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Sun P, Wang J, Ilyasova T, Shumadalova A, Agaverdiev M, Wang C. The function of miRNAs in the process of kidney development. Noncoding RNA Res 2023; 8:593-601. [PMID: 37680850 PMCID: PMC10480480 DOI: 10.1016/j.ncrna.2023.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs (ncRNAs) that typically consist of 19-25 nucleotides in length. These molecules function as essential regulators of gene expression by selectively binding to complementary target sequences within messenger RNA (mRNA) molecules, consequently exerting a negative impact on gene expression at the post-transcriptional level. By modulating the stability and translation efficiency of target mRNAs, miRNAs play pivotal roles in diverse biological processes, including the intricate orchestration of organ development. Among these processes, the development of the kidney has emerged as a key area of interest regarding miRNA function. Intriguingly, recent investigations have uncovered a subset of miRNAs that exhibit remarkably high expression levels in the kidney, signifying their close association with kidney development and diseases affecting this vital organ. This growing body of evidence strongly suggests that miRNAs serve as crucial regulators, actively shaping both the physiological processes governing kidney function and the pathological events leading to renal disorders. This comprehensive review aims to provide an up-to-date overview of the latest research progress regarding miRNAs and their involvement in kidney development. By examining the intricate interplay between miRNAs and the molecular pathways driving kidney development, this review seeks to elucidate the underlying mechanisms through which miRNAs exert their regulatory functions. Furthermore, an in-depth exploration of the role played by miRNAs in the occurrence and progression of renal dysplasia will be presented. Renal dysplasia represents a significant developmental anomaly characterized by abnormal kidney tissue formation, and miRNAs have emerged as key players in this pathological process. By shedding light on the intricate network of miRNA-mediated regulatory mechanisms involved in kidney dysplasia, this review aims to provide valuable insights for the diagnosis and research of diseases associated with aberrant kidney development.
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Affiliation(s)
- Pengfei Sun
- Tianjin Baodi Hospital/Baodi Clinical College of Tianjin Medical University, Tianjin, 301800, China
| | - Jiaqi Wang
- Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081, China
| | - Tatiana Ilyasova
- Department of Internal Diseases, Bashkir State Medical University, Ufa, Republic of Bashkortostan 450008, Russia
| | - Alina Shumadalova
- Department of General Chemistry, Bashkir State Medical University, 3 Lenin Street, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Murad Agaverdiev
- Department of Urology, Bashkir State Medical University, 450008, Ufa, Russian Federation
| | - Chunlei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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2
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Dash SN, Patnaik L. Flight for fish in drug discovery: a review of zebrafish-based screening of molecules. Biol Lett 2023; 19:20220541. [PMID: 37528729 PMCID: PMC10394424 DOI: 10.1098/rsbl.2022.0541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/13/2023] [Indexed: 08/03/2023] Open
Abstract
Human disease and biological practices are modelled in zebrafish (Danio rerio) at various phases of drug development as well as toxicity evaluation. The zebrafish is ideal for in vivo pathological research and high-resolution investigation of disease progress. Zebrafish has an advantage over other mammalian models, it is cost-effective, it has external development and embryo transparency, easy to apply genetic manipulations, and open to both forward and reverse genetic techniques. Drug screening in zebrafish is suitable for target identification, illness modelling, high-throughput screening of compounds for inhibition or prevention of disease phenotypes and developing new drugs. Several drugs that have recently entered the clinic or clinical trials have their origins in zebrafish. The sophisticated screening methods used in zebrafish models are expected to play a significant role in advancing drug development programmes. This review highlights the current developments in drug discovery processes, including understanding the action of drugs in the context of disease and screening novel candidates in neurological diseases, cardiovascular diseases, glomerulopathies and cancer. Additionally, it summarizes the current techniques and approaches for the selection of small molecules and current technical limitations on the execution of zebrafish drug screening tests.
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Affiliation(s)
- Surjya Narayan Dash
- Institute of Biotechnology, Biocenter 2. Viikinkaari, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Lipika Patnaik
- Environmental Science Laboratory, Department of Zoology, COE in Environment and Public Health, Ravenshaw University, Cuttack 751003, Odisha, India
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3
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Hawkins MR, Wingert RA. Zebrafish as a Model to Study Retinoic Acid Signaling in Development and Disease. Biomedicines 2023; 11:biomedicines11041180. [PMID: 37189798 DOI: 10.3390/biomedicines11041180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Retinoic acid (RA) is a metabolite of vitamin A (retinol) that plays various roles in development to influence differentiation, patterning, and organogenesis. RA also serves as a crucial homeostatic regulator in adult tissues. The role of RA and its associated pathways are well conserved from zebrafish to humans in both development and disease. This makes the zebrafish a natural model for further interrogation into the functions of RA and RA-associated maladies for the sake of basic research, as well as human health. In this review, we explore both foundational and recent studies using zebrafish as a translational model for investigating RA from the molecular to the organismal scale.
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Affiliation(s)
- Matthew R Hawkins
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
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4
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Nguyen TK, Petrikas M, Chambers BE, Wingert RA. Principles of Zebrafish Nephron Segment Development. J Dev Biol 2023; 11:jdb11010014. [PMID: 36976103 PMCID: PMC10052950 DOI: 10.3390/jdb11010014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Nephrons are the functional units which comprise the kidney. Each nephron contains a number of physiologically unique populations of specialized epithelial cells that are organized into discrete domains known as segments. The principles of nephron segment development have been the subject of many studies in recent years. Understanding the mechanisms of nephrogenesis has enormous potential to expand our knowledge about the basis of congenital anomalies of the kidney and urinary tract (CAKUT), and to contribute to ongoing regenerative medicine efforts aimed at identifying renal repair mechanisms and generating replacement kidney tissue. The study of the zebrafish embryonic kidney, or pronephros, provides many opportunities to identify the genes and signaling pathways that control nephron segment development. Here, we describe recent advances of nephron segment patterning and differentiation in the zebrafish, with a focus on distal segment formation.
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Affiliation(s)
- Thanh Khoa Nguyen
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Madeline Petrikas
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brooke E Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556, USA
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5
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Drummond BE, Ercanbrack WS, Wingert RA. Modeling Podocyte Ontogeny and Podocytopathies with the Zebrafish. J Dev Biol 2023; 11:jdb11010009. [PMID: 36810461 PMCID: PMC9944608 DOI: 10.3390/jdb11010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Podocytes are exquisitely fashioned kidney cells that serve an essential role in the process of blood filtration. Congenital malformation or damage to podocytes has dire consequences and initiates a cascade of pathological changes leading to renal disease states known as podocytopathies. In addition, animal models have been integral to discovering the molecular pathways that direct the development of podocytes. In this review, we explore how researchers have used the zebrafish to illuminate new insights about the processes of podocyte ontogeny, model podocytopathies, and create opportunities to discover future therapies.
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Gerhardt LMS, McMahon AP. Identifying Common Molecular Mechanisms in Experimental and Human Acute Kidney Injury. Semin Nephrol 2022; 42:151286. [PMID: 36402654 PMCID: PMC11017289 DOI: 10.1016/j.semnephrol.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acute kidney injury (AKI) is a highly prevalent, heterogeneous syndrome, associated with increased short- and long-term mortality. A multitude of different factors cause AKI including ischemia, sepsis, nephrotoxic drugs, and urinary tract obstruction. Upon injury, the kidney initiates an intrinsic repair program that can result in adaptive repair with regeneration of damaged nephrons and functional recovery of epithelial activity, or maladaptive repair and persistence of damaged epithelial cells with a characteristic proinflammatory, profibrotic molecular signature. Maladaptive repair is linked to disease progression from AKI to chronic kidney disease. Despite extensive efforts, no therapeutic strategies provide consistent benefit to AKI patients. Since kidney biopsies are rarely performed in the acute injury phase in humans, most of our understanding of AKI pathophysiology is derived from preclinical AKI models. This raises the question of how well experimental models of AKI reflect the molecular and cellular mechanisms underlying human AKI? Here, we provide a brief overview of available AKI models, discuss their strengths and limitations, and consider important aspects of the AKI response in mice and humans, with a particular focus on the role of proximal tubule cells in adaptive and maladaptive repair.
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Affiliation(s)
- Louisa M S Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA.
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
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Xiang X, Dong G, Zhu J, Zhang G, Dong Z. Inhibition of HDAC3 protects against kidney cold storage/transplantation injury and allograft dysfunction. Clin Sci (Lond) 2022; 136:45-60. [PMID: 34918039 DOI: 10.1042/cs20210823] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022]
Abstract
Cold storage/rewarming is an inevitable process for kidney transplantation from deceased donors, which correlates closely with renal ischemia-reperfusion injury (IRI) and the occurrence of delayed graft function. Histone deacetylases (HDAC) are important epigenetic regulators, but their involvement in cold storage/rewarming injury in kidney transplantation is unclear. In the present study, we showed a dynamic change of HDAC3 in a mouse model of kidney cold storage followed by transplantation. We then demonstrated that the selective HDAC3 inhibitor RGFP966 could reduce acute tubular injury and cell death after prolonged cold storage with transplantation. RGFP966 also improved renal function, kidney repair and tubular integrity when the transplanted kidney became the sole life-supporting graft in the recipient mouse. In vitro, cold storage of proximal tubular cells followed by rewarming induced remarkable cell death, which was suppressed by RGFP966 or knockdown of HDAC3 with shRNA. Inhibition of HDAC3 decreased the mitochondrial pathway of apoptosis and preserved mitochondrial membrane potential. Collectively, HDAC3 plays a pathogenic role in cold storage/rewarming injury in kidney transplantation, and its inhibition may be a therapeutic option.
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Affiliation(s)
- Xiaohong Xiang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, GA, U.S.A
| | - Guie Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, GA, U.S.A
| | - Jiefu Zhu
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
- Center of Nephrology and Dialysis, Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Gang Zhang
- Center of Organ Transplantation, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Dong
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, GA, U.S.A
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Marchione AD, Thompson Z, Kathrein KL. DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development. Brief Funct Genomics 2021:elab022. [PMID: 33782688 DOI: 10.1093/bfgp/elab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/21/2023] Open
Abstract
The complex processes necessary for embryogenesis require a gene regulatory network that is complex and systematic. Gene expression regulates development and organogenesis, but this process is altered and fine-tuned by epigenetic regulators that facilitate changes in the chromatin landscape. Epigenetic regulation of embryogenesis adjusts the chromatin structure by modifying both DNA through methylation and nucleosomes through posttranslational modifications of histone tails. The zebrafish is a well-characterized model organism that is a quintessential tool for studying developmental biology. With external fertilization, low cost and high fecundity, the zebrafish are an efficient tool for studying early developmental stages. Genetic manipulation can be performed in vivo resulting in quick identification of gene function. Large-scale genome analyses including RNA sequencing, chromatin immunoprecipitation and chromatin structure all are feasible in the zebrafish. In this review, we highlight the key events in zebrafish development where epigenetic regulation plays a critical role from the early stem cell stages through differentiation and organogenesis.
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Molecular Mechanisms of Renal Progenitor Regulation: How Many Pieces in the Puzzle? Cells 2021; 10:cells10010059. [PMID: 33401654 PMCID: PMC7823786 DOI: 10.3390/cells10010059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Kidneys of mice, rats and humans possess progenitors that maintain daily homeostasis and take part in endogenous regenerative processes following injury, owing to their capacity to proliferate and differentiate. In the glomerular and tubular compartments of the nephron, consistent studies demonstrated that well-characterized, distinct populations of progenitor cells, localized in the parietal epithelium of Bowman capsule and scattered in the proximal and distal tubules, could generate segment-specific cells in physiological conditions and following tissue injury. However, defective or abnormal regenerative responses of these progenitors can contribute to pathologic conditions. The molecular characteristics of renal progenitors have been extensively studied, revealing that numerous classical and evolutionarily conserved pathways, such as Notch or Wnt/β-catenin, play a major role in cell regulation. Others, such as retinoic acid, renin-angiotensin-aldosterone system, TLR2 (Toll-like receptor 2) and leptin, are also important in this process. In this review, we summarize the plethora of molecular mechanisms directing renal progenitor responses during homeostasis and following kidney injury. Finally, we will explore how single-cell RNA sequencing could bring the characterization of renal progenitors to the next level, while knowing their molecular signature is gaining relevance in the clinic.
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Shi W, Huang Y, Zhao X, Xie Z, Dong W, Li R, Chen Y, Li Z, Wang W, Ye Z, Liu S, Zhang L, Liang X. Histone deacetylase 4 mediates high glucose-induced podocyte apoptosis via upregulation of calcineurin. Biochem Biophys Res Commun 2020; 533:1061-1068. [PMID: 33019979 DOI: 10.1016/j.bbrc.2020.09.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 09/26/2020] [Indexed: 01/28/2023]
Abstract
Hyperglycemia promotes podocyte apoptosis and plays an important role in the pathogenesis of diabetic nephropathy (DN). Calcium/calcineurin (CaN) signaling is critical for podocyte apoptosis. Therefore, it is essential to elucidate the mechanisms underlying the regulation of CaN signaling. Recent studies reported that histone deacetylase 4 (HDAC4) is involved in podocyte apoptosis in DN. The aim of this study was to determine whether HDAC4 mediates the regulation of CaN and to elucidate the function of HDAC4 in high glucose (HG)-induced podocyte apoptosis. First, we identified the expression of HDAC4 was upregulated in podocytes of patients with DN. In vitro, the results also indicate that the mRNA and protein expression levels of HDAC4 were increased in HG-cultured podocytes. Silencing and overexpression of HDAC4 markedly decreased and increased CaN expression, respectively. Meanwhile, HG-induced podocyte apoptosis was abrogated by HDAC4-knockdown with subsequent decreased Bax expression and increased Bcl-2 expression. In contrast, overexpression of HDAC4 increased podocyte apoptosis and Bax expression, as well as decreased Bcl-2 expression. In addition, podocyte apoptosis induced by HDAC4 overexpression was effectively rescued by FK506, a pharmacological inhibitor of CaN, which was accompanied by decreased Bax and increased Bcl-2 expression. As a novel finding, HG-induced podocyte apoptosis is mediated by the HDAC4/CaN signaling pathway, which presents a promising target for therapeutic intervention in DN.
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Affiliation(s)
- Wanxin Shi
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Ying Huang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Xingchen Zhao
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zhiyong Xie
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Wei Dong
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Ruizhao Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yuanhan Chen
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zhuo Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Wenjian Wang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shuangxin Liu
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Li Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| | - Xinling Liang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
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Liu M, Qiao Z, Zhang Y, Zhan P, Yi F. Histone Deacetylases Take Center Stage on Regulation of Podocyte Function. KIDNEY DISEASES (BASEL, SWITZERLAND) 2020; 6:236-246. [PMID: 32903938 PMCID: PMC7445693 DOI: 10.1159/000507117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/10/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Podocytes (highly specialized and terminally differentiated epithelial cells) are integral components of the glomerular filtration barrier that are vulnerable to a variety of injuries and, as a result, they undergo a series of changes ranging from hypertrophy to detachment and apoptosis. Podocyte injury is a major determinant in proteinuric kidney disease and identification of potential therapeutic targets for preventing podocyte injury has clinical importance. Although numerous studies have achieved dramatic advances in the understanding of podocyte biology and its relevance to renal injury, few effective and specific therapies are available. SUMMARY Epigenetic modifications have been proven to play important roles in the pathogenesis of kidney diseases. Among them, histone deacetylase (HDAC)-mediated epigenetic acetylation in the kidney has attracted much attention, which may play multiple roles in both kidney development and the pathogenesis of kidney disease. Recent studies have demonstrated that HDAC protect against podocyte injury by regulation of inflammation, apoptosis, autophagy, mitochondrial function, and insulin resistance. In this review, we summarize recent advances in the understanding of the functions and regulatory mechanisms of HDAC in podocytes and associated proteinuric kidney diseases. In addition, we provide evidence of the potential therapeutic effects of HDAC inhibitors for proteinuric kidney disease. KEY MESSAGES Pharmacological targeting of HDAC-mediated epigenetic processes may open new therapeutic avenues for chronic kidney disease.
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Affiliation(s)
| | | | | | | | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
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Wen X, Li S, Frank A, Chen X, Emlet D, Hukriede NA, Kellum JA. Time-dependent effects of histone deacetylase inhibition in sepsis-associated acute kidney injury. Intensive Care Med Exp 2020; 8:9. [PMID: 32034542 PMCID: PMC7007462 DOI: 10.1186/s40635-020-0297-3] [Citation(s) in RCA: 8] [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: 10/08/2019] [Accepted: 01/29/2020] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Sepsis, a dysregulated host response to infection with results in organ dysfunction, has been a major challenge to the development of effective therapeutics. Sepsis-associated acute kidney injury (S-AKI) results in a 3-5-fold increase in the risk of hospital mortality compared to sepsis alone. The development of therapies to reverse S-AKI could therefore significantly affect sepsis outcomes. However, the translation of therapies from preclinical studies into humans requires model systems that recapitulate clinical scenarios and the development of renal fibrosis indicative of the transition from acute to chronic kidney disease. RESULTS Here we characterized a murine model of S-AKI induced by abdominal sepsis developing into a chronic phenotype. We applied a small molecule histone deacetylase-8 inhibitor, UPHD186, and found that early treatment, beginning at 48 h post-sepsis, worsened renal outcome accompanied by decreasing mononuclear cell infiltration in the kidney, skewing cells into a pro-inflammatory phenotype, and increased pro-fibrotic gene expression, while delayed treatment, beginning at 96 h post-sepsis, after the acute inflammation in the kidney had subsided, resulted in improved survival and kidney histology presumably through promoting proliferation and inhibiting fibrosis. CONCLUSIONS These findings not only present a clinically relevant S-AKI model, but also introduce a timing dimension into S-AKI therapeutic interventions that delayed treatment with UPHD186 may enhance renal histologic repair. Our results provide novel insights into successful repair of kidney injury and sepsis therapy.
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Affiliation(s)
- Xiaoyan Wen
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
| | - Shengnan Li
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
| | - Alicia Frank
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
| | - Xiukai Chen
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
| | - David Emlet
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
| | - Neil A Hukriede
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John A Kellum
- Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, 3347 Forbes Ave, Suite 220, Pittsburgh, PA, 15213, USA.
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miR-29b attenuates histone deacetylase-4 mediated podocyte dysfunction and renal fibrosis in diabetic nephropathy. J Diabetes Metab Disord 2019; 19:13-27. [PMID: 32550152 DOI: 10.1007/s40200-019-00469-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023]
Abstract
Purpose As epigenetic modifications like chromatin histone modifications have been suggested to play a role in the pathophysiology of Diabetic Nephropathy (DN) and are also found to be regulated by microRNAs. Our main purpose was to explore the role of microRNA in histone modulations associated with DN. There is downregulation of miR-29b due to advanced glycation end products in diabetes. Histone Deacetylase-4 (HDAC4) is amongst the histone modulators which promotes podocytes' impairment and upregulates transforming growth factor-1 (TGF-β1) leading to renal fibrosis. Moreover, macrophage infiltration causes podocytes' apoptosis and IL-6 mediated inflammation. As miR-29b is downregulated in diabetes and HDAC4, TGF-β1 and IL-6 could be the possible therapeutic targets in DN, our study was focussed on unveiling the role of miR-29b in modulation of HDAC4 and hence, in podocyte dysfunction and renal fibrosis in DN. Methods In silico analysis and luciferase assay were done to study the interaction between miR-29b and HDAC4. In-vitro DN model was developed in podocytes and miR-29b mimics were transfected. Also, podocytes were co-cultured with macrophage and miR-29b mimics were transfected. At the end, in-vivo DN model was generated in C57BL/6 J male mice and the effect of miR-29b mimics was reconfirmed. Results It was found that miR-29b targets the 3' untranslated region of HDAC4. In both in-vitro and in-vivo DN model, downregulation of miR-29b and subsequent increase in HDAC4 expression was observed. The miR-29b mimics suppressed podocytes' inflammation mediated through macrophages and attenuated HDAC4 expression, glomerular damage and renal fibrosis. Conclusion This study concludes that miR-29b regulates the expression of HDAC4 which plays a role in controlling renal fibrosis and podocytes' impairment in DN.
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Gliozzi ML, Espiritu EB, Shipman KE, Rbaibi Y, Long KR, Roy N, Duncan AW, Lazzara MJ, Hukriede NA, Baty CJ, Weisz OA. Effects of Proximal Tubule Shortening on Protein Excretion in a Lowe Syndrome Model. J Am Soc Nephrol 2019; 31:67-83. [PMID: 31676724 DOI: 10.1681/asn.2019020125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/24/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Lowe syndrome (LS) is an X-linked recessive disorder caused by mutations in OCRL, which encodes the enzyme OCRL. Symptoms of LS include proximal tubule (PT) dysfunction typically characterized by low molecular weight proteinuria, renal tubular acidosis (RTA), aminoaciduria, and hypercalciuria. How mutant OCRL causes these symptoms isn't clear. METHODS We examined the effect of deleting OCRL on endocytic traffic and cell division in newly created human PT CRISPR/Cas9 OCRL knockout cells, multiple PT cell lines treated with OCRL-targeting siRNA, and in orcl-mutant zebrafish. RESULTS OCRL-depleted human cells proliferated more slowly and about 10% of them were multinucleated compared with fewer than 2% of matched control cells. Heterologous expression of wild-type, but not phosphatase-deficient, OCRL prevented the accumulation of multinucleated cells after acute knockdown of OCRL but could not rescue the phenotype in stably edited knockout cell lines. Mathematic modeling confirmed that reduced PT length can account for the urinary excretion profile in LS. Both ocrl mutant zebrafish and zebrafish injected with ocrl morpholino showed truncated expression of megalin along the pronephric kidney, consistent with a shortened S1 segment. CONCLUSIONS Our data suggest a unifying model to explain how loss of OCRL results in tubular proteinuria as well as the other commonly observed renal manifestations of LS. We hypothesize that defective cell division during kidney development and/or repair compromises PT length and impairs kidney function in LS patients.
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Affiliation(s)
| | | | | | | | | | - Nairita Roy
- Department of Pathology, McGowan Institute for Regenerative Medicine, and Pittsburgh Liver Research Center, Pittsburgh, Pennsylvania
| | - Andrew W Duncan
- Department of Pathology, McGowan Institute for Regenerative Medicine, and Pittsburgh Liver Research Center, Pittsburgh, Pennsylvania
| | - Matthew J Lazzara
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia; and
| | - Neil A Hukriede
- Department of Developmental Biology, and.,Center for Critical Care Nephrology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Ora A Weisz
- Renal-Electrolyte Division, Department of Medicine,
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15
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Kellum JA, Wen X, de Caestecker MP, Hukriede NA. Sepsis-Associated Acute Kidney Injury: A Problem Deserving of New Solutions. Nephron Clin Pract 2019; 143:174-178. [PMID: 31018211 DOI: 10.1159/000500167] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022] Open
Abstract
Sepsis-associated acute kidney injury (S-AKI) significantly worsens patient prognosis, and recent evidence suggests that the injury process begins early and may be sustained by therapies used to treat the sepsis (e.g., fluids resuscitation, antibiotics). While efforts to develop less-injurious treatments are making progress, some degree of secondary injury is to be expected. So too is the inevitable nature of organ injury, which is often present at the time the patient seeks medical attention. We recently found that most patients presenting with septic shock and developing AKI had evidence of kidney damage at the time of, or within 24 h of their admission. In such patients, prevention is not a viable option, as injury has already occurred by the time of presentation. Since S-AKI patients are at increased risk of developing chronic kidney disease, a fundamental target for interventions in S-AKI is to prevent fibrosis (maladaptive repair) while stimulating regeneration (proliferation of viable epithelial cells). Using a pathway-agnostic, proliferation-based phenotypic assay, we discovered phenylthiobutanoic acid, a small molecule histone deacetylase inhibitor, that enhances renal recovery and reduces fibrosis in both zebrafish and mouse models of AKI.
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Affiliation(s)
- John A Kellum
- Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA, .,Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,
| | - Xiaoyan Wen
- Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark P de Caestecker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Neil A Hukriede
- Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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16
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Brilli Skvarca L, Han HI, Espiritu EB, Missinato MA, Rochon ER, McDaniels MD, Bais AS, Roman BL, Waxman JS, Watkins SC, Davidson AJ, Tsang M, Hukriede NA. Enhancing regeneration after acute kidney injury by promoting cellular dedifferentiation in zebrafish. Dis Model Mech 2019; 12:dmm.037390. [PMID: 30890583 PMCID: PMC6505474 DOI: 10.1242/dmm.037390] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Acute kidney injury (AKI) is a serious disorder for which there are limited treatment options. Following injury, native nephrons display limited regenerative capabilities, relying on the dedifferentiation and proliferation of renal tubular epithelial cells (RTECs) that survive the insult. Previously, we identified 4-(phenylthio)butanoic acid (PTBA), a histone deacetylase inhibitor (HDI), as an enhancer of renal recovery, and showed that PTBA treatment increased RTEC proliferation and reduced renal fibrosis. Here, we investigated the regenerative mechanisms of PTBA in zebrafish models of larval renal injury and adult cardiac injury. With respect to renal injury, we showed that delivery of PTBA using an esterified prodrug (UPHD25) increases the reactivation of the renal progenitor gene Pax2a, enhances dedifferentiation of RTECs, reduces Kidney injury molecule-1 (Kim-1) expression, and lowers the number of infiltrating macrophages. Further, we found that the effects of PTBA on RTEC proliferation depend upon retinoic acid signaling and demonstrate that the therapeutic properties of PTBA are not restricted to the kidney but also increase cardiomyocyte proliferation and decrease fibrosis following cardiac injury in adult zebrafish. These studies provide key mechanistic insights into how PTBA enhances tissue repair in models of acute injury and lay the groundwork for translating this novel HDI into the clinic. This article has an associated First Person interview with the joint first authors of the paper. Summary: Mortality associated with AKI is in part due to limited treatments available to ameliorate injury. The authors identify a compound that accelerates AKI recovery and promotes cellular dedifferentiation.
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Affiliation(s)
- Lauren Brilli Skvarca
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hwa In Han
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eugenel B Espiritu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Maria A Missinato
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Elizabeth R Rochon
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Michael D McDaniels
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Abha S Bais
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Beth L Roman
- Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Joshua S Waxman
- Heart Institute, Molecular Cardiovascular Biology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Simon C Watkins
- Department of Cell Biology and Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alan J Davidson
- Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA .,Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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17
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Han HI, Skvarca LB, Espiritu EB, Davidson AJ, Hukriede NA. The role of macrophages during acute kidney injury: destruction and repair. Pediatr Nephrol 2019; 34:561-569. [PMID: 29383444 PMCID: PMC6066473 DOI: 10.1007/s00467-017-3883-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 12/29/2017] [Indexed: 12/21/2022]
Abstract
Acute kidney injury (AKI) is defined by a rapid decline in renal function. Regardless of the initial cause of injury, the influx of immune cells is a common theme during AKI. While an inflammatory response is critical for the initial control of injury, a prolonged response can negatively affect tissue repair. In this review, we focus on the role of macrophages, from early inflammation to resolution, during AKI. These cells serve as the innate defense system by phagocytosing cellular debris and pathogenic molecules and bridge communication with the adaptive immune system by acting as antigen-presenting cells and secreting cytokines. While many immune cells function to initiate inflammation, macrophages play a complex role throughout AKI. This complexity is driven by their functional plasticity: the ability to polarize from a "pro-inflammatory" phenotype to a "pro-reparative" phenotype. Importantly, experimental and translational studies indicate that macrophage polarization opens the possibility to generate novel therapeutics to promote repair during AKI. A thorough understanding of the biological roles these phagocytes play during both injury and repair is necessary to understand the limitations while furthering the therapeutic application.
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Affiliation(s)
- Hwa I. Han
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Lauren B. Skvarca
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Eugenel B. Espiritu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Alan J. Davidson
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Neil A. Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States of America,Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, PA, United States of America,Correspondence: Dr. Neil A. Hukriede, Department of Developmental Biology, University of Pittsburgh School of Medicine, 3501 5th Ave., 5061 BST3, Pittsburgh, PA 15213. Phone: 412-648-9918;
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18
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Russell JO, Ko S, Monga SP, Shin D. Notch Inhibition Promotes Differentiation of Liver Progenitor Cells into Hepatocytes via sox9b Repression in Zebrafish. Stem Cells Int 2019; 2019:8451282. [PMID: 30992706 PMCID: PMC6434270 DOI: 10.1155/2019/8451282] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/12/2019] [Indexed: 02/08/2023] Open
Abstract
Liver regeneration after most forms of injury is mediated through the proliferation of hepatocytes. However, when hepatocyte proliferation is impaired, such as during chronic liver disease, liver progenitor cells (LPCs) arising from the biliary epithelial cell (BEC) compartment can give rise to hepatocytes to mediate hepatic repair. Promotion of LPC-to-hepatocyte differentiation in patients with chronic liver disease could serve as a potentially new therapeutic option, but first requires the identification of the molecular mechanisms driving this process. Notch signaling has been identified as an important signaling pathway promoting the BEC fate during development and has also been implicated in regulating LPC differentiation during regeneration. SRY-related HMG box transcription factor 9 (Sox9) is a direct target of Notch signaling in the liver, and Sox9 has also been shown to promote the BEC fate during development. We have recently shown in a zebrafish model of LPC-driven liver regeneration that inhibition of Hdac1 activity through MS-275 treatment enhances sox9b expression in LPCs and impairs LPC-to-hepatocyte differentiation. Therefore, we hypothesized that inhibition of Notch signaling would promote LPC-to-hepatocyte differentiation by repressing sox9b expression in zebrafish. We ablated the hepatocytes of Tg(fabp10a:CFP-NTR) larvae and blocked Notch activation during liver regeneration through treatment with γ-secretase inhibitor LY411575 and demonstrated enhanced induction of Hnf4a in LPCs. Alternatively, enhancing Notch signaling via Notch3 intracellular domain (N3ICD) overexpression impaired Hnf4a induction. Hepatocyte ablation in sox9b heterozygous mutant embryos enhanced Hnf4a induction, while BEC-specific Sox9b overexpression impaired LPC-to-hepatocyte differentiation. Our results establish the Notch-Sox9b signaling axis as inhibitory to LPC-to-hepatocyte differentiation in a well-established in vivo LPC-driven liver regeneration model.
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Affiliation(s)
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, USA
| | - Satdarshan P. Monga
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Donghun Shin
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
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19
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Ko S, Russell JO, Tian J, Gao C, Kobayashi M, Feng R, Yuan X, Shao C, Ding H, Poddar M, Singh S, Locker J, Weng HL, Monga SP, Shin D. Hdac1 Regulates Differentiation of Bipotent Liver Progenitor Cells During Regeneration via Sox9b and Cdk8. Gastroenterology 2019; 156:187-202.e14. [PMID: 30267710 PMCID: PMC6309465 DOI: 10.1053/j.gastro.2018.09.039] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND & AIMS Upon liver injury in which hepatocyte proliferation is compromised, liver progenitor cells (LPCs), derived from biliary epithelial cells (BECs), differentiate into hepatocytes. Little is known about the mechanisms of LPC differentiation. We used zebrafish and mouse models of liver injury to study the mechanisms. METHODS We used transgenic zebrafish, Tg(fabp10a:CFP-NTR), to study the effects of compounds that alter epigenetic factors on BEC-mediated liver regeneration. We analyzed zebrafish with disruptions of the histone deacetylase 1 gene (hdac1) or exposed to MS-275 (an inhibitor of Hdac1, Hdac2, and Hdac3). We also analyzed zebrafish with mutations in sox9b, fbxw7, kdm1a, and notch3. Zebrafish larvae were collected and analyzed by whole-mount immunostaining and in situ hybridization; their liver tissues were collected for quantitative reverse transcription polymerase chain reaction. We studied mice in which hepatocyte-specific deletion of β-catenin (Ctnnb1flox/flox mice injected with Adeno-associated virus serotype 8 [AAV8]-TBG-Cre) induces differentiation of LPCs into hepatocytes after a choline-deficient, ethionine-supplemented (CDE) diet. Liver tissues were collected and analyzed by immunohistochemistry and immunoblots. We performed immunohistochemical analyses of liver tissues from patients with compensated or decompensated cirrhosis or acute on chronic liver failure (n = 15). RESULTS Loss of Hdac1 activity in zebrafish blocked differentiation of LPCs into hepatocytes by increasing levels of sox9b mRNA and reduced differentiation of LPCs into BECs by increasing levels of cdk8 mRNA, which encodes a negative regulator gene of Notch signaling. We identified Notch3 as the receptor that regulates differentiation of LPCs into BECs. Loss of activity of Kdm1a, a lysine demethylase that forms repressive complexes with Hdac1, produced the same defects in differentiation of LPCs into hepatocytes and BECs as observed in zebrafish with loss of Hdac1 activity. Administration of MS-275 to mice with hepatocyte-specific loss of β-catenin impaired differentiation of LPCs into hepatocytes after the CDE diet. HDAC1 was expressed in reactive ducts and hepatocyte buds of liver tissues from patients with cirrhosis. CONCLUSIONS Hdac1 regulates differentiation of LPCs into hepatocytes via Sox9b and differentiation of LPCs into BECs via Cdk8, Fbxw7, and Notch3 in zebrafish with severe hepatocyte loss. HDAC1 activity was also required for differentiation of LPCs into hepatocytes in mice with liver injury after the CDE diet. These pathways might be manipulated to induce LPC differentiation for treatment of patients with advanced liver diseases.
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Affiliation(s)
- Sungjin Ko
- Department of Developmental Biology, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania; Department of Pathology, Pittsburgh, Pennsylvania.
| | | | - Jianmin Tian
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA
| | - Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Rilu Feng
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiaodong Yuan
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chen Shao
- Department of Pathology, Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Huiguo Ding
- Department of Gastroenterology and Hepatology, Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Minakshi Poddar
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
| | - Sucha Singh
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
| | - Joseph Locker
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA
| | - Hong-Lei Weng
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Satdarshan P. Monga
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, USA,Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Donghun Shin
- Department of Developmental Biology, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, Pittsburgh, Pennsylvania.
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20
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Khaliq M, Ko S, Liu Y, Wang H, Sun Y, Solnica-Krezel L, Shin D. Stat3 Regulates Liver Progenitor Cell-Driven Liver Regeneration in Zebrafish. Gene Expr 2018; 18:157-170. [PMID: 29690953 PMCID: PMC6190120 DOI: 10.3727/105221618x15242506133273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
After liver injury, regeneration manifests as either (1) hepatocytes proliferating to restore the lost hepatocyte mass or (2) if hepatocyte proliferation is compromised, biliary epithelial cells (BECs) dedifferentiating into liver progenitor cells (LPCs), which subsequently differentiate into hepatocytes. Following pharmacogenetic ablation of hepatocytes in Tg(fabp10a:CFP-NTR) zebrafish, resulting in severe liver injury, signal transducer and activator of transcription 3 (Stat3) and its target gene and negative regulator, socs3a, were upregulated in regenerating livers. Using either Stat3 inhibitors, JSI-124 and S3I-201, or stat3 zebrafish mutants, we investigated the role of Stat3 in LPC-driven liver regeneration. Although Stat3 suppression reduced the size of regenerating livers, BEC dedifferentiation into LPCs was unaffected. However, regenerating livers displayed a delay in LPC-to-hepatocyte differentiation and a significant reduction in the number of BECs. While no difference in cell death was detected, Stat3 inhibition significantly reduced LPC proliferation. Notably, stat3 mutants phenocopied the effects of Stat3 chemical inhibitors, although the mutant phenotype was incompletely penetrant. Intriguingly, a subset of socs3a mutants also displayed a lower number of BECs in regenerating livers. We conclude that the Stat3/Socs3a pathway is necessary for the proper timing of LPC-to-hepatocyte differentiation and establishing the proper number of BECs during LPC-driven liver regeneration.
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Affiliation(s)
- Mehwish Khaliq
- *Department of Developmental Biology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sungjin Ko
- *Department of Developmental Biology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yinzi Liu
- †Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hualin Wang
- ‡China Zebrafish Resource Center, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Yonghua Sun
- ‡China Zebrafish Resource Center, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Lila Solnica-Krezel
- †Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Donghun Shin
- *Department of Developmental Biology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
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21
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Kearney M, Cooper PR, Smith AJ, Duncan HF. Epigenetic Approaches to the Treatment of Dental Pulp Inflammation and Repair: Opportunities and Obstacles. Front Genet 2018; 9:311. [PMID: 30131827 PMCID: PMC6090030 DOI: 10.3389/fgene.2018.00311] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Concerns over the cost and destructive nature of dental treatment have led to the call for novel minimally invasive, biologically based restorative solutions. For patients with toothache, this has resulted in a shift from invasive root-canal-treatment (RCT) toward more conservative vital-pulp-treatment (VPT) procedures, aimed to protect the pulp and harness its natural regenerative capacity. If the dental pulp is exposed, as long as the infection and inflammation can be controlled, conservative therapies can promote the formation of new tertiary dentine in a stem cell-led reparative process. Crucially, the volume and quality of new dentine is dependent on the material applied; however, currently available dental-materials are limited by non-specific action, cytotoxicity and poor clinical handling. Looking to the future, an improved understanding of the cellular regulators of pulpal inflammation and associated repair mechanisms is critical to predict pulpal responses and devise novel treatment strategies. Epigenetic modifications of DNA-associated proteins and the influences of non-coding RNAs have been demonstrated to control the self-renewal of stem cell populations as well as regulate mineralised tissue development and repair. Notably, the stability of microRNAs and their relative ease of sampling from pulpal blood highlight their potential for application as diagnostic inflammatory biomarkers, while increased understanding of their actions will not only enhance our knowledge of pulpal disease and repair, but also identify novel molecular targets. The potential therapeutic application of epigenetic modifying agents, DNA-methyltransferase-inhibitors (DNMTi) and histone-deacetylase-inhibitors (HDACi), have been shown to promote mineralisation and repair processes in dental-pulp-cell (DPC) populations as well as induce the release of bioactive dentine-matrix-components. Consequently, HDACis and DNMTis have the potential to enhance tertiary dentinogenesis by influencing the cellular and tissue processes at low concentrations with minimal side effects, providing an opportunity to develop a topically placed, inexpensive bio-inductive restorative material. The aim of this review is to highlight the potential role of epigenetic approaches in the treatment of the damaged dental pulp, considering the opportunities and obstacles, such as off-target effects, delivery mechanisms, for the therapeutic use of miRNA as an inflammatory biomarker or molecular target, before discussing the application of HDACi and DNMTi to the damaged pulp to stimulate repair.
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Affiliation(s)
- Michaela Kearney
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Paul R. Cooper
- Oral Biology, School of Dentistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Anthony J. Smith
- Oral Biology, School of Dentistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Henry F. Duncan
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College Dublin, University of Dublin, Dublin, Ireland
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22
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Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
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23
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Allinovi M, De Chiara L, Angelotti ML, Becherucci F, Romagnani P. Anti-fibrotic treatments: A review of clinical evidence. Matrix Biol 2018; 68-69:333-354. [DOI: 10.1016/j.matbio.2018.02.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 02/06/2023]
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24
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Wang L, Zhang L, Hou Q, Zhu X, Chen Z, Liu Z. Triptolide attenuates proteinuria and podocyte apoptosis via inhibition of NF-κB/GADD45B. Sci Rep 2018; 8:10843. [PMID: 30022148 PMCID: PMC6052061 DOI: 10.1038/s41598-018-29203-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 07/06/2018] [Indexed: 12/14/2022] Open
Abstract
Podocyte injury is a primary contributor to proteinuria. Triptolide is a major active component of Tripterygium wilfordii Hook F that exhibits potent antiproteinuric effects. We used our previously developed in vivo zebrafish model of inducible podocyte-target injury and found that triptolide treatment effectively alleviated oedema, proteinuria and foot process effacement. Triptolide also inhibited podocyte apoptosis in our zebrafish model and in vitro. We also examined the mechanism of triptolide protection of podocyte. Whole-genome expression profiles of cultured podocytes demonstrated that triptolide treatment downregulated apoptosis pathway-related GADD45B expression. Specific overexpression of gadd45b in zebrafish podocytes abolished the protective effects of triptolide. GADD45B is a mediator of podocyte apoptosis that contains typical NF-κB binding sites in the promoter region, and NF-κB p65 primarily transactivates this gene. Triptolide inhibited NF-κB signalling activation and binding of NF-κB to the GADD45B promoter. Taken together, our findings demonstrated that triptolide attenuated proteinuria and podocyte apoptosis via inhibition of NF-κB/GADD45B signalling, which provides a new understanding of the antiproteinuric effects of triptolide in glomerular diseases.
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Affiliation(s)
- Ling Wang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Liwen Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Qing Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Xiaodong Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Zhaohong Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.
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25
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Rothschild SC, Lee HJ, Ingram SR, Mohammadi DK, Walsh GS, Tombes RM. Calcium signals act through histone deacetylase to mediate pronephric kidney morphogenesis. Dev Dyn 2018; 247:807-817. [PMID: 29633426 DOI: 10.1002/dvdy.24632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/30/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease is the most common monogenetic kidney disorder and is linked to mutations in PKD1 and PKD2. PKD2, a Ca2+ -conducting TRP channel enriched in ciliated cells and gated by extracellular signals, is necessary to activate the multifunctional Ca2+/ calmodulin-dependent protein kinase type 2 (CaMK-II), enabling kidney morphogenesis and cilia stability. RESULTS In this study, antisense morpholino oligonucleotides and pharmacological compounds were employed to investigate the roles of class II HDAC family members (HDAC 4, 5, and 6) in Zebrafish kidney development. While all three class II HDAC genes were expressed throughout the embryo during early development, HDAC5-morphant embryos exhibited anterior cysts and destabilized cloacal cilia, similar to PKD2 and CaMK-II morphants. In contrast, HDAC4-morphant embryos exhibited elongated cloacal cilia and lacked anterior kidney defects. Suppression of HDAC4 partially reversed the cilia shortening and anterior convolution defects caused by CaMK-II deficiency, whereas HDAC5 loss exacerbated these defects. EGFP-HDAC4, but not EGFP-HDAC5, translocated into the nucleus upon CaMK-II suppression in pronephric kidney cells. CONCLUSIONS These results support a model by which activated CaMK-II sequesters HDAC4 in the cytosol to enable primary cilia formation and kidney morphogenesis. Developmental Dynamics 247:807-817, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Hunter J Lee
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Sarah R Ingram
- Life Sciences, Virginia Commonwealth University, Richmond, Virginia
| | - Daniel K Mohammadi
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Gregory S Walsh
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Robert M Tombes
- Life Sciences, Virginia Commonwealth University, Richmond, Virginia
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26
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Lazzeri E, Angelotti ML, Peired A, Conte C, Marschner JA, Maggi L, Mazzinghi B, Lombardi D, Melica ME, Nardi S, Ronconi E, Sisti A, Antonelli G, Becherucci F, De Chiara L, Guevara RR, Burger A, Schaefer B, Annunziato F, Anders HJ, Lasagni L, Romagnani P. Endocycle-related tubular cell hypertrophy and progenitor proliferation recover renal function after acute kidney injury. Nat Commun 2018; 9:1344. [PMID: 29632300 PMCID: PMC5890293 DOI: 10.1038/s41467-018-03753-4] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/08/2018] [Indexed: 12/29/2022] Open
Abstract
Acute kidney injury (AKI) is considered largely reversible based on the capacity of surviving tubular cells to dedifferentiate and replace lost cells via cell division. Here we show by tracking individual tubular cells in conditional Pax8/Confetti mice that kidney function is recovered after AKI despite substantial tubular cell loss. Cell cycle and ploidy analysis upon AKI in conditional Pax8/FUCCI2aR mice and human biopsies identify endocycle-mediated hypertrophy of tubular cells. By contrast, a small subset of Pax2+ tubular progenitors enriches via higher stress resistance and clonal expansion and regenerates necrotic tubule segments, a process that can be enhanced by suitable drugs. Thus, renal functional recovery upon AKI involves remnant tubular cell hypertrophy via endocycle and limited progenitor-driven regeneration that can be pharmacologically enhanced.
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Affiliation(s)
- Elena Lazzeri
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Maria Lucia Angelotti
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Anna Peired
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Carolina Conte
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Julian A Marschner
- Division of Nephrology, Medizinische Klinik and Poliklinik IV, Klinikum der LMU München, Munich, Germany
| | - Laura Maggi
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | | | - Duccio Lombardi
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Maria Elena Melica
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Sara Nardi
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Elisa Ronconi
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Alessandro Sisti
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Nephrology Unit and Meyer Children's University Hospital, Florence, Italy
| | - Giulia Antonelli
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | | | - Letizia De Chiara
- Nephrology Unit and Meyer Children's University Hospital, Florence, Italy
| | - Ricardo Romero Guevara
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Beat Schaefer
- Department of Oncology and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Francesco Annunziato
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Hans-Joachim Anders
- Division of Nephrology, Medizinische Klinik and Poliklinik IV, Klinikum der LMU München, Munich, Germany
| | - Laura Lasagni
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy
| | - Paola Romagnani
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy.
- Excellence Centre for Research, Transfer and High Education for the development of DE NOVO Therapies (DENOTHE), Florence, Italy.
- Nephrology Unit and Meyer Children's University Hospital, Florence, Italy.
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27
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Russell JO, Ko S, Saggi HS, Singh S, Poddar M, Shin D, Monga SP. Bromodomain and Extraterminal (BET) Proteins Regulate Hepatocyte Proliferation in Hepatocyte-Driven Liver Regeneration. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1389-1405. [PMID: 29545201 DOI: 10.1016/j.ajpath.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/20/2022]
Abstract
Bromodomain and extraterminal (BET) proteins recruit key components of basic transcriptional machinery to promote gene expression. Aberrant expression and mutations in BET genes have been identified in many malignancies. Small molecule inhibitors of BET proteins such as JQ1 have shown efficacy in preclinical cancer models, including affecting growth of hepatocellular carcinoma. BET proteins also regulate cell proliferation in nontumor settings. We recently showed that BET proteins regulate cholangiocyte-driven liver regeneration. Here, we studied the role of BET proteins in hepatocyte-driven liver regeneration in partial hepatectomy (PHx) and acetaminophen-induced liver injury models in mice and zebrafish. JQ1 was injected 2 or 16 hours after PHx in mice to determine effect on hepatic injury, regeneration, and signaling. Mice treated with JQ1 after PHx displayed increased liver injury and a near-complete inhibition of hepatocyte proliferation. Levels of Ccnd1 mRNA and Cyclin D1 protein were reduced in animals injected with JQ1 16 hours after PHx and were even further reduced in animals injected with JQ1 2 hours after PHx. JQ1-treated zebrafish larvae after acetaminophen-induced injury also displayed notably impaired hepatocyte proliferation. In both models, Wnt signaling was prominently suppressed by JQ1. Our results show that BET proteins regulate hepatocyte proliferation-driven liver regeneration, and Wnt signaling is particularly sensitive to BET protein inhibition.
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Affiliation(s)
- Jacquelyn O Russell
- Department of Pathology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania
| | - Sungjin Ko
- Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Department of Developmental Biology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania
| | - Harvinder S Saggi
- Department of Pathology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania
| | - Sucha Singh
- Department of Pathology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania
| | - Minakshi Poddar
- Department of Pathology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania
| | - Donghun Shin
- Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Department of Developmental Biology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania.
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, University of Pittsburgh, School of Medicine Pittsburgh, Pennsylvania.
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28
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Abstract
Zebrafish are increasingly used to perform phenotypic screens to identify agents that can alter physiology in a whole organismal context. Here, we describe an automated high-content chemical screen using transgenic zebrafish embryos to identify small molecules that modulate Fibroblast Growth Factor Signaling. High content multi-well screening was further refined with a particular emphasis on automated imaging and quantification that increases sensitivity and throughput of whole organism chemical screens.
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Affiliation(s)
- Manush Saydmohammed
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, 5062 Biomedical Science Tower 3, Pittsburgh, PA, 15260, USA
| | - Michael Tsang
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, 5062 Biomedical Science Tower 3, Pittsburgh, PA, 15260, USA.
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29
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Abstract
No therapies have been shown to improve outcomes in patients with acute kidney injury (AKI). Given the high morbidity and mortality associated with AKI this represents an important unmet medical need. A common feature of all of the therapeutic development efforts for AKI is that none were driven by target selection or preclinical modeling that was based primarily on human data. This is important when considering a heterogeneous and dynamic condition such as AKI, in which in the absence of more accurate molecular classifications, clinical cohorts are likely to include patients with different types of injury at different stages in the injury and repair continuum. The National Institutes of Health precision medicine initiative offers an opportunity to address this. By creating a molecular tissue atlas of AKI, defining patient subgroups, and identifying critical cells and pathways involved in human AKI, this initiative has the potential to transform our current approach to therapeutic discovery. In this review, we discuss the opportunities and challenges that this initiative presents, with a specific focus on AKI, what additional efforts will be needed to apply these discoveries to therapeutic development, and how we believe this effort might lead to the development of new therapeutics for subsets of patients with AKI.
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Affiliation(s)
- Mark de Caestecker
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Raymond Harris
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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30
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Gehrig J, Pandey G, Westhoff JH. Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases. Front Pediatr 2018; 6:183. [PMID: 30003073 PMCID: PMC6031734 DOI: 10.3389/fped.2018.00183] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic disorders account for a wide range of renal diseases emerging during childhood and adolescence. Due to the utilization of modern biochemical and biomedical techniques, the number of identified disease-associated genes is increasing rapidly. Modeling of congenital human disease in animals is key to our understanding of the biological mechanism underlying pathological processes and thus developing novel potential treatment options. The zebrafish (Danio rerio) has been established as a versatile small vertebrate organism that is widely used for studying human inherited diseases. Genetic accessibility in combination with elegant experimental methods in zebrafish permit modeling of human genetic diseases and dissecting the perturbation of underlying cellular networks and physiological processes. Beyond its utility for genetic analysis and pathophysiological and mechanistic studies, zebrafish embryos, and larvae are amenable for phenotypic screening approaches employing high-content and high-throughput experiments using automated microscopy. This includes large-scale chemical screening experiments using genetic models for searching for disease-modulating compounds. Phenotype-based approaches of drug discovery have been successfully performed in diverse zebrafish-based screening applications with various phenotypic readouts. As a result, these can lead to the identification of candidate substances that are further examined in preclinical and clinical trials. In this review, we discuss zebrafish models for inherited kidney disease as well as requirements and considerations for the technical realization of drug screening experiments in zebrafish.
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Affiliation(s)
- Jochen Gehrig
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany
| | - Gunjan Pandey
- Acquifer is a Division of Ditabis, Digital Biomedical Imaging Systems AG, Pforzheim, Germany.,Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Jens H Westhoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
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31
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Hukriede N, Vogt A, de Caestecker M. Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury. Nephron Clin Pract 2017; 137:268-272. [PMID: 28614822 DOI: 10.1159/000476079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/24/2017] [Indexed: 12/29/2022] Open
Abstract
The cellular responses that occur following acute kidney injury (AKI) are complex and dynamic, involving multiple cells types and molecular pathways. For this reason, early selection of defined molecular targets for therapeutic intervention is unlikely to be effective in complex in vivo models of AKI, let alone Phase 3 clinical trials in patients with even more complex AKI pathobiology. Phenotypic screening using zebrafish provides an attractive alternative that does not require prior knowledge of molecular targets and may identify compounds that modify multiple targets that might be missed in more traditional target-based screens. In this review, we discuss results of an academic drug discovery campaign that used zebrafish as a primary screening tool to discover compounds with favorable absorption, metabolism, and toxicity that enhance repair when given late after injury in multiple models of AKI. We discuss how this screening campaign is being integrated into a more comprehensive, phenotypic, and target-based screen for lead compound optimization.
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Affiliation(s)
- Neil Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
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32
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Duncan HF, Smith AJ, Fleming GJP, Partridge NC, Shimizu E, Moran GP, Cooper PR. The Histone-Deacetylase-Inhibitor Suberoylanilide Hydroxamic Acid Promotes Dental Pulp Repair Mechanisms Through Modulation of Matrix Metalloproteinase-13 Activity. J Cell Physiol 2017; 231:798-816. [PMID: 26264761 DOI: 10.1002/jcp.25128] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/23/2022]
Abstract
Direct application of histone-deacetylase-inhibitors (HDACis) to dental pulp cells (DPCs) induces chromatin changes, promoting gene expression and cellular-reparative events. We have previously demonstrated that HDACis (valproic acid, trichostatin A) increase mineralization in dental papillae-derived cell-lines and primary DPCs by stimulation of dentinogenic gene expression. Here, we investigated novel genes regulated by the HDACi, suberoylanilide hydroxamic acid (SAHA), to identify new pathways contributing to DPC differentiation. SAHA significantly compromised DPC viability only at relatively high concentrations (5 μM); while low concentrations (1 μM) SAHA did not increase apoptosis. HDACi-exposure for 24 h induced mineralization-per-cell dose-dependently after 2 weeks; however, constant 14d SAHA-exposure inhibited mineralization. Microarray analysis (24 h and 14 days) of SAHA exposed cultures highlighted that 764 transcripts showed a significant >2.0-fold change at 24 h, which reduced to 36 genes at 14 days. 59% of genes were down-regulated at 24 h and 36% at 14 days, respectively. Pathway analysis indicated SAHA increased expression of members of the matrix metalloproteinase (MMP) family. Furthermore, SAHA-supplementation increased MMP-13 protein expression (7 d, 14 days) and enzyme activity (48 h, 14 days). Selective MMP-13-inhibition (MMP-13i) dose-dependently accelerated mineralization in both SAHA-treated and non-treated cultures. MMP-13i-supplementation promoted expression of several mineralization-associated markers, however, HDACi-induced cell migration and wound healing were impaired. Data demonstrate that short-term low-dose SAHA-exposure promotes mineralization in DPCs by modulating gene pathways and tissue proteases. MMP-13i further increased mineralization-associated events, but decreased HDACi cell migration indicating a specific role for MMP-13 in pulpal repair processes. Pharmacological inhibition of HDAC and MMP may provide novel insights into pulpal repair processes with significant translational benefit. J. Cell. Physiol. 231: 798-816, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Henry F Duncan
- Division of Restorative Dentistry and Periodontology, Dublin Dental University Hospital, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland
| | - Anthony J Smith
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
| | - Garry J P Fleming
- Material Science Unit, Dublin Dental University Hospital, Trinity College Dublin, Ireland
| | - Nicola C Partridge
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York
| | - Emi Shimizu
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York
| | - Gary P Moran
- Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College Dublin, Ireland
| | - Paul R Cooper
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
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33
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Pronephric tubule formation in zebrafish: morphogenesis and migration. Pediatr Nephrol 2017; 32:211-216. [PMID: 26942753 DOI: 10.1007/s00467-016-3353-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 01/14/2023]
Abstract
The nephron is the functional subunit of the vertebrate kidney and plays important osmoregulatory and excretory roles during embryonic development and in adulthood. Despite its central role in kidney function, surprisingly little is known about the molecular and cellular processes that control nephrogenesis. The zebrafish pronephric kidney, comprising two nephrons, provides a visually accessible and genetically tractable model system for a better understanding of nephron formation. Using this system, various developmental processes, including the commitment of mesoderm to a kidney fate, renal tubule proliferation, and migration, can be studied during nephrogenesis. Here, we discuss some of these processes in zebrafish with a focus on the pathways that influence renal tubule cell morphogenesis.
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34
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Abstract
Animal models have been an invaluable means to advance biomedical research as they provide experimental avenues for cellular and molecular investigations of disease pathology. The zebrafish (Danio rerio) is a good alternative to mammalian models that can be used to apply powerful genetic experimental methods normally used in invertebrates to answer questions about vertebrate development and disease. In the case of the kidney, the zebrafish has proven itself to be an applicable and versatile experimental system, mainly due to the simplicity of its pronephros, which contains two nephrons that possess conserved structural and physiological aspects with mammalian nephrons. Numerous genes that were not previously related to kidney conditions have now been linked to renal diseases by applying genetic screening with the zebrafish. In fact, a large collection of mutations that affect nephron formation and function were generated through phenotype-based forward screens. Complementary reverse genetic approaches have also been insightful, with methods spanning the use of antisense morpholino oligonucleotides to genome editing approaches such as the CRISPR/Cas9 system, to selectively knock down or knock out genes of interest to see if they produce kidney phenotypes. Acute kidney injury (AKI) has also been easily modeled in the zebrafish by injecting nephrotoxins, directly inducing damage through surgical intervention, or by generating transgenic lines that express compounds in a tissue-specific manner that when exposed to certain drugs promote an apoptotic response within cells. In this chapter, we provide an overview of these various approaches as well as discuss many of the contributions that have been achieved through the use of zebrafish to model kidney disease.
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35
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36
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Epigenetics of Renal Development and Disease. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:565-573. [PMID: 28018145 PMCID: PMC5168832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An understanding of epigenetics is indispensable to our understanding of gene regulation under normal and pathological states. This knowledge will help with designing better therapeutic approaches in regenerative tissue medicine. Epigenetics allows us to parse out the mechanisms by which transcriptional regulators gain access to specific gene loci thereby imprinting epigenetic information affecting chromatin function. This epigenetic memory forms the basis of cell lineage specification in multicellular organisms. Post-translational modifications to DNA and histones in the nucleosome core form characteristic epigenetic codes which are distinct for self-renewing and primed progenitor cell populations. Studies of chromatin modifiers and modifications in renal development and disease have been gaining momentum. Both congenital and adult renal diseases have a gene-environment component, which involves alterations to the epigenetic information imprinted during development. This epigenetic memory must be characterized to establish optimal treatment of both acute and chronic renal diseases.
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37
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White DT, Eroglu AU, Wang G, Zhang L, Sengupta S, Ding D, Rajpurohit SK, Walker SL, Ji H, Qian J, Mumm JS. ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates. Nat Protoc 2016; 11:2432-2453. [PMID: 27831568 DOI: 10.1038/nprot.2016.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The zebrafish has emerged as an important model for whole-organism small-molecule screening. However, most zebrafish-based chemical screens have achieved only mid-throughput rates. Here we describe a versatile whole-organism drug discovery platform that can achieve true high-throughput screening (HTS) capacities. This system combines our automated reporter quantification in vivo (ARQiv) system with customized robotics, and is termed 'ARQiv-HTS'. We detail the process of establishing and implementing ARQiv-HTS: (i) assay design and optimization, (ii) calculation of sample size and hit criteria, (iii) large-scale egg production, (iv) automated compound titration, (v) dispensing of embryos into microtiter plates, and (vi) reporter quantification. We also outline what we see as best practice strategies for leveraging the power of ARQiv-HTS for zebrafish-based drug discovery, and address technical challenges of applying zebrafish to large-scale chemical screens. Finally, we provide a detailed protocol for a recently completed inaugural ARQiv-HTS effort, which involved the identification of compounds that elevate insulin reporter activity. Compounds that increased the number of insulin-producing pancreatic beta cells represent potential new therapeutics for diabetic patients. For this effort, individual screening sessions took 1 week to conclude, and sessions were performed iteratively approximately every other day to increase throughput. At the conclusion of the screen, more than a half million drug-treated larvae had been evaluated. Beyond this initial example, however, the ARQiv-HTS platform is adaptable to almost any reporter-based assay designed to evaluate the effects of chemical compounds in living small-animal models. ARQiv-HTS thus enables large-scale whole-organism drug discovery for a variety of model species and from numerous disease-oriented perspectives.
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Affiliation(s)
- David T White
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, USA
| | - Arife Unal Eroglu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guohua Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Liyun Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sumitra Sengupta
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Surendra K Rajpurohit
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, USA
| | - Steven L Walker
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, USA
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38
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Mazzinghi B, Romagnani P, Lazzeri E. Biologic modulation in renal regeneration. Expert Opin Biol Ther 2016; 16:1403-1415. [DOI: 10.1080/14712598.2016.1219336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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39
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Epigenetics mechanisms in renal development. Pediatr Nephrol 2016; 31:1055-60. [PMID: 26493068 PMCID: PMC4841758 DOI: 10.1007/s00467-015-3228-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/03/2023]
Abstract
Appreciation for the role of epigenetic modifications in the diagnosis and treatment of diseases is fast gaining attention. Treatment of chronic kidney disease stemming from diabetes or hypertension as well as Wilms tumor will all profit from knowledge of the changes in the epigenomic landscapes. To do so, it is essential to characterize the epigenomic modifiers and their modifications under normal physiological conditions. The transcription factor Pax2 was identified as a major epigenetic player in the early specification of the kidney. Notably, the progenitors of all nephrons that reside in the cap mesenchyme display a unique bivalent histone signature (expressing repressive epigenetic marks alongside activation marks) on lineage-specific genes. These cells are deemed poised for differentiation and commitment to the nephrogenic lineage. In response to the appropriate inducing signal, these genes lose their repressive histone marks, which allow for their expression in nascent nephron precursors. Such knowledge of the epigenetic landscape and the resultant cell fate or behavior in the developing kidney will greatly improve the overall success in designing regenerative strategies and tissue reprogramming methodologies from pluripotent cells.
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40
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Poureetezadi SJ, Wingert RA. Little fish, big catch: zebrafish as a model for kidney disease. Kidney Int 2016; 89:1204-10. [PMID: 27165832 DOI: 10.1016/j.kint.2016.01.031] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/13/2016] [Accepted: 01/21/2016] [Indexed: 02/08/2023]
Abstract
The zebrafish, Danio rerio, is a relevant vertebrate model for biomedical research and translational studies because of its broad genetic conservation with humans. In recent years, scientists have formulated a growing list of zebrafish kidney disease paradigms, the study of which has contributed a multitude of insights into the basic biology of human conditions and even identified potential therapeutic agents. Conversely, there are also distinctive aspects of zebrafish biology lacking in higher vertebrates, such as the capacity to heal without lasting scar formation after tissue damage and the ability to generate nephrons throughout their lifespan, which makes the zebrafish uniquely suited to study regeneration in the context of the kidney. Here, we review several informative zebrafish models of kidney disease and discuss their future applications in nephrology.
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Affiliation(s)
- Shahram Jevin Poureetezadi
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, USA.
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41
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Drummond BE, Wingert RA. Insights into kidney stem cell development and regeneration using zebrafish. World J Stem Cells 2016; 8:22-31. [PMID: 26981168 PMCID: PMC4766248 DOI: 10.4252/wjsc.v8.i2.22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/28/2015] [Accepted: 01/11/2016] [Indexed: 02/06/2023] Open
Abstract
Kidney disease is an escalating global health problem, for which the formulation of therapeutic approaches using stem cells has received increasing research attention. The complexity of kidney anatomy and function, which includes the diversity of renal cell types, poses formidable challenges in the identification of methods to generate replacement structures. Recent work using the zebrafish has revealed their high capacity to regenerate the integral working units of the kidney, known as nephrons, following acute injury. Here, we discuss these findings and explore the ways that zebrafish can be further utilized to gain a deeper molecular appreciation of renal stem cell biology, which may uncover important clues for regenerative medicine.
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42
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Skrypnyk NI, Sanker S, Skvarca LB, Novitskaya T, Woods C, Chiba T, Patel K, Goldberg ND, McDermott L, Vinson PN, Calcutt MW, Huryn DM, Vernetti LA, Vogt A, Hukriede NA, de Caestecker MP. Delayed treatment with PTBA analogs reduces postinjury renal fibrosis after kidney injury. Am J Physiol Renal Physiol 2015; 310:F705-F716. [PMID: 26661656 DOI: 10.1152/ajprenal.00503.2015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/03/2015] [Indexed: 02/07/2023] Open
Abstract
No therapies have been shown to accelerate recovery or prevent fibrosis after acute kidney injury (AKI). In part, this is because most therapeutic candidates have to be given at the time of injury and the diagnosis of AKI is usually made too late for drugs to be efficacious. Strategies to enhance post-AKI repair represent an attractive approach to address this. Using a phenotypic screen in zebrafish, we identified 4-(phenylthio)butanoic acid (PTBA), which promotes proliferation of embryonic kidney progenitor cells (EKPCs), and the PTBA methyl ester UPHD25, which also increases postinjury repair in ischemia-reperfusion and aristolochic acid-induced AKI in mice. In these studies, a new panel of PTBA analogs was evaluated. Initial screening was performed in zebrafish EKPC assays followed by survival assays in a gentamicin-induced AKI larvae zebrafish model. Using this approach, we identified UPHD186, which in contrast to UPHD25, accelerates recovery and reduces fibrosis when administered several days after ischemia-reperfusion AKI and reduces fibrosis after unilateral ureteric obstruction in mice. UPHD25 and 186 are efficiently metabolized to the active analog PTBA in liver and kidney microsome assays, indicating both compounds may act as PTBA prodrugs in vivo. UPHD186 persists longer in the circulation than UPHD25, suggesting that sustained levels of UPHD186 may increase efficacy by acting as a reservoir for renal metabolism to PTBA. These findings validate use of zebrafish EKPC and AKI assays as a drug discovery strategy for molecules that reduce fibrosis in multiple AKI models and can be administered days after initiation of injury.
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Affiliation(s)
- Nataliya I Skrypnyk
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Subramaniam Sanker
- Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Tatiana Novitskaya
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Clara Woods
- Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Takuto Chiba
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Kevin Patel
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Natasha D Goldberg
- Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lee McDermott
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Paige N Vinson
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| | - M Wade Calcutt
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee
| | - Donna M Huryn
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lawrence A Vernetti
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andreas Vogt
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Neil A Hukriede
- Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark P de Caestecker
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, Tennessee; .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
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43
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Chiba T, Skrypnyk NI, Skvarca LB, Penchev R, Zhang KX, Rochon ER, Fall JL, Paueksakon P, Yang H, Alford CE, Roman BL, Zhang MZ, Harris R, Hukriede NA, de Caestecker MP. Retinoic Acid Signaling Coordinates Macrophage-Dependent Injury and Repair after AKI. J Am Soc Nephrol 2015; 27:495-508. [PMID: 26109319 DOI: 10.1681/asn.2014111108] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/04/2015] [Indexed: 12/13/2022] Open
Abstract
Retinoic acid (RA) has been used therapeutically to reduce injury and fibrosis in models of AKI, but little is known about the regulation of this pathway and what role it has in regulating injury and repair after AKI. In these studies, we show that RA signaling is activated in mouse and zebrafish models of AKI, and that these responses limit the extent of injury and promote normal repair. These effects were mediated through a novel mechanism by which RA signaling coordinated the dynamic equilibrium of inflammatory M1 spectrum versus alternatively activated M2 spectrum macrophages. Our data suggest that locally synthesized RA represses proinflammatory macrophages, thereby reducing macrophage-dependent injury post-AKI, and activates RA signaling in injured tubular epithelium, which in turn promotes alternatively activated M2 spectrum macrophages. Because RA signaling has an essential role in kidney development but is repressed in the adult, these findings provide evidence of an embryonic signaling pathway that is reactivated after AKI and involved in reducing injury and enhancing repair.
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Affiliation(s)
- Takuto Chiba
- Division of Nephrology, Department of Medicine, Departments of Cell and Developmental Biology, and
| | | | | | | | | | | | | | | | - Haichun Yang
- Pathology, Vanderbilt University, Nashville, Tennessee
| | - Catherine E Alford
- Department of Pathology and Laboratory Medicine, Veteran Affairs Tennessee Valley Health Authority, Nashville, Tennessee; and
| | | | | | | | - Neil A Hukriede
- Departments of Developmental Biology, Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark P de Caestecker
- Division of Nephrology, Department of Medicine, Departments of Cell and Developmental Biology, and
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44
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Duncan HF, Smith AJ, Fleming GJP, Cooper PR. Epigenetic modulation of dental pulp stem cells: implications for regenerative endodontics. Int Endod J 2015; 49:431-46. [PMID: 26011759 DOI: 10.1111/iej.12475] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/24/2015] [Indexed: 12/28/2022]
Abstract
Dental pulp stem cells (DPSCs) offer significant potential for use in regenerative endodontics, and therefore, identifying cellular regulators that control stem cell fate is critical to devising novel treatment strategies. Stem cell lineage commitment and differentiation are regulated by an intricate range of host and environmental factors of which epigenetic influence is considered vital. Epigenetic modification of DNA and DNA-associated histone proteins has been demonstrated to control cell phenotype and regulate the renewal and pluripotency of stem cell populations. The activities of the nuclear enzymes, histone deacetylases, are increasingly being recognized as potential targets for pharmacologically inducing stem cell differentiation and dedifferentiation. Depending on cell maturity and niche in vitro, low concentration histone deacetylase inhibitor (HDACi) application can promote dedifferentiation of several post-natal and mouse embryonic stem cell populations and conversely increase differentiation and accelerate mineralization in DPSC populations, whilst animal studies have shown an HDACi-induced increase in stem cell marker expression during organ regeneration. Notably, both HDAC and DNA methyltransferase inhibitors have also been demonstrated to dramatically increase the reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) for use in regenerative therapeutic procedures. As the regulation of cell fate will likely remain the subject of intense future research activity, this review aims to describe the current knowledge relating to stem cell epigenetic modification, focusing on the role of HDACi on alteration of DPSC phenotype, whilst presenting the potential for therapeutic application as part of regenerative endodontic regimens.
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Affiliation(s)
- H F Duncan
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College, Dublin, Ireland
| | - A J Smith
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
| | - G J P Fleming
- Material Science Unit, Dublin Dental University Hospital, Trinity College, Dublin, Ireland
| | - P R Cooper
- Oral Biology, School of Dentistry, University of Birmingham, Birmingham, UK
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45
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Cirio MC, de Caestecker MP, Hukriede NA. Zebrafish Models of Kidney Damage and Repair. CURRENT PATHOBIOLOGY REPORTS 2015; 3:163-170. [PMID: 28690924 PMCID: PMC5497754 DOI: 10.1007/s40139-015-0080-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The vertebrate kidney possesses the capacity to repair damaged nephrons, and this potential is conserved regardless of the complexity of species-specific kidneys. However, many aquatic vertebrates possess the ability to not only repair existing nephrons, but also generate new nephrons after injury. Adult zebrafish have the ability to recover from acute renal injury not only by replacing lost injured epithelial cells of endogenous nephrons, but by also generating de novo nephrons. This strong regeneration potential, along with other unique characteristics such as the high degree of genetic conservation with humans, the ease of harvesting externally fertilized, transparent embryos, the accessibility to larval and adult kidneys, and the ability to perform whole organism phenotypic small molecule screens, has positioned zebrafish as a unique vertebrate model to study kidney injury. In this review, we provide an overview of the contribution of zebrafish larvae/adult studies to the understanding of renal regeneration, diseases, and therapeutic discovery.
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Affiliation(s)
- Maria Cecilia Cirio
- Instituto de Fisiología, Biología Molecular y Neurociencias-Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mark P de Caestecker
- Division of Nephrology, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, PA, USA
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46
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Atlas of Cellular Dynamics during Zebrafish Adult Kidney Regeneration. Stem Cells Int 2015; 2015:547636. [PMID: 26089919 PMCID: PMC4451991 DOI: 10.1155/2015/547636] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022] Open
Abstract
The zebrafish is a useful animal model to study the signaling pathways that orchestrate kidney regeneration, as its renal nephrons are simple, yet they maintain the biological complexity inherent to that of higher vertebrate organisms including mammals. Recent studies have suggested that administration of the aminoglycoside antibiotic gentamicin in zebrafish mimics human acute kidney injury (AKI) through the induction of nephron damage, but the timing and details of critical phenotypic events associated with the regeneration process, particularly in existing nephrons, have not been characterized. Here, we mapped the temporal progression of cellular and molecular changes that occur during renal epithelial regeneration of the proximal tubule in the adult zebrafish using a platform of histological and expression analysis techniques. This work establishes the timing of renal cell death after gentamicin injury, identifies proliferative compartments within the kidney, and documents gene expression changes associated with the regenerative response of proliferating cells. These data provide an important descriptive atlas that documents the series of events that ensue after damage in the zebrafish kidney, thus availing a valuable resource for the scientific community that can facilitate the implementation of zebrafish research to delineate the mechanisms that control renal regeneration.
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47
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McKee RA, Wingert RA. Zebrafish Renal Pathology: Emerging Models of Acute Kidney Injury. CURRENT PATHOBIOLOGY REPORTS 2015; 3:171-181. [PMID: 25973344 PMCID: PMC4419198 DOI: 10.1007/s40139-015-0082-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The renal system is vital to maintain homeostasis in the body, where the kidneys contain nephron functional units that remove metabolic waste from the bloodstream, regulate fluids, and balance electrolytes. Severe organ damage from toxins or ischemia that occurs abruptly can cause acute kidney injury (AKI) in which there is a rapid, life-threatening loss of these activities. Humans have a limited but poorly understood ability to regenerate damaged nephrons after AKI. However, researchers studying AKI in vertebrate animal models such as mammals, and more recently the zebrafish, have documented robust regeneration within the nephron blood filter and tubule following injury. Further, zebrafish kidneys contain progenitors that create new nephrons after AKI. Here, we review investigations in zebrafish which have established a series of exciting renal pathology paradigms that complement existing AKI models and can be implemented to discover insights into kidney regeneration and the roles of stem cells.
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Affiliation(s)
- Robert A. McKee
- Department of Biological Sciences, Center for Zebrafish Research, Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Rebecca A. Wingert
- Department of Biological Sciences, Center for Zebrafish Research, Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN 46556 USA
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48
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Levine MH, Wang Z, Bhatti TR, Wang Y, Aufhauser DD, McNeal S, Liu Y, Cheraghlou S, Han R, Wang L, Hancock WW. Class-specific histone/protein deacetylase inhibition protects against renal ischemia reperfusion injury and fibrosis formation. Am J Transplant 2015; 15:965-73. [PMID: 25708614 PMCID: PMC5493154 DOI: 10.1111/ajt.13106] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 01/25/2023]
Abstract
Renal ischemia-reperfusion injury (IRI) is a common cause of renal dysfunction and renal failure. Histone/protein deacetylases (HDACs) regulate gene accessibility and higher order protein structures and may alter cellular responses to a variety of stresses. We investigated whether use of pan- and class-specific HDAC inhibitors (HDACi) could improve IRI tolerance in the kidney. Using a model of unilateral renal IRI, we investigated early renal function after IRI, and calculated fibrosis after IRI using an automated scoring system. We found that pan-HDAC inhibition using trichostatin (TSA) yielded significant renal functional benefit at 24-96 hours (p < 0.001). Treated mice developed significantly less fibrosis at 30 days (p < 0.0004). Class I HDAC inhibition with MS-275 yielded similar effects. Protection from fibrosis formation was also noted in a cold ischemia transplant model (p < 0.008) with a trend toward improved cold ischemic survival in TSA-treated mice. These effects were not accompanied by induction of typical ischemic tolerance pathways or by priming of heat shock protein expression. In fact, heat shock protein 70 deletion or overexpression did not alter renal ischemia tolerance. Micro-RNA 21, known to be enhanced in vitro in renal tubular cells that survive stress, was enhanced by treatment with HDACi, pointing to possible mechanism.
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Affiliation(s)
- M. H. Levine
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA,Department of Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Z. Wang
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA
| | - T. R. Bhatti
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Y. Wang
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA
| | - D. D. Aufhauser
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA
| | - S. McNeal
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA
| | - Y. Liu
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - S. Cheraghlou
- Department of Surgery, Transplant Surgery, University of Pennsylvania, Philadelphia, PA
| | - R. Han
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - L. Wang
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - W. W. Hancock
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
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49
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Rennekamp AJ, Peterson RT. 15 years of zebrafish chemical screening. Curr Opin Chem Biol 2014; 24:58-70. [PMID: 25461724 DOI: 10.1016/j.cbpa.2014.10.025] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/13/2022]
Abstract
In 2000, the first chemical screen using living zebrafish in a multi-well plate was reported. Since then, more than 60 additional screens have been published describing whole-organism drug and pathway discovery projects in zebrafish. To investigate the scope of the work reported in the last 14 years and to identify trends in the field, we analyzed the discovery strategies of 64 primary research articles from the literature. We found that zebrafish screens have expanded beyond the use of developmental phenotypes to include behavioral, cardiac, metabolic, proliferative and regenerative endpoints. Additionally, many creative strategies have been used to uncover the mechanisms of action of new small molecules including chemical phenocopy, genetic phenocopy, mutant rescue, and spatial localization strategies.
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Affiliation(s)
- Andrew J Rennekamp
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Randall T Peterson
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
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50
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Poureetezadi SJ, Donahue EK, Wingert RA. A manual small molecule screen approaching high-throughput using zebrafish embryos. J Vis Exp 2014:e52063. [PMID: 25407322 PMCID: PMC4353429 DOI: 10.3791/52063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology due to their considerable degree of genetic conservation with humans. Chemical genetics entails testing the effect that small molecules have on a biological process and is becoming a popular translational research method to identify therapeutic compounds. Zebrafish are specifically appealing to use for chemical genetics because of their ability to produce large clutches of transparent embryos, which are externally fertilized. Furthermore, zebrafish embryos can be easily drug treated by the simple addition of a compound to the embryo media. Using whole-mount in situ hybridization (WISH), mRNA expression can be clearly visualized within zebrafish embryos. Together, using chemical genetics and WISH, the zebrafish becomes a potent whole organism context in which to determine the cellular and physiological effects of small molecules. Innovative advances have been made in technologies that utilize machine-based screening procedures, however for many labs such options are not accessible or remain cost-prohibitive. The protocol described here explains how to execute a manual high-throughput chemical genetic screen that requires basic resources and can be accomplished by a single individual or small team in an efficient period of time. Thus, this protocol provides a feasible strategy that can be implemented by research groups to perform chemical genetics in zebrafish, which can be useful for gaining fundamental insights into developmental processes, disease mechanisms, and to identify novel compounds and signaling pathways that have medically relevant applications.
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Affiliation(s)
| | - Eric K Donahue
- Department of Biological Sciences, University of Notre Dame
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