor-positive primary MN. Results H3K4 me3 exhibited a pattern of nuclear expression in podocytes of the kidneys from patients with MN. The overlapping expression of H3K4 me3 and cathepsin L (a potent endoprotease causing the breakdown of actin-associated protein within lysosomal compartments in kidney podocytes) were higher in patients with MN compared with the controls. Histone H3K4 me3 in kidney podocytes was negatively correlated with synaptopodin, an actin-associated protein in podocytes, and the expression was positively correlated with the proteinuria levels in patients with MN. Histone H3K4 me3 levels were elevated in podocytes of LPS-treated mice, combined with an increase in podocyte swelling, an elevation of serum creatinine and urine albumin, increased cathepsin L, and decreased synaptopodin expression. Histone H3K4 me3 levels at the cathepsin L promoter were elevated in LPS-exposed mouse kidneys. The administration of shRNA against MLL3 (an H3K4 methyltransferase) to LPS-treated mice and cultured podocytes co-cultured with LPS-stimulated macrophages ameliorated podocyte swelling, an elevation in the serum creatinine and urine albumin levels and an increased expression of histone H3K4 me3 and cathepsin L, and a decreased expression of synaptopodin and increase in histone H3K4 me3 levels at the cathepsin L promoter. Conclusions Histone H3K4 me3 upregulation may be involved in podocyte dysfunction and the pathophysiology of MN. Targeting this epigenetic signature of histone H3K4 me3 followed by modulating the actin dynamics may be an effective strategy to ameliorate the consequences of MN.
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Affiliation(s)
- Takayuki Fujino
- Department of Internal Medicine, Cardiovascular Respiratory and Neurology and Nephrology Division, Asahikawa Medical University, Midorigaoka Higashi 2-1-1-1, Asahikawa, 078-8510, Japan.
| | - Naoyuki Hasebe
- Department of Internal Medicine, Cardiovascular Respiratory and Neurology and Nephrology Division, Asahikawa Medical University, Midorigaoka Higashi 2-1-1-1, Asahikawa, 078-8510, Japan
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Zhu Y, Bai K, Yu J, Guo M. Association Between Histone Methyltransferase hSETD1A and Prognosis in Patients With Triple-Negative Breast Cancer After Surgery: A Retrospective Study in the Chinese Female Population. Medicine (Baltimore) 2016; 95:e3783. [PMID: 27227949 PMCID: PMC4902373 DOI: 10.1097/md.0000000000003783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Breast cancer, the most common cancer in women, is a serious public health issue. Triple-negative breast cancer (TNBC), which lacks expression of the estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2, accounts for ∼15% of breast cancer cases. Treatment of TNBC patients has proven difficult because of the lack of expression of hormone receptors. We conducted a retrospective study to investigate the prognostic impact of histone methyltransferase, hSETD1A, on overall survival in TNBC cases after surgery. In total, 159 TNBC cases were enrolled and clinicopathological characteristics were obtained from medical records. hSETD1A status of each subject was determined using immunohistochemistry. The chi-squared test was used to compare 5-year overall survival rates of all subjects according to clinical characteristics, and both univariate and multivariate analyses were conducted to calculate the hazard ratios and 95% confidence intervals. Advanced tumor-node-metastasis stage stage, larger tumor size, vascular invasion, metastasis in the initial diagnosis, and hSETD1A expression were correlated with worse outcome. Among all factors identified, metastasis in the initial diagnosis had the greatest impact on survival. The results indicated that hSETD1A positivity was correlated with shorter survival among TNBC cases, suggesting it may serve as a prognostic biomarker for patients with TNBC.
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Affiliation(s)
- YanYan Zhu
- From the Department of General Surgery (YZ, JY), Jinshan Hospital, Fudan University, Shanghai, China; Department of Hepatobiliary Surgery (KB), Fuzong Clinical College, Fujian Medical University, Fuzhou City, Fujian Province, China; and Department of Breast Surgery (MG), Affiliated Hospital of Hebei University of Engineering, Handan, Hebei Province, China
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Abstract
PURPOSE OF REVIEW Recent advances in epigenetics indicate the involvement of several epigenetic modifications in the pathogenesis of acute kidney injury (AKI). The purpose of this review is to summarize our understanding of recent advances in the epigenetic regulation of AKI and provide mechanistic insight into the role of acetylation, methylation, and microRNA expression in the pathological processes of AKI. RECENT FINDINGS Enhancement of protein acetylation by pharmacological inhibition of histone deacetylases leads to more severe tubular injury and impairment of renal structural and functional recovery. The changes in promoter DNA methylation occur in the kidney with ischemia/reperfusion. microRNA expression is associated with regulation of both renal injury and regeneration after AKI. SUMMARY Recent studies on epigenetic regulation indicate that acetylation, methylation, and microRNA expression are critically implicated in the pathogenesis of AKI. Strategies targeting epigenetic processes may hold a therapeutic potential for patients with AKI.
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Siddiqi FS, Majumder S, Thai K, Abdalla M, Hu P, Advani SL, White KE, Bowskill BB, Guarna G, Dos Santos CC, Connelly KA, Advani A. The Histone Methyltransferase Enzyme Enhancer of Zeste Homolog 2 Protects against Podocyte Oxidative Stress and Renal Injury in Diabetes. J Am Soc Nephrol 2015; 27:2021-34. [PMID: 26534922 DOI: 10.1681/asn.2014090898] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/22/2015] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulation of oxidative stress is emerging as a critical mediator of diabetic nephropathy. In diabetes, oxidative damage occurs when there is an imbalance between reactive oxygen species generation and enzymatic antioxidant repair. Here, we investigated the function of the histone methyltransferase enzyme enhancer of zeste homolog 2 (EZH2) in attenuating oxidative injury in podocytes, focusing on its regulation of the endogenous antioxidant inhibitor thioredoxin interacting protein (TxnIP). Pharmacologic or genetic depletion of EZH2 augmented TxnIP expression and oxidative stress in podocytes cultured under high-glucose conditions. Conversely, EZH2 upregulation through inhibition of its regulatory microRNA, microRNA-101, downregulated TxnIP and attenuated oxidative stress. In diabetic rats, depletion of EZH2 decreased histone 3 lysine 27 trimethylation (H3K27me3), increased glomerular TxnIP expression, induced podocyte injury, and augmented oxidative stress and proteinuria. Chromatin immunoprecipitation sequencing revealed H3K27me3 enrichment at the promoter of the transcription factor Pax6, which was upregulated on EZH2 depletion and bound to the TxnIP promoter, controlling expression of its gene product. In high glucose-exposed podocytes and the kidneys of diabetic rats, the lower EZH2 expression detected coincided with upregulation of Pax6 and TxnIP. Finally, in a gene expression array, TxnIP was among seven of 30,854 genes upregulated by high glucose, EZH2 depletion, and the combination thereof. Thus, EZH2 represses the transcription factor Pax6, which controls expression of the antioxidant inhibitor TxnIP, and in diabetes, downregulation of EZH2 promotes oxidative stress. These findings expand the extent to which epigenetic processes affect the diabetic kidney to include antioxidant repair.
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Affiliation(s)
- Ferhan S Siddiqi
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Syamantak Majumder
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Kerri Thai
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Moustafa Abdalla
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics and George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada; and
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Kathryn E White
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bridgit B Bowskill
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Giuliana Guarna
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Claudia C Dos Santos
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Kim A Connelly
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada;
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Majumder S, Advani A. The epigenetic regulation of podocyte function in diabetes. J Diabetes Complications 2015; 29:1337-44. [PMID: 26344726 DOI: 10.1016/j.jdiacomp.2015.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/06/2015] [Accepted: 07/11/2015] [Indexed: 10/23/2022]
Abstract
Chronic hyperglycemia early in the course of diabetes confers a sustained increase in the risk of complications development. In recent years, efforts to understand the molecular basis for this "metabolic memory" have focused on epigenetic mechanisms as a means by which transient high glucose can cause persistent and propagated changes in cell function. For instance, in vascular endothelial cells, smooth muscle cells and peripheral blood cells, temporary exposure to high glucose causes changes in epigenetic marks that promote a shift towards a pro-inflammatory phenotype. However, the influence of epigenetic processes in complications development extends beyond their contribution to metabolic memory. Podocytes, for example, are terminally differentiated cells of the renal glomerulus whose injury is a major contributor to the pathogenesis of nephropathy. Over recent months, several reports have emerged describing the essential actions of histone-modifying enzymes and DNA methylation patterns (the two principal epigenetic mechanisms) in maintaining podocyte integrity, especially under diabetic conditions. Here, we review the known and potential role of epigenetic processes within podocytes, focusing on the evidence linking these processes to oxidative stress, crosstalk with tubule cells, autophagy and slit-pore protein expression. Whether podocytes themselves exhibit a metabolic memory awaits to be seen.
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MESH Headings
- Acetylation
- Animals
- Autophagy
- DNA Methylation
- Diabetes Complications/genetics
- Diabetes Complications/metabolism
- Diabetes Complications/pathology
- Diabetes Mellitus, Type 1/complications
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Epigenesis, Genetic
- Evidence-Based Medicine
- Gene Expression Regulation, Developmental
- Histones/metabolism
- Humans
- Models, Biological
- Oxidative Stress
- Podocytes/metabolism
- Podocytes/pathology
- Protein Processing, Post-Translational
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Affiliation(s)
- Syamantak Majumder
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada.
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Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) refer to a spectrum of structural renal malformations and are the leading cause of end-stage renal disease in children. The genetic diagnosis of CAKUT has proven to be challenging due to genetic and phenotypic heterogeneity and incomplete genetic penetrance. Monogenic causes of CAKUT have been identified using different approaches, including single gene screening, and gene panel and whole exome sequencing. The majority of the identified mutations, however, lack substantial evidence to support a pathogenic role in CAKUT. Copy number variants or single nucleotide variants that are associated with CAKUT have also been identified. Numerous studies support the influence of epigenetic and environmental factors on kidney development and the natural history of CAKUT, suggesting that the pathogenesis of this syndrome is multifactorial. In this Review we describe the current knowledge regarding the genetic susceptibility underlying CAKUT and the approaches used to investigate the genetic basis of CAKUT. We outline the associated environmental risk factors and epigenetic influences on CAKUT and discuss the challenges and strategies used to fully address the involvement and interplay of these factors in the pathogenesis of the disease.
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Grahammer F, Benzing T, Huber TB. New insights into mechanisms of glomerular injury and repair from the 10th International Podocyte Conference 2014. Kidney Int 2015; 87:885-93. [DOI: 10.1038/ki.2015.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 01/17/2023]
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Abraham S, Paknikar R, Bhumbra S, Luan D, Garg R, Dressler GR, Patel SR. The Groucho-associated phosphatase PPM1B displaces Pax transactivation domain interacting protein (PTIP) to switch the transcription factor Pax2 from a transcriptional activator to a repressor. J Biol Chem 2015; 290:7185-94. [PMID: 25631048 DOI: 10.1074/jbc.m114.607424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pax genes encode developmental regulatory proteins that specify cell lineages and tissues in metazoans. Upon binding to DNA through the conserved paired domain, Pax proteins can recruit both activating and repressing complexes that imprint distinct patterns of histone methylation associated with either gene activation or silencing. How the switch from Pax-mediated activation to repression is regulated remains poorly understood. In this report, we identify the phosphatase PPM1B as an essential component of the Groucho4 repressor complex that is recruited by Pax2 to chromatin. PPM1B can dephosphorylate the Pax2 activation domain and displace the adaptor protein PTIP, thus inhibiting H3K4 methylation and gene activation. Loss of PPM1B prevents Groucho-mediated gene repression. Thus, PPM1B helps switch Pax2 from a transcriptional activator to a repressor protein. This can have profound implications for developmental regulation by Pax proteins and suggests a model for imprinting specific epigenetic marks depending on the availability of co-factors.
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Affiliation(s)
| | | | | | - Danny Luan
- From the Departments of Internal Medicine and
| | - Rohan Garg
- From the Departments of Internal Medicine and
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Ranghini EJ, Dressler GR. Evidence for intermediate mesoderm and kidney progenitor cell specification by Pax2 and PTIP dependent mechanisms. Dev Biol 2015; 399:296-305. [PMID: 25617721 DOI: 10.1016/j.ydbio.2015.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/19/2014] [Accepted: 01/11/2015] [Indexed: 11/30/2022]
Abstract
Activation of the Pax2 gene marks the intermediate mesoderm shortly after gastrulation, as the mesoderm becomes compartmentalized into paraxial, intermediate, and lateral plate. Using an EGFP knock-in allele of Pax2 to identify and sort cells of the intermediate mesodermal lineage, we compared gene expression patterns in EGFP positive cells that were heterozygous or homozygous null for Pax2. Thus, we identified critical regulators of intermediate mesoderm and kidney development whose expression depended on Pax2 function. In cell culture models, Pax2 is thought to recruit epigenetic modifying complex to imprint activating histone methylation marks through interactions with the adaptor protein PTIP. In kidney organ culture, conditional PTIP deletion showed that many Pax2 target genes, which were activated early in renal progenitor cells, remained on once activated, whereas Pax2 target genes expressed later in kidney development were unable to be fully activated without PTIP. In Pax2 mutants, we also identified a set of genes whose expression was up-regulated in EGFP positive cells and whose expression was consistent with a cell fate transformation to paraxial mesoderm and its derivatives. These data provide evidence that Pax2 specifies the intermediate mesoderm and renal epithelial cells through epigenetic mechanisms and in part by repressing paraxial mesodermal fate.
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Affiliation(s)
- Egon J Ranghini
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory R Dressler
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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35
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Dressler GR, Patel SR. Epigenetics in kidney development and renal disease. Transl Res 2015; 165:166-76. [PMID: 24958601 PMCID: PMC4256142 DOI: 10.1016/j.trsl.2014.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 11/21/2022]
Abstract
The study of epigenetics is intimately linked and inseparable from developmental biology. Many of the genes that imprint epigenetic information on chromatin function during the specification of cell lineages in the developing embryo. These include the histone methyltransferases and their cofactors of the Polycomb and Trithorax gene families. How histone methylation is established and what regulates the tissue and locus specificity of histone methylation is an emerging area of research. The embryonic kidney is used as a model to understand how DNA-binding proteins can specify cell lineages and how such proteins interact directly with the histone methylation machinery to generate a unique epigenome for particular tissues and cell types. In adult tissues, histone methylation marks must be maintained for normal gene expression patterns. In chronic and acute renal disease, epigenetic marks are being characterized and correlated with the establishment of metabolic memory, in part to explain the persistence of pathologies even when optimal treatment modalities are used. Thus, the state of the epigenome in adult cells must be considered when attempting to alleviate or alter gene expression patterns in disease.
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Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance. Nat Commun 2014; 5:5815. [PMID: 25519973 PMCID: PMC4284801 DOI: 10.1038/ncomms6815] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 11/10/2014] [Indexed: 12/16/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is involved in gene regulation and development; however, its precise function, molecular targets and underlying mechanisms during development are poorly understood. Here we show that LSD1 is required for neuronal progenitor cell (NPC) maintenance during cortical development. A ChIP-seq analysis identified a LSD1-binding site (LBAL) downstream of Atrophin1 (ATN1). Surprisingly, tranylcypromine (LSD1 inhibitor) treatment increased H3K4 methylation at LBAL, leading to ATN1 repression and NPC differentiation. Knockdown of LSD1 and ATN1 phenocopied each other in inducing NPC premature differentiation and depletion, which could be rescued by ATN1 overexpression, suggesting that LSD1 controls NPC differentiation via regulation of ATN1 methylation status and expression. The involvement of LSD1 in ATN1 expression and NPC maintenance were confirmed in knockout mice. These findings hint at the potential application for the clinical drug, tranylcypromine, in the prevention and/or treatment of ATN1-associated degenerative disease, dentatorubral-pallidoluysian atrophy. Histone modification is critical for gene expression regulation during development. Here, the authors show that the demethylase LSD1 and its target gene ATN1 are responsible for maintenance of neural progenitor cells during mouse cortical development.
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37
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Hayashi K, Itoh H. Transcription Factors and Epigenetic Modulation: Its Therapeutic Implication in Chronic Kidney Disease. Arch Immunol Ther Exp (Warsz) 2014; 63:193-6. [DOI: 10.1007/s00005-014-0326-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/18/2014] [Indexed: 11/24/2022]
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38
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Kopan R, Chen S, Little M. Nephron progenitor cells: shifting the balance of self-renewal and differentiation. Curr Top Dev Biol 2014; 107:293-331. [PMID: 24439811 DOI: 10.1016/b978-0-12-416022-4.00011-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Within the developing mammalian kidney, several populations of progenitors form the discrete cellular components of the final organ. Fate mapping experiments revealed the cap mesenchyme (CM) to be the progenitor population for all nephron epithelial cells, whereas the neighboring stromal mesenchyme gives rise to mesangial, pericytic, renin-producing and interstitial cells. The collecting ducts are derived from a population of progenitors at the ureteric bud (UB) tip and a proportion of the endothelium is also derived from a dedicated mesenchymal progenitor. The stroma, CM, and UB interact to create spatially defined niches at the periphery of the developing organ. While the UB tip population persist, the CM represents a transient progenitor population that is exhausted to set the final organ size. The timing of CM exhaustion, and hence the final organ structure, is sensitive to disruptions such as premature birth. Here we will discuss our current understanding of the molecular processes allowing these populations to balance cell survival, self-renewal, support of branching, and maintain capacity to commit to differentiation.
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Affiliation(s)
- Raphael Kopan
- Department of Developmental Biology, Washington University, St. Louis, Missouri, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio, USA.
| | - Shuang Chen
- Department of Developmental Biology, Washington University, St. Louis, Missouri, USA
| | - Melissa Little
- Department of Developmental Biology, Washington University, St. Louis, Missouri, USA; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
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Abstract
Epigenetics refers to functionally relevant modifications of the genome that do not involve a change in the nucleotide sequence. Examples of such modifications are DNA methylation and histone modifications. Both modifications serve to regulate gene expression without altering the underlying DNA sequence. The epigenome encodes critical information to regulate gene expression. The cellular epigenome is established during development and differentiation and maintained during cell division. These instructions are different in each cell type; therefore, the epigenome is cell-type-specific. Nutrient availability and other environmental factors cause changes in the epigenome. Recent research suggests the critical contribution of the epigenome to the development of complex gene-environmental diseases including chronic kidney diseases.
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Abstract
The development of the mammalian kidney has been studied at the genetic, biochemical, and cell biological level for more than 40 years. As such, detailed mechanisms governing early patterning, cell lineages, and inductive interactions have been well described. How genes interact to specify the renal epithelial cells of the nephrons and how this specification is relevant to maintaining normal renal function is discussed. Implicit in the development of the kidney are epigenetic mechanisms that mark renal cell types and connect certain developmental regulatory factors to chromatin modifications that control gene expression patterns and cellular physiology. In adults, such regulatory factors and their epigenetic pathways may function in regeneration and may be disturbed in disease processes.
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Bechtel-Walz W, Huber TB. Chromatin dynamics in kidney development and function. Cell Tissue Res 2014; 356:601-8. [PMID: 24817101 DOI: 10.1007/s00441-014-1884-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
Abstract
Epigenetic mechanisms are fundamental key features of developing cells connecting developmental regulatory factors to chromatin modification. Changes in the environment during renal development can have long-lasting effects on the permanent tissue structure and the level of expression of important functional genes. These changes are believed to contribute to kidney disease occurrence and progression. Although the mechanisms of early patterning and cell fate have been well described for renal development, little is known about associated epigenetic modifications and their impact on how genes interact to specify the renal epithelial cells of nephrons and how this specification is relevant to maintaining normal renal function. A better understanding of the renal cell-specific epigenetic modifications and the interaction of different cell types to form this highly complex organ will not only help to better understand developmental defects and early loss of kidney function in children, but also help to understand and improve chronic disease progression, cell regeneration and renal aging.
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Affiliation(s)
- Wibke Bechtel-Walz
- Renal Division, University Hospital Freiburg, Breisacher Str. 66, 79106, Freiburg, Germany,
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Mechanisms of gene activation and repression by Pax proteins in the developing kidney. Pediatr Nephrol 2014; 29:589-95. [PMID: 23996452 PMCID: PMC3944099 DOI: 10.1007/s00467-013-2603-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
Abstract
During embryonic development, DNA binding proteins help specify and restrict the fates of pluripotent stem cells. In the developing kidney, Pax2 proteins are among the earliest markers for the renal epithelial cell lineage, with expression in the mesenchyme and in proliferating epithelia. The Pax2 protein is essential for interpreting inductive signals emanating from the ureteric bud such that the kidney mesenchyme can convert to epithelia. The biochemistry of Pax protein function is being studied in a variety of model systems. Through interactions with the adaptor Pax transactivation-domain interacting protein (PTIP), Pax proteins can recruit members of the Trithorax family of histone methyltransferases to imprint activating epigenetic marks on chromatin. However, interactions with the corepressor Groucho-related gene-4 (Grg4) protein can inhibit activation and instead recruit Polycomb repressor complexes to promote target-gene silencing. We present a model whereby the regulated interactions of Pax proteins with available cofactor-mediated activation or gene silencing at different stages of development. The implications for establishing and maintaining the epigenome are discussed.
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The aging kidney revisited: a systematic review. Ageing Res Rev 2014; 14:65-80. [PMID: 24548926 DOI: 10.1016/j.arr.2014.02.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 01/10/2023]
Abstract
As for the whole human body, the kidney undergoes age-related changes which translate in an inexorable and progressive decline in renal function. Renal aging is a multifactorial process where gender, race and genetic background and several key-mediators such as chronic inflammation, oxidative stress, the renin-angiotensin-aldosterone (RAAS) system, impairment in kidney repair capacities and background cardiovascular disease play a significant role. Features of the aging kidney include macroscopic and microscopic changes and important functional adaptations, none of which is pathognomonic of aging. The assessment of renal function in the framework of aging is problematic and the question whether renal aging should be considered as a physiological or pathological process remains a much debated issue. Although promising dietary and pharmacological approaches have been tested to retard aging processes or renal function decline in the elderly, proper lifestyle modifications, as those applicable to the general population, currently represent the most plausible approach to maintain kidney health.
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Tampe B, Zeisberg M. Evidence for the involvement of epigenetics in the progression of renal fibrogenesis. Nephrol Dial Transplant 2013; 29 Suppl 1:i1-i8. [DOI: 10.1093/ndt/gft361] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sadler T, Scarpa M, Rieder F, West G, Stylianou E. Cytokine-induced chromatin modifications of the type I collagen alpha 2 gene during intestinal endothelial-to-mesenchymal transition. Inflamm Bowel Dis 2013; 19:1354-64. [PMID: 23635716 PMCID: PMC3684204 DOI: 10.1097/mib.0b013e318281f37a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Fibrosis of the intestine is currently an irreversible complication of inflammatory bowel disease; yet, little is understood of the underlying pathogenesis and antifibrotic strategies remain elusive. To develop effective therapies, knowledge of the mechanism of transcription and excessive deposition of type I collagen, a hallmark of fibrosis, is needed. We have shown previously that endothelial-to-mesenchymal transition (EndoMT) contributes to the pool of intestinal fibrotic cells and that a cytokine cocktail (interleukin 1-β, tumor necrosis factor α, and transforming growth factor β) induces collagen I alpha 2 (COL1A2) mRNA and protein. METHODS Chromatin immunoprecipitation assays on pure cultures of human intestinal mucosal endothelial cells undergoing EndoMT were performed with antibodies to specific histone modifications and RNA polymerase II. Reverse transcriptase-PCR was used to quantify the levels of Col1A2 and endothelial-specific von Willebrand factor (vWF) mRNA. RESULTS We showed that cytokines induce selective chromatin modifications (histone 4 hyperacetylation, and hypermethylation of histone 3) and phosphorylated RNA polymerase II at the COL1A2 promoter. Hypoacetylated and hypomethylated histone 3 was detected on the repressed vWF gene. Prolonged exposure to cytokines (16 days) retained hyperacetylation of select lysines in H4 on the COL1A2 promoter. Removal of cytokines after 16 days and continued culture for 10 days showed persistent hyperacetylation at lysine 16 in histone H4. CONCLUSIONS This is the first study to show that COL1A2 gene expression is associated with cytokine-induced, temporally ordered, and persistent chromatin modifications and suggests that these are important determinants of gene expression in EndoMT and intestinal fibrosis.
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Affiliation(s)
- Tammy Sadler
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Melania Scarpa
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Melania Scarpa, current address: Istituto Oncologico Veneto, I.R.C.C.S., Padua, Italy
| | - Florian Rieder
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, 44195, USA
| | - Gail West
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Eleni Stylianou
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, 44195, USA,To who correspondence should be addressed: Dr. Eleni Stylianou, B.Sc. Ph.D., Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195. Tel: 216-445-7156; Fax: 216-636-0104,
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Developmental programming of hypertension and kidney disease. Int J Nephrol 2012; 2012:760580. [PMID: 23251800 PMCID: PMC3516001 DOI: 10.1155/2012/760580] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/18/2012] [Accepted: 10/21/2012] [Indexed: 02/05/2023] Open
Abstract
A growing body of evidence supports the concept that changes in the intrauterine milieu during "sensitive" periods of embryonic development or in infant diet after birth affect the developing individual, resulting in general health alterations later in life. This phenomenon is referred to as "developmental programming" or "developmental origins of health and disease." The risk of developing late-onset diseases such as hypertension, chronic kidney disease (CKD), obesity or type 2 diabetes is increased in infants born prematurely at <37 weeks of gestation or in low birth weight (LBW) infants weighing <2,500 g at birth. Both genetic and environmental events contribute to the programming of subsequent risks of CKD and hypertension in premature or LBW individuals. A number of observations suggest that susceptibility to subsequent CKD and hypertension in premature or LBW infants is mediated, at least in part, by reduced nephron endowment. The major factors influencing in utero environment that are associated with a low final nephron number include uteroplacental insufficiency, maternal low-protein diet, hyperglycemia, vitamin A deficiency, exposure to or interruption of endogenous glucocorticoids, and ethanol exposure. This paper discusses the effect of premature birth, LBW, intrauterine milieu, and infant feeding on the development of hypertension and renal disease in later life as well as examines the role of the kidney in developmental programming of hypertension and CKD.
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Schwab KR, Smith GD, Dressler GR. Arrested spermatogenesis and evidence for DNA damage in PTIP mutant testes. Dev Biol 2012; 373:64-71. [PMID: 23063797 DOI: 10.1016/j.ydbio.2012.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 10/03/2012] [Accepted: 10/05/2012] [Indexed: 11/17/2022]
Abstract
The differentiation of mature sperm from male germ cells requires both chromatin remodeling and compaction as well as DNA double stranded break repair of sister chromatids. We examined the function of PTIP, a protein implicated in both DNA repair and histone methylation, during spermatogenesis by using a conditional, inducible mutation in adult male mice. Loss of PTIP led to the developmental arrest of spermatocytes, testicular atrophy, and infertility. By immunostaining with specific markers for different stages of spermatogenesis and for proteins involved in DNA damage and repair mechanisms, we conclude that the lack of PTIP results in genomic instability and DNA damage resulting in the cessation of spermatogenesis in meiosis I. These data underscore the importance of PTIP in the DNA repair process associated with the development of mature spermatozoa.
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Reddy MA, Park JT, Natarajan R. Epigenetic modifications and diabetic nephropathy. Kidney Res Clin Pract 2012; 31:139-50. [PMID: 26894019 PMCID: PMC4716094 DOI: 10.1016/j.krcp.2012.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/30/2012] [Accepted: 07/09/2012] [Indexed: 01/15/2023] Open
Abstract
Diabetic nephropathy (DN) is a major complication associated with both type 1 and type 2 diabetes, and a leading cause of end-stage renal disease. Conventional therapeutic strategies are not fully efficacious in the treatment of DN, suggesting an incomplete understanding of the gene regulation mechanisms involved in its pathogenesis. Furthermore, evidence from clinical trials has demonstrated a "metabolic memory" of prior exposure to hyperglycemia that continues to persist despite subsequent glycemic control. This remains a major challenge in the treatment of DN and other vascular complications. Epigenetic mechanisms such as DNA methylation, nucleosomal histone modifications, and noncoding RNAs control gene expression through regulation of chromatin structure and function and post-transcriptional mechanisms without altering the underlying DNA sequence. Emerging evidence indicates that multiple factors involved in the etiology of diabetes can alter epigenetic mechanisms and regulate the susceptibility to diabetes complications. Recent studies have demonstrated the involvement of histone lysine methylation in the regulation of key fibrotic and inflammatory genes related to diabetes complications including DN. Interestingly, histone lysine methylation persisted in vascular cells even after withdrawal from the diabetic milieu, demonstrating a potential role of epigenetic modifications in metabolic memory. Rapid advances in high-throughput technologies in the fields of genomics and epigenomics can lead to the identification of genome-wide alterations in key epigenetic modifications in vascular and renal cells in diabetes. Altogether, these findings can lead to the identification of potential predictive biomarkers and development of novel epigenetic therapies for diabetes and its associated complications.
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Affiliation(s)
| | | | - Rama Natarajan
- Department of Diabetes, Beckman Research Institute of City of Hope, Duarte, California, USA
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Soofi A, Levitan I, Dressler GR. Two novel EGFP insertion alleles reveal unique aspects of Pax2 function in embryonic and adult kidneys. Dev Biol 2012; 365:241-50. [PMID: 22410172 DOI: 10.1016/j.ydbio.2012.02.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 02/02/2012] [Accepted: 02/24/2012] [Indexed: 01/28/2023]
Abstract
The Pax2 gene encodes a DNA binding protein with multiple functions in the developing intermediate mesoderm and urogenital tract. Loss of Pax2 in mice results in the complete absence of kidneys, ureters, and sex specific epithelial structures derived from the intermediate mesoderm in both males and females. In this report, we describe two new alleles of Pax2 created by inserting the enhanced green fluorescent protein coding region into the 5' untranslated leader sequence. One allele is a hypomorph that generates less protein and exhibits structural defects in kidneys and ureters upon homozygosity. A second allele is a true null that can be used to image Pax2 expressing cells in a mutant background. Organ culture and embryo analyses point to a loss of epithelial cell polarity and increased mobility in cells that have deleted Pax2 function. These experiments provide new insight into the role of Pax2 protein levels in determining correct renal architecture and cell fate. These new Pax2 alleles are valuable genetic reagents for in vivo studies of urogenital development.
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Affiliation(s)
- Abdul Soofi
- Dept. of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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Hou L, Zhang X, Wang D, Baccarelli A. Environmental chemical exposures and human epigenetics. Int J Epidemiol 2012; 41:79-105. [PMID: 22253299 PMCID: PMC3304523 DOI: 10.1093/ije/dyr154] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 02/06/2023] Open
Abstract
Every year more than 13 million deaths worldwide are due to environmental pollutants, and approximately 24% of diseases are caused by environmental exposures that might be averted through preventive measures. Rapidly growing evidence has linked environmental pollutants with epigenetic variations, including changes in DNA methylation, histone modifications and microRNAs. Environ mental chemicals and epigenetic changes All of these mechanisms are likely to play important roles in disease aetiology, and their modifications due to environmental pollutants might provide further understanding of disease aetiology, as well as biomarkers reflecting exposures to environmental pollutants and/or predicting the risk of future disease. We summarize the findings on epigenetic alterations related to environmental chemical exposures, and propose mechanisms of action by means of which the exposures may cause such epigenetic changes. We discuss opportunities, challenges and future directions for future epidemiology research in environmental epigenomics. Future investigations are needed to solve methodological and practical challenges, including uncertainties about stability over time of epigenomic changes induced by the environment, tissue specificity of epigenetic alterations, validation of laboratory methods, and adaptation of bioinformatic and biostatistical methods to high-throughput epigenomics. In addition, there are numerous reports of epigenetic modifications arising following exposure to environmental toxicants, but most have not been directly linked to disease endpoints. To complete our discussion, we also briefly summarize the diseases that have been linked to environmental chemicals-related epigenetic changes.
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Affiliation(s)
- Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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