1
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Yoshida T, Latt KZ, Rosenberg AZ, Santo BA, Myakala K, Ishimoto Y, Zhao Y, Shrivastav S, Jones BA, Yang X, Wang XX, Tutino VM, Sarder P, Levi M, Okamoto K, Winkler CA, Kopp JB. PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy. eLife 2024; 12:RP91260. [PMID: 39207915 PMCID: PMC11361708 DOI: 10.7554/elife.91260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
HIV disease remains prevalent in the USA and chronic kidney disease remains a major cause of morbidity in HIV-1-positive patients. Host double-stranded RNA (dsRNA)-activated protein kinase (PKR) is a sensor for viral dsRNA, including HIV-1. We show that PKR inhibition by compound C16 ameliorates the HIV-associated nephropathy (HIVAN) kidney phenotype in the Tg26 transgenic mouse model, with reversal of mitochondrial dysfunction. Combined analysis of single-nucleus RNA-seq and bulk RNA-seq data revealed that oxidative phosphorylation was one of the most downregulated pathways and identified signal transducer and activator of transcription (STAT3) as a potential mediating factor. We identified in Tg26 mice a novel proximal tubular cell cluster enriched in mitochondrial transcripts. Podocytes showed high levels of HIV-1 gene expression and dysregulation of cytoskeleton-related genes, and these cells dedifferentiated. In injured proximal tubules, cell-cell interaction analysis indicated activation of the pro-fibrogenic PKR-STAT3-platelet-derived growth factor (PDGF)-D pathway. These findings suggest that PKR inhibition and mitochondrial rescue are potential novel therapeutic approaches for HIVAN.
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Affiliation(s)
- Teruhiko Yoshida
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Khun Zaw Latt
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins Medical InstitutionsBaltimoreUnited States
| | - Briana A Santo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at BuffaloBuffaloUnited States
| | - Komuraiah Myakala
- Polycystic Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Yu Ishimoto
- Frederick National Laboratory for Cancer Research, NCI, NIHFrederickUnited States
| | - Yongmei Zhao
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown UniversityWashingtonUnited States
| | - Shashi Shrivastav
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Bryce A Jones
- Polycystic Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Xiaoping Yang
- Department of Pathology, Johns Hopkins Medical InstitutionsBaltimoreUnited States
| | - Xiaoxin X Wang
- Polycystic Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Vincent M Tutino
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at BuffaloBuffaloUnited States
| | - Pinaki Sarder
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at BuffaloBuffaloUnited States
- College of Medicine, University of FloridaGainesvilleUnited States
| | - Moshe Levi
- Polycystic Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
| | - Koji Okamoto
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
- Nephrology Endocrinology and Vascular Medicine, Tohoku University HospitalSendaiJapan
| | - Cheryl A Winkler
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown UniversityWashingtonUnited States
| | - Jeffrey B Kopp
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIHBethesdaUnited States
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2
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Kato M, Chen Z, Das S, Wu X, Wang J, Li A, Chen W, Tsark W, Tunduguru R, Lanting L, Wang M, Moore R, Kalkum M, Abdollahi M, Natarajan R. Long non-coding RNA lncMGC mediates the expression of TGF-β-induced genes in renal cells via nucleosome remodelers. Front Mol Biosci 2023; 10:1204124. [PMID: 37325470 PMCID: PMC10266347 DOI: 10.3389/fmolb.2023.1204124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Background: MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) play key roles in diabetic kidney disease (DKD). The miR-379 megacluster of miRNAs and its host transcript lnc-megacluster (lncMGC) are regulated by transforming growth factor-β (TGF-β), increased in the glomeruli of diabetic mice, and promote features of early DKD. However, biochemical functions of lncMGC are unknown. Here, we identified lncMGC-interacting proteins by in vitro-transcribed lncMGC RNA pull down followed by mass spectrometry. We also created lncMGC-knockout (KO) mice by CRISPR-Cas9 editing and used primary mouse mesangial cells (MMCs) from the KO mice to examine the effects of lncMGC on the gene expression related to DKD, changes in promoter histone modifications, and chromatin remodeling. Methods: In vitro-transcribed lncMGC RNA was mixed with lysates from HK2 cells (human kidney cell line). lncMGC-interacting proteins were identified by mass spectrometry. Candidate proteins were confirmed by RNA immunoprecipitation followed by qPCR. Cas9 and guide RNAs were injected into mouse eggs to create lncMGC-KO mice. Wild-type (WT) and lncMGC-KO MMCs were treated with TGF-β, and RNA expression (by RNA-seq and qPCR) and histone modifications (by chromatin immunoprecipitation) and chromatin remodeling/open chromatin (by Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq) were examined. Results: Several nucleosome remodeling factors including SMARCA5 and SMARCC2 were identified as lncMGC-interacting proteins by mass spectrometry, and confirmed by RNA immunoprecipitation-qPCR. MMCs from lncMGC-KO mice showed no basal or TGF-β-induced expression of lncMGC. Enrichment of histone H3K27 acetylation and SMARCA5 at the lncMGC promoter was increased in TGF-β-treated WT MMCs but significantly reduced in lncMGC-KO MMCs. ATAC peaks at the lncMGC promoter region and many other DKD-related loci including Col4a3 and Col4a4 were significantly lower in lncMGC-KO MMCs compared to WT MMCs in the TGF-β-treated condition. Zinc finger (ZF), ARID, and SMAD motifs were enriched in ATAC peaks. ZF and ARID sites were also found in the lncMGC gene. Conclusion: lncMGC RNA interacts with several nucleosome remodeling factors to promote chromatin relaxation and enhance the expression of lncMGC itself and other genes including pro-fibrotic genes. The lncMGC/nucleosome remodeler complex promotes site-specific chromatin accessibility to enhance DKD-related genes in target kidney cells.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Sadhan Das
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Arthur Li
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Wei Chen
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Walter Tsark
- Transgenic Mouse Facility, Center for Comparative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Ragadeepthi Tunduguru
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Roger Moore
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Markus Kalkum
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
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3
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Fan GH, Wei RL, Wei XY, Zhang CZ, Qi ZT, Xie HY, Zheng SS, Xu X. Key factors and potential drug combinations of nonalcoholic steatohepatitis: Bioinformatic analysis and experimental validation-based study. Hepatobiliary Pancreat Dis Int 2021; 20:433-451. [PMID: 34233850 DOI: 10.1016/j.hbpd.2021.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/11/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Nonalcoholic fatty liver disease and its advanced stage, nonalcoholic steatohepatitis (NASH), are the major cause of hepatocellular carcinoma (HCC) and other end-stage liver disease. However, the potential mechanism and therapeutic strategies have not been clarified. This study aimed to identify potential roles of miRNA/mRNA axis in the pathogenesis and drug combinations in the treatment of NASH. METHODS Microarray GSE59045 and GSE48452 were downloaded from the Gene Expression Omnibus and analyzed using R. Then we obtained differentially expressed genes (DE-genes). DAVID database was used for Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis. Protein-protein interaction (PPI) networks were used for the identification of hub genes. We found upstream regulators of hub genes using miRTarBase. The expression and correlation of key miRNA and its targets were detected by qPCR. Drug Pair Seeker was employed to predict drug combinations against NASH. The expression of miRNA and hub genes in HCC was identified in the Cancer Genome Atlas database and Human Protein Atlas database. RESULTS Ninety-four DE-genes were accessed. GO and KEGG analysis showed that these predicted genes were linked to lipid metabolism. Eleven genes were identified as hub genes in PPI networks, and they were highly expressed in cells with vigorous lipid metabolism. hsa-miR-335-5p was the upstream regulator of 9 genes in the 11 hub genes, and it was identified as a key miRNA. The hub genes were highly expressed in NASH models, while hsa-miR-335-5p was lowly expressed. The correlation of miRNA-mRNA was established by qPCR. Functional verification indicated that hsa-miR-335-5p had inhibitory effect on the development of NASH. Finally, drug combinations were predicted and the expression of miRNA and hub genes in HCC was identified. CONCLUSIONS In the study, potential miRNA-mRNA pathways related to NASH were identified. Targeting these pathways may be novel strategies against NASH.
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Affiliation(s)
- Guang-Han Fan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Rong-Li Wei
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xu-Yong Wei
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Chen-Zhi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Zhe-Tuo Qi
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hai-Yang Xie
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Shu-Sen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Department of Hepatobiliary and Pancreatic Surgery, Shulan (Hangzhou) Hospital, Hangzhou 310000, China
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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4
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Meijboom KE, Volpato V, Monzón-Sandoval J, Hoolachan JM, Hammond SM, Abendroth F, de Jong OG, Hazell G, Ahlskog N, Wood MJ, Webber C, Bowerman M. Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy. JCI Insight 2021; 6:e149446. [PMID: 34236053 PMCID: PMC8410072 DOI: 10.1172/jci.insight.149446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by loss of survival motor neuron (SMN) protein. While SMN restoration therapies are beneficial, they are not a cure. We aimed to identify potentially novel treatments to alleviate muscle pathology combining transcriptomics, proteomics, and perturbational data sets. This revealed potential drug candidates for repurposing in SMA. One of the candidates, harmine, was further investigated in cell and animal models, improving multiple disease phenotypes, including lifespan, weight, and key molecular networks in skeletal muscle. Our work highlights the potential of multiple and parallel data-driven approaches for the development of potentially novel treatments for use in combination with SMN restoration therapies.
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Affiliation(s)
- Katharina E Meijboom
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Viola Volpato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Jimena Monzón-Sandoval
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Suzan M Hammond
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Paediatrics, John Radcliffe Hospital and.,MDUK Oxford Neuromuscular Centre, University of Oxford, United Kingdom
| | - Frank Abendroth
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom.,Institute of Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Olivier G de Jong
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Gareth Hazell
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Nina Ahlskog
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Paediatrics, John Radcliffe Hospital and
| | - Matthew Ja Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,Department of Paediatrics, John Radcliffe Hospital and.,MDUK Oxford Neuromuscular Centre, University of Oxford, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Melissa Bowerman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,School of Medicine, Keele University, Staffordshire, United Kingdom.,Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, United Kingdom
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5
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Liu L, Ma F, Hao Y, Yi Z, Yu X, Xu B, Wei C, Hu J. Integrative Informatics Analysis of Transcriptome and Identification of Interacted Genes in the Glomeruli and Tubules in CKD. Front Med (Lausanne) 2021; 7:615306. [PMID: 33644086 PMCID: PMC7906987 DOI: 10.3389/fmed.2020.615306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022] Open
Abstract
Chronic kidney disease (CKD) is a complex disease in which the renal function is compromised chronically. Many studies have indicated the crosstalk between the tubule and the glomerulus in CKD progression. However, our understanding of the interaction of tubular and glomerular injury remains incomplete. In this study, we applied a meta-analysis approach on the transcriptome of the tubules and glomeruli of CKD patients to identify differentially expressed genes (DEGs) signature. Functional analysis of pathways and Gene Ontology found that tubular DEGs were mainly involved in cell assembly and remodeling, glomerular DEGs in cell proliferation and apoptosis, and overlapping DEGs mainly in immune response. Correlation analysis was performed to identify the associated DEGs in the tubules and glomeruli. Secreted protein comparison and verification experiments indicated that WFDC2 from the tubule could downregulate PEX19 mRNA and protein levels at the glomeruli in diabetic kidney disease (DKD). This study revealed the distinctive pathways of the tubules and glomeruli and identified interacted genes during CKD progression.
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Affiliation(s)
- Lingyun Liu
- Department of Andrology, The First Hospital of Jilin University, Jilin, China
| | - Fuzhe Ma
- Department of Nephrology, The First Hospital of Jilin University, Jilin, China
| | - Yuanyuan Hao
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Zhengzi Yi
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Xiaoxia Yu
- Division of Nephrology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Bo Xu
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Chengguo Wei
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jinghai Hu
- Department of Urology, The First Hospital of Jilin University, Jilin, China
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6
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Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC. Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. Diabetes 2021; 70:589-602. [PMID: 33067313 PMCID: PMC7881868 DOI: 10.2337/db20-0580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
Diabetic kidney disease (DKD) remains the most common cause of kidney failure, and the treatment options are insufficient. Here, we used a connectivity mapping approach to first collect 15 gene expression signatures from 11 DKD-related published independent studies. Then, by querying the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 data set, we identified drugs and other bioactive small molecules that are predicted to reverse these gene signatures in the diabetic kidney. Among the top consensus candidates, we selected a PLK1 inhibitor (BI-2536) for further experimental validation. We found that PLK1 expression was increased in the glomeruli of both human and mouse diabetic kidneys and localized largely in mesangial cells. We also found that BI-2536 inhibited mesangial cell proliferation and extracellular matrix in vitro and ameliorated proteinuria and kidney injury in DKD mice. Further pathway analysis of the genes predicted to be reversed by the PLK1 inhibitor was of members of the TNF-α/NF-κB, JAK/STAT, and TGF-β/Smad3 pathways. In vitro, either BI-2536 treatment or knockdown of PLK1 dampened the NF-κB and Smad3 signal transduction and transcriptional activation. Together, these results suggest that the PLK1 inhibitor BI-2536 should be further investigated as a novel therapy for DKD.
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Affiliation(s)
- Lu Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zichen Wang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ruijie Liu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhengzhe Li
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer Lin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Megan L Wojciechowicz
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jiyi Huang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Renal Section, James J. Peters Veterans Affair Medical Center, Bronx, NY
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7
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Current Therapies in Nephrotic Syndrome: HDAC inhibitors, an Emerging Therapy for Kidney Diseases. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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8
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Egerman MA, Campbell KN. Podocyte histone deacetylase activity inhibition as a therapeutic strategy for glomerular disease. Kidney Int 2020; 96:1266-1268. [PMID: 31759482 DOI: 10.1016/j.kint.2019.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/21/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Marc A Egerman
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kirk N Campbell
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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9
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Williams VR, Konvalinka A, Song X, Zhou X, John R, Pei Y, Scholey JW. Connectivity mapping of a chronic kidney disease progression signature identified lysine deacetylases as novel therapeutic targets. Kidney Int 2020; 98:116-132. [PMID: 32418621 DOI: 10.1016/j.kint.2020.01.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/25/2022]
Abstract
Tubulointerstitial injury is an important determinant of chronic kidney disease progression, yet treatment is limited. Accordingly, we derived a chronic kidney disease progression signature based on aging and disease in Col4a3-/- mice, a model associated with proteinuria and progressive loss of kidney function. Computational drug repurposing with the Connectivity Map identified vorinostat, a lysine deacetylase inhibitor, as a candidate treatment to reverse progression signature gene expression. Vorinostat administration significantly increased the lifespan of Col4a3-/- mice and attenuated tubulointerstitial fibrosis and JNK phosphorylation in the kidneys of Col4a3-/- mice. In vitro, vorinostat reduced albumin- and angiotensin II-induced activation of canonical mitogen-activated protein kinases in kidney tubular epithelial cells. Finally, a subset of murine progression signature genes was differentially expressed across kidney transcriptomic data from patients with focal segmental glomerulosclerosis, IgA nephropathy, and diabetic nephropathy. Thus, our findings suggest that lysine deacetylase inhibition may be a novel treatment to chronic kidney disease associated with proteinuria and progressive tubulointerstitial injury.
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Affiliation(s)
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Division of Nephrology, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Xuewen Song
- Division of Nephrology, University Health Network, Toronto, Canada
| | - Xiaohua Zhou
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Rohan John
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology, University Health Network, Toronto, Canada
| | - York Pei
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Division of Nephrology, University Health Network, Toronto, Canada
| | - James W Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Division of Nephrology, University Health Network, Toronto, Canada; Department of Physiology, University of Toronto, Toronto, Canada
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10
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Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021211] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form of perturbations. Such resources enable the characterization of signatures from novel perturbations based on similarity; provide a global view of the space of many themed perturbations; and allow the ability to predict cellular, tissue, and organismal phenotypes for perturbagens. A signature search engine enables hypothesis generation by finding connections between query signatures and the database of signatures. This framework has been used to identify connections between small molecules and their targets, to discover cell-specific responses to perturbations and ways to reverse disease expression states with small molecules, and to predict small-molecule mimickers for existing drugs. This review provides a historical perspective and the current state of connectivity mapping resources with a focus on both methodology and community implementations.
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Affiliation(s)
- Alexandra B. Keenan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan L. Wojciechowicz
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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11
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Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. Comput Struct Biotechnol J 2019; 17:843-853. [PMID: 31316728 PMCID: PMC6611921 DOI: 10.1016/j.csbj.2019.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/27/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023] Open
Abstract
Aging is a major driver for chronic kidney disease (CKD) and the counterbalancing of aging processes holds promise to positively impact disease development and progression. In this study we generated a signature of renal age-associated genes (RAAGs) based on six different data sources including transcriptomics data as well as data extracted from scientific literature and dedicated databases. Protein abundance in renal tissue of the 634 identified RAAGs was studied next to the analysis of affected molecular pathways. RAAG expression profiles were furthermore analysed in a cohort of 63 CKD patients with available follow-up data to determine association with CKD progression. 23 RAAGs were identified showing concordant regulation in renal aging and CKD progression. This set was used as input to computationally screen for compounds with the potential of reversing the RAAG/CKD signature on the transcriptional level. Among the top-ranked drugs we identified atorvastatin, captopril, valsartan, and rosiglitazone, which are widely used in clinical practice for the treatment of patients with renal and cardiovascular diseases. Their positive impact on the RAAG/CKD signature could be validated in an in-vitro model of renal aging. In summary, we have (i) consolidated a set of RAAGs, (ii) determined a subset of RAAGs with concordant regulation in CKD progression, and (iii) identified a set of compounds capable of reversing the proposed RAAG/CKD signature.
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12
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Hansen J, Galatioto J, Caescu CI, Arnaud P, Calizo RC, Spronck B, Murtada SI, Borkar R, Weinberg A, Azeloglu EU, Bintanel-Morcillo M, Gallo JM, Humphrey JD, Jondeau G, Boileau C, Ramirez F, Iyengar R. Systems pharmacology-based integration of human and mouse data for drug repurposing to treat thoracic aneurysms. JCI Insight 2019; 4:127652. [PMID: 31167969 DOI: 10.1172/jci.insight.127652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Marfan syndrome (MFS) is associated with mutations in fibrillin-1 that predispose afflicted individuals to progressive thoracic aortic aneurysm (TAA) leading to dissection and rupture of the vessel wall. Here we combined computational and experimental approaches to identify and test FDA-approved drugs that may slow or even halt aneurysm progression. Computational analyses of transcriptomic data derived from the aortas of MFS patients and MFS mice (Fbn1mgR/mgR mice) predicted that subcellular pathways associated with reduced muscle contractility are key TAA determinants that could be targeted with the GABAB receptor agonist baclofen. Systemic administration of baclofen to Fbn1mgR/mgR mice validated our computational prediction by mitigating arterial disease progression at the cellular and physiological levels. Interestingly, baclofen improved muscle contraction-related subcellular pathways by upregulating a different set of genes than those downregulated in the aorta of vehicle-treated Fbn1mgR/mgR mice. Distinct transcriptomic profiles were also associated with drug-treated MFS and wild-type mice. Thus, systems pharmacology approaches that compare patient- and mouse-derived transcriptomic data for subcellular pathway-based drug repurposing represent an effective strategy to identify potential new treatments of human diseases.
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Affiliation(s)
- Jens Hansen
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josephine Galatioto
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cristina I Caescu
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pauline Arnaud
- Département de Génétique et Centre de Référence Maladies Rares Syndrome de Marfan et Pathologies Apparentées, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France.,LVTS, INSERM U1148, Université Paris Diderot, Hôpital Bichat, Paris, France
| | - Rhodora C Calizo
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bart Spronck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
| | - Sae-Il Murtada
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
| | - Roshan Borkar
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Alan Weinberg
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Evren U Azeloglu
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maria Bintanel-Morcillo
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Jay D Humphrey
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
| | - Guillaume Jondeau
- Département de Génétique et Centre de Référence Maladies Rares Syndrome de Marfan et Pathologies Apparentées, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France.,LVTS, INSERM U1148, Université Paris Diderot, Hôpital Bichat, Paris, France
| | - Catherine Boileau
- Département de Génétique et Centre de Référence Maladies Rares Syndrome de Marfan et Pathologies Apparentées, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France.,LVTS, INSERM U1148, Université Paris Diderot, Hôpital Bichat, Paris, France
| | - Francesco Ramirez
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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13
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Dolomatov S, Zukow W, Novikov N, Markaryan A, Eremeeva E. EXPRESSION OF THE RENIN-ANGIOTENSIN SYSTEM COMPONENTS IN ONCOLOGIC DISEASES. Acta Clin Croat 2019; 58:354-364. [PMID: 31819334 PMCID: PMC6884393 DOI: 10.20471/acc.2019.58.02.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The literature devoted to changes in the expression of the renin-angiotensin system (RAS) proteins of cancer cells was analyzed. The dynamics of RAS protein expression in malignant tumors and the possible role of epigenetic mechanisms in these processes are briefly reviewed. Through research of the epigenetic mechanisms in cancer, principally new techniques for their correction based on the use of selective regulatory systems of covalent modification of histone proteins (for example, deacetylase inhibitor) and microRNA synthesis technologies have been developed. Literature data show promising pharmacological correction of epigenetic modification of chromatin in the treatment of cancer.
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Affiliation(s)
| | - Walery Zukow
- 1Department of Medical Biology, Medical Academy SI Georgievsky, Crimea Federal University, Simferopol, Russian Federation jurisdiction; 2Faculty of Earth, Nicolaus Copernicus University, Toruń, Poland; 3A. Tsyb Medical Radiological Research Center, branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Kaluga Region, Russian Federation
| | - Nikolay Novikov
- 1Department of Medical Biology, Medical Academy SI Georgievsky, Crimea Federal University, Simferopol, Russian Federation jurisdiction; 2Faculty of Earth, Nicolaus Copernicus University, Toruń, Poland; 3A. Tsyb Medical Radiological Research Center, branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Kaluga Region, Russian Federation
| | - Alexandra Markaryan
- 1Department of Medical Biology, Medical Academy SI Georgievsky, Crimea Federal University, Simferopol, Russian Federation jurisdiction; 2Faculty of Earth, Nicolaus Copernicus University, Toruń, Poland; 3A. Tsyb Medical Radiological Research Center, branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Kaluga Region, Russian Federation
| | - Elena Eremeeva
- 1Department of Medical Biology, Medical Academy SI Georgievsky, Crimea Federal University, Simferopol, Russian Federation jurisdiction; 2Faculty of Earth, Nicolaus Copernicus University, Toruń, Poland; 3A. Tsyb Medical Radiological Research Center, branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Kaluga Region, Russian Federation
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14
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Regan-Fendt KE, Xu J, DiVincenzo M, Duggan MC, Shakya R, Na R, Carson WE, Payne PRO, Li F. Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. NPJ Syst Biol Appl 2019; 5:6. [PMID: 30820351 PMCID: PMC6391384 DOI: 10.1038/s41540-019-0085-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Systems biology perspectives are crucial for understanding the pathophysiology of complex diseases, and therefore hold great promise for the discovery of novel treatment strategies. Drug combinations have been shown to improve durability and reduce resistance to available first-line therapies in a variety of cancers; however, traditional drug discovery approaches are prohibitively cost and labor-intensive to evaluate large-scale matrices of potential drug combinations. Computational methods are needed to efficiently model complex interactions of drug target pathways and identify mechanisms underlying drug combination synergy. In this study, we employ a computational approach, SynGeNet (Synergy from Gene expression and Network mining), which integrates transcriptomics-based connectivity mapping and network centrality analysis to analyze disease networks and predict drug combinations. As an exemplar of a disease in which combination therapies demonstrate efficacy in genomic-specific contexts, we investigate malignant melanoma. We employed SynGeNet to generate drug combination predictions for each of the four major genomic subtypes of melanoma (BRAF, NRAS, NF1, and triple wild type) using publicly available gene expression and mutation data. We validated synergistic drug combinations predicted by our method across all genomic subtypes using results from a high-throughput drug screening study across. Finally, we prospectively validated the drug combination for BRAF-mutant melanoma that was top ranked by our approach, vemurafenib (BRAF inhibitor) + tretinoin (retinoic acid receptor agonist), using both in vitro and in vivo models of BRAF-mutant melanoma and RNA-sequencing analysis of drug-treated melanoma cells to validate the predicted mechanisms. Our approach is applicable to a wide range of disease domains, and, importantly, can model disease-relevant protein subnetworks in precision medicine contexts.
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Affiliation(s)
- Kelly E Regan-Fendt
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Jielin Xu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Mallory DiVincenzo
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Megan C Duggan
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Reena Shakya
- Target Validation Shared Resource, The Ohio State University, Columbus, OH, USA
| | - Ryejung Na
- Target Validation Shared Resource, The Ohio State University, Columbus, OH, USA
| | - William E Carson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip R O Payne
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA
| | - Fuhai Li
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA.
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15
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Yang X, Huang WT, Wu HY, He RQ, Ma J, Liu AG, Chen G. Novel drug candidate for the treatment of several soft‑tissue sarcoma histologic subtypes: A computational method using survival‑associated gene signatures for drug repurposing. Oncol Rep 2019; 41:2241-2253. [PMID: 30816547 PMCID: PMC6412453 DOI: 10.3892/or.2019.7033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/22/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic treatment options for soft tissue sarcomas (STSs) have remained unchanged despite the need for novel drug candidates to improve STS outcomes. Drug repurposing involves the application of clinical drugs to different diseases, reducing development time, and cost. It has also become a fast and effective way to identify drug candidates. The present study used a computational method to screen three drug-gene interaction databases for novel drug candidates for the treatment of several common STS histologic subtypes through drug repurposing. STS survival-associated genes were generated by conducting a univariate cox regression analysis using The Cancer Genome Atlas survival data. These genes were then applied to three databases (the Connectivity Map, the Drug Gene Interaction Database and the L1000 Fireworks Display) to identify drug candidates for STS treatment. Additionally, pathway analysis and molecular docking were conducted to evaluate the molecular mechanisms of the candidate drug. Bepridil was identified as a potential candidate for several STS histologic subtype treatments by overlapping the screening results from three drug-gene interaction databases. The pathway analysis with the Kyoto Encyclopedia of Genes and Genomes predicted that Bepridil may target CRK, fibroblast growth factor receptor 4 (FGFR4), laminin subunit β1 (LAMB1), phosphoinositide-3-kinase regulatory subunit 2 (PIK3R2), WNT5A, cluster of differentiation 47 (CD47), elastase, neutrophil expressed (ELANE), 15-hydroxyprostaglandin dehydrogenase (HPGD) and protein kinase cβ (PRKCB) to suppress STS development. Further molecular docking simulation suggested a relatively stable binding selectivity between Bepridil and eight proteins (CRK, FGFR4, LAMB1, PIK3R2, CD47, ELANE, HPGD, and PRKCB). In conclusion, a computational method was used to identify Bepridil as a potential candidate for the treatment of several common STS histologic subtypes. Experimental validation of these in silico results is necessary before clinical translation can occur.
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Affiliation(s)
- Xia Yang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Wen-Ting Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Hua-Yu Wu
- Department of Cell Biology and Genetics, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - An-Gui Liu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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16
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Inoue K, Gan G, Ciarleglio M, Zhang Y, Tian X, Pedigo CE, Cavanaugh C, Tate J, Wang Y, Cross E, Groener M, Chai N, Wang Z, Justice A, Zhang Z, Parikh CR, Wilson FP, Ishibe S. Podocyte histone deacetylase activity regulates murine and human glomerular diseases. J Clin Invest 2019; 129:1295-1313. [PMID: 30776024 DOI: 10.1172/jci124030] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
We identified 2 genes, histone deacetylase 1 (HDAC1) and HDAC2, contributing to the pathogenesis of proteinuric kidney diseases, the leading cause of end-stage kidney disease. mRNA expression profiling from proteinuric mouse glomeruli was linked to Connectivity Map databases, identifying HDAC1 and HDAC2 with the differentially expressed gene set reversible by HDAC inhibitors. In numerous progressive glomerular disease models, treatment with valproic acid (a class I HDAC inhibitor) or SAHA (a pan-HDAC inhibitor) mitigated the degree of proteinuria and glomerulosclerosis, leading to a striking increase in survival. Podocyte HDAC1 and HDAC2 activities were increased in mice podocytopathy models, and podocyte-associated Hdac1 and Hdac2 genetic ablation improved proteinuria and glomerulosclerosis. Podocyte early growth response 1 (EGR1) was increased in proteinuric patients and mice in an HDAC1- and HDAC2-dependent manner. Loss of EGR1 in mice reduced proteinuria and glomerulosclerosis. Longitudinal analysis of the multicenter Veterans Aging Cohort Study demonstrated a 30% reduction in mean annual loss of estimated glomerular filtration rate, and this effect was more pronounced in proteinuric patients receiving valproic acid. These results strongly suggest that inhibition of HDAC1 and HDAC2 activities may suppress the progression of human proteinuric kidney diseases through the regulation of EGR1.
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Affiliation(s)
| | - Geliang Gan
- Yale School of Public Health, Department of Biostatistics, Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Maria Ciarleglio
- Yale School of Public Health, Department of Biostatistics, Yale Center for Analytical Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yan Zhang
- State Key Laboratory of Organ Failure Research, Nanfang Hospital.,Department of Cardiology, Nanfang Hospital, and.,Center for Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | | | | | - Corey Cavanaugh
- Department of Internal Medicine, and.,Program of Applied Translational Research, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Janet Tate
- VA Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Ying Wang
- Department of Internal Medicine, and
| | | | | | | | - Zhen Wang
- Department of Internal Medicine, and
| | - Amy Justice
- Department of Internal Medicine, and.,VA Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, Nanfang Hospital.,Department of Cardiology, Nanfang Hospital, and.,Center for Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Chirag R Parikh
- Department of Internal Medicine, Division of Nephrology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francis P Wilson
- Department of Internal Medicine, and.,Program of Applied Translational Research, Yale University School of Medicine, New Haven, Connecticut, USA
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17
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Pang JS, Li ZK, Lin P, Wang XD, Chen G, Yan HB, Li SH. The underlying molecular mechanism and potential drugs for treatment in papillary renal cell carcinoma: A study based on TCGA and Cmap datasets. Oncol Rep 2019; 41:2089-2102. [PMID: 30816528 PMCID: PMC6412146 DOI: 10.3892/or.2019.7014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
Papillary renal cell carcinoma (PRCC) accounts for 15–20% of all kidney neoplasms and continually attracts attention due to the increase in the incidents in which it occurs. The molecular mechanism of PRCC remains unclear and the efficacy of drugs that treat PRCC lacks sufficient evidence in clinical trials. Therefore, it is necessary to investigate the underlying mechanism in the development of PRCC and identify additional potential anti-PRCC drugs for its treatment. The differently expressed genes (DEGs) of PRCC were identified, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for functional annotation. Then, potential drugs for PRCC treatment were predicted by Connectivity Map (Cmap) based on DEGs. Furthermore, the latent function of query drugs in PRCC was explored by integrating drug-target, drug-pathway and drug-protein interactions. In total, 627 genes were screened as DEGs, and these DEGs were annotated using KEGG pathway analyses and were clearly associated with the complement and coagulation cascades, amongst others. Then, 60 candidate drugs, as predicted based on DEGs, were obtained from the Cmap database. Vorinostat was considered as the most promising drug for detailed discussion. Following protein-protein interaction (PPI) analysis and molecular docking, vorinostat was observed to interact with C3 and ANXN1 proteins, which are the upregulated hub genes and may serve as oncologic therapeutic targets in PRCC. Among the top 20 metabolic pathways, several significant pathways, such as complement and coagulation cascades and cell adhesion molecules, may greatly contribute to the development and progression of PRCC. Following the performance of the PPI network and molecular docking tests, vorinostat exhibited a considerable and promising application in PRCC treatment by targeting C3 and ANXN1.
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Affiliation(s)
- Jin-Shu Pang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zhe-Kun Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Peng Lin
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Dong Wang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Hai-Biao Yan
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Sheng-Hua Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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18
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Rednor SJ, Ross MJ. Molecular Mechanisms of Injury in HIV-Associated Nephropathy. Front Med (Lausanne) 2018; 5:177. [PMID: 29930940 PMCID: PMC5999756 DOI: 10.3389/fmed.2018.00177] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/22/2018] [Indexed: 11/15/2022] Open
Abstract
HIV-associated nephropathy (HIVAN) is an important cause of secondary focal glomerulosclerosis that occurs primarily in persons of African ancestry with advanced HIV disease. Although HIVAN is characterized by severe proteinuria and rapid progression to end stage renal disease without treatment, the phenotype is markedly attenuated by treatment with antiretroviral medications. HIV infection of glomerular and tubular epithelial cells and subsequent viral gene expression is a key contributor to HIVAN pathogenesis and the kidney can serve as reservoir for HIV strains that differ those in blood. HIV gene expression in renal epithelial cells leads to dysregulation of cellular pathways including cell cycle, inflammation, cell death, and cytoskeletal homeostasis. Polymorphisms in the APOL1 gene explain the marked predilection of HIVAN to occur in persons of African descent and HIVAN. Since HIVAN has the strongest association with APOL1 genotype of any of the APOL1-associated nephropathies, studies to determine the mechanisms by which HIV and APOL1 risk variants together promote kidney injury hold great promise to improve our understanding of the pathogenesis of APOL1-mediated kidney diseases.
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Affiliation(s)
- Samuel J Rednor
- Division of Nephrology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, United States
| | - Michael J Ross
- Division of Nephrology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, United States.,Department of Development and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States
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19
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Histone deacetylase inhibitors protect against cisplatin-induced acute kidney injury by activating autophagy in proximal tubular cells. Cell Death Dis 2018; 9:322. [PMID: 29476062 PMCID: PMC5833747 DOI: 10.1038/s41419-018-0374-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/23/2018] [Accepted: 02/05/2018] [Indexed: 12/17/2022]
Abstract
Histone deacetylase inhibitors (HDACi) have therapeutic effects in models of various renal diseases including acute kidney injury (AKI); however, the underlying mechanism remains unclear. Here we demonstrate that two widely tested HDACi (suberoylanilide hydroxamic acid (SAHA) and trichostatin A (TSA)) protect the kidneys in cisplatin-induced AKI by enhancing autophagy. In cultured renal proximal tubular cells, SAHA and TSA enhanced autophagy during cisplatin treatment. We further verified the protective effect of TSA against cisplatin-induced apoptosis in these cells. Notably, inhibition of autophagy by chloroquine or by autophagy gene 7 (Atg7) ablation diminished the protective effect of TSA. In mice, TSA increased autophagy in renal proximal tubules and protected against cisplatin-induced AKI. The in vivo effect of TSA was also abolished by chloroquine and by Atg7 knockout specifically from renal proximal tubules. Mechanistically, TSA stimulated AMPK and inactivated mTOR during cisplatin treatment of proximal tubule cells and kidneys in mice. Together, these results suggest that HDACi may protect kidneys by activating autophagy in proximal tubular cells.
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20
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Brum AM, van de Peppel J, Nguyen L, Aliev A, Schreuders-Koedam M, Gajadien T, van der Leije CS, van Kerkwijk A, Eijken M, van Leeuwen JPTM, van der Eerden BCJ. Using the Connectivity Map to discover compounds influencing human osteoblast differentiation. J Cell Physiol 2018; 233:4895-4906. [PMID: 29194609 DOI: 10.1002/jcp.26298] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/28/2017] [Indexed: 12/24/2022]
Abstract
Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. Identification of factors influencing osteoblast differentiation and bone formation is very important. Previously, we identified parbendazole to be a novel compound that stimulates osteogenic differentiation of human mesenchymal stromal cells (hMSCs), using gene expression profiling and bioinformatic analyzes, including the Connectivity Map (CMap), as an in-silico approach. The aim for this paper is to identify additional compounds affecting osteoblast differentiation using the CMap. Gene expression profiling was performed on hMSCs differentiated to osteoblasts using Illumina microarrays. Our osteoblast gene signature, the top regulated genes 6 hr after induction by dexamethasone, was uploaded into CMap (www.broadinstitute.org/cmap/). Through this approach we identified compounds with gene signatures positively correlating (withaferin-A, calcium folinate, amylocaine) or negatively correlating (salbutamol, metaraminol, diprophylline) to our osteoblast gene signature. All positively correlating compounds stimulated osteogenic differentiation, as indicated by increased mineralization compared to control treated cells. One of three negatively correlating compounds, salbutamol, inhibited dexamethasone-induced osteoblastic differentiation, while the other two had no effect. Based on gene expression data of withaferin-A and salbutamol, we identified HMOX1 and STC1 as being strongly differentially expressed . shRNA knockdown of HMOX1 or STC1 in hMSCs inhibited osteoblast differentiation. These results confirm that the CMap is a powerful approach to identify positively compounds that stimulate osteogenesis of hMSCs, and through this approach we can identify genes that play an important role in osteoblast differentiation and could be targets for novel bone anabolic therapies.
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Affiliation(s)
- Andrea M Brum
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Linh Nguyen
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Abidin Aliev
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Tarini Gajadien
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | | | - B C J van der Eerden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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21
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Talevi A. Drug repositioning: current approaches and their implications in the precision medicine era. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1424535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alan Talevi
- Laboratory of Research and Development of Bioactive Compounds – Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata, La Plata, Argentina
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22
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Expression and activity of angiotensin-regulating enzymes is associated with prognostic outcome in clear cell renal cell carcinoma patients. PLoS One 2017; 12:e0181711. [PMID: 28809959 PMCID: PMC5557356 DOI: 10.1371/journal.pone.0181711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 07/06/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of the intrarenal renin-angiotensin system (iRAS), which regulates angiogenesis, cell differentiation and proliferation, has opened new perspectives in the knowledge of kidney carcinogenesis. In this study we analyzed the immunohistochemical expression and fluorimetric activity of four key peptidases of iRAS in tumor tissue (n = 144) and serum samples (n = 128) from patients with renal neoplasms. Neutral endopeptidase (NEP/CD10), Angiotensin-converting enzyme-2 (ACE2), and aminopeptidase A (APA) were expressed in tumor cells whilst Angiotensin-converting enzyme (ACE) was expressed in the endothelial cells of intratumor blood vessels. The expression of ACE, ACE2 and NEP/CD10 was highest in clear cell renal cell carcinoma (CCRCC) and papillary renal cell carcinoma (PRCC). The expression of these enzymes correlated with CCRCC aggressiveness. In addition, NEP/CD10 correlated with 15-year overall survival. On the other hand, APA expression was decreased in CCRCC with higher grade and stage. The loss of expression of APA independently correlated with a worse 15-year overall survival. Serum activity of ACE2, NEP/CD10 and APA was significantly higher in renal tumor patients than in healthy subjects. Serum ACE activity was lower in high grade and metastatic CCRCC patients, and NEP/CD10 activity was negatively correlated with UISS (UCLA Integrated Staging System) and SSIGN (Mayo Clinic stage, size, grade and necrosis model) scores and with overall survival of CCRCC patients. These results suggest a metabolic imbalance of iRAS in renal tumors. This finding should be taken into account in the search of new diagnostic, prognostic and therapeutic tools for this disease.
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23
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Schena FP, Nistor I, Curci C. Transcriptomics in kidney biopsy is an untapped resource for precision therapy in nephrology: a systematic review. Nephrol Dial Transplant 2017; 33:1094-1102. [DOI: 10.1093/ndt/gfx211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Ionut Nistor
- Nephrology Department, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
- Methods Support Team ERBP, Ghent University, Ghent, Belgium
| | - Claudia Curci
- University of Bari, Bari, Italy
- Schena Foundation, Valenzano, Italy
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24
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Regan KE, Payne PR, Li F. Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017; 2017:247-256. [PMID: 28815138 PMCID: PMC5543336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Computational methods for drug combination predictions are needed to identify effective therapies that improve durability and prevent drug resistance in an efficient manner. In this paper, we present SynGeNet, a computational method that integrates transcriptomics data characterizing disease and drug z-score profiles with network mining algorithms in order to predict synergistic drug combinations. We compare SynGeNet to other available transcriptomics-based tools to predict drug combinations validated across melanoma cell lines in three genotype groups: BRAF-mutant, NRAS-mutant and combined. We showed that SynGeNet outperforms other available tools in predicting validated drug combinations and single agents tested as part of additional drug pairs. Interestingly, we observed that the performance of SynGeNet decreased when the network construction step was removed and improved when the proportion of matched-genotype validation cell lines increased. These results suggest that delineating functional information from transcriptomics data via network mining and genomic features can improve drug combination predictions.
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Affiliation(s)
- Kelly E. Regan
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Philip R.O. Payne
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA
| | - Fuhai Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
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25
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Wanner N, Bechtel-Walz W. Epigenetics of kidney disease. Cell Tissue Res 2017; 369:75-92. [PMID: 28286899 DOI: 10.1007/s00441-017-2588-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation and histone modifications determine renal programming and the development and progression of renal disease. The identification of the way in which the renal cell epigenome is altered by environmental modifiers driving the onset and progression of renal diseases has extended our understanding of the pathophysiology of kidney disease progression. In this review, we focus on current knowledge concerning the implications of epigenetic modifications during renal disease from early development to chronic kidney disease progression including renal fibrosis, diabetic nephropathy and the translational potential of identifying new biomarkers and treatments for the prevention and therapy of chronic kidney disease and end-stage kidney disease.
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Affiliation(s)
- Nicola Wanner
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Center for Systems Biology (ZBSA), Albert-Ludwigs-University, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
| | - Wibke Bechtel-Walz
- Department of Medicine IV, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Renal Division, University Hospital Freiburg, Breisacher Strasse 66, 79106, Freiburg, Germany.
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26
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Malard F, Harousseau JL, Mohty M. Multiple myeloma treatment at relapse after autologous stem cell transplantation: A practical analysis. Cancer Treat Rev 2016; 52:41-47. [PMID: 27888768 DOI: 10.1016/j.ctrv.2016.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/19/2016] [Accepted: 11/05/2016] [Indexed: 11/30/2022]
Abstract
Over the past decade, significant advances have been made in the field of multiple myeloma. Introduction of the so-called novel agents, proteasome inhibitors (PI) and immunomodulatory drugs (IMiD), and improved supportive care have resulted in significantly better outcome. Standard first line treatment in fit patients include PI and IMiD based induction, high dose melphalan with autologous hematopoietic stem cell transplantation (ASCT) and consolidation/maintenance. However, despite these progresses MM remains incurable for the majority of patients and most patients will relapse. Next generation PI (carfilzomib, ixazomib) and IMiD (pomalidomide) and new therapeutic classes: monoclonal antibody (elotuzumab, daratumumab) and pan-deacetylase inhibitors (panobinostat) have been successfully evaluated in relapse multiple myeloma. Some of these new agents are now approved for multiple myeloma treatment at relapse. However choosing the most appropriate treatment at relapse may be difficult. This review sum up the most important studies and provide evidence to choose the most relevant therapeutic strategy for relapse after ASCT, based on disease, patient and previous treatment related parameters.
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Affiliation(s)
- F Malard
- Department of Haematology, Saint Antoine Hospital, Paris, France; INSERM UMRs 938, Paris, France; Université Pierre et Marie Curie, Paris, France.
| | | | - M Mohty
- Department of Haematology, Saint Antoine Hospital, Paris, France; INSERM UMRs 938, Paris, France; Université Pierre et Marie Curie, Paris, France
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27
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Urinary peptidomics provides a noninvasive humanized readout of diabetic nephropathy in mice. Kidney Int 2016; 90:1045-1055. [DOI: 10.1016/j.kint.2016.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/25/2016] [Accepted: 06/16/2016] [Indexed: 01/31/2023]
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28
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Schneider L, Stöckel D, Kehl T, Gerasch A, Ludwig N, Leidinger P, Huwer H, Tenzer S, Kohlbacher O, Hildebrandt A, Kaufmann M, Gessler M, Keller A, Meese E, Graf N, Lenhof HP. DrugTargetInspector: An assistance tool for patient treatment stratification. Int J Cancer 2016; 138:1765-76. [PMID: 26501925 DOI: 10.1002/ijc.29897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/16/2015] [Accepted: 10/08/2015] [Indexed: 12/21/2022]
Abstract
Cancer is a large class of diseases that are characterized by a common set of features, known as the Hallmarks of cancer. One of these hallmarks is the acquisition of genome instability and mutations. This, combined with high proliferation rates and failure of repair mechanisms, leads to clonal evolution as well as a high genotypic and phenotypic diversity within the tumor. As a consequence, treatment and therapy of malignant tumors is still a grand challenge. Moreover, under selective pressure, e.g., caused by chemotherapy, resistant subpopulations can emerge that then may lead to relapse. In order to minimize the risk of developing multidrug-resistant tumor cell populations, optimal (combination) therapies have to be determined on the basis of an in-depth characterization of the tumor's genetic and phenotypic makeup, a process that is an important aspect of stratified medicine and precision medicine. We present DrugTargetInspector (DTI), an interactive assistance tool for treatment stratification. DTI analyzes genomic, transcriptomic, and proteomic datasets and provides information on deregulated drug targets, enriched biological pathways, and deregulated subnetworks, as well as mutations and their potential effects on putative drug targets and genes of interest. To demonstrate DTI's broad scope of applicability, we present case studies on several cancer types and different types of input -omics data. DTI's integrative approach allows users to characterize the tumor under investigation based on various -omics datasets and to elucidate putative treatment options based on clinical decision guidelines, but also proposing additional points of intervention that might be neglected otherwise. DTI can be freely accessed at http://dti.bioinf.uni-sb.de.
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Affiliation(s)
- Lara Schneider
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Daniel Stöckel
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Andreas Gerasch
- Center for Bioinformatics, Eberhard-Karls-University, Tübingen, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Petra Leidinger
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Hanno Huwer
- Department of Cardiothoracic Surgery, Völklingen Heart Center, Völklingen, Germany
| | - Stefan Tenzer
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, Eberhard-Karls-University, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andreas Hildebrandt
- Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michael Kaufmann
- Center for Bioinformatics, Eberhard-Karls-University, Tübingen, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
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29
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Rapid Identification of Potential Drugs for Diabetic Nephropathy Using Whole-Genome Expression Profiles of Glomeruli. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1634730. [PMID: 27069916 PMCID: PMC4812204 DOI: 10.1155/2016/1634730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/25/2016] [Accepted: 02/08/2016] [Indexed: 12/26/2022]
Abstract
Objective. To investigate potential drugs for diabetic nephropathy (DN) using whole-genome expression profiles and the Connectivity Map (CMAP). Methodology. Eighteen Chinese Han DN patients and six normal controls were included in this study. Whole-genome expression profiles of microdissected glomeruli were measured using the Affymetrix human U133 plus 2.0 chip. Differentially expressed genes (DEGs) between late stage and early stage DN samples and the CMAP database were used to identify potential drugs for DN using bioinformatics methods. Results. (1) A total of 1065 DEGs (FDR < 0.05 and fold change > 1.5) were found in late stage DN patients compared with early stage DN patients. (2) Piperlongumine, 15d-PGJ2 (15-delta prostaglandin J2), vorinostat, and trichostatin A were predicted to be the most promising potential drugs for DN, acting as NF-κB inhibitors, histone deacetylase inhibitors (HDACIs), PI3K pathway inhibitors, or PPARγ agonists, respectively. Conclusion. Using whole-genome expression profiles and the CMAP database, we rapidly predicted potential DN drugs, and therapeutic potential was confirmed by previously published studies. Animal experiments and clinical trials are needed to confirm both the safety and efficacy of these drugs in the treatment of DN.
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30
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Wang Z, Zeng C, Villar VAM, Chen SY, Konkalmatt P, Wang X, Asico LD, Jones JE, Yang Y, Sanada H, Felder RA, Eisner GM, Weir MR, Armando I, Jose PA. Human GRK4γ142V Variant Promotes Angiotensin II Type I Receptor-Mediated Hypertension via Renal Histone Deacetylase Type 1 Inhibition. Hypertension 2015; 67:325-34. [PMID: 26667412 DOI: 10.1161/hypertensionaha.115.05962] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022]
Abstract
The influence of a single gene on the pathogenesis of essential hypertension may be difficult to ascertain, unless the gene interacts with other genes that are germane to blood pressure regulation. G-protein-coupled receptor kinase type 4 (GRK4) is one such gene. We have reported that the expression of its variant hGRK4γ(142V) in mice results in hypertension because of impaired dopamine D1 receptor. Signaling through dopamine D1 receptor and angiotensin II type I receptor (AT1R) reciprocally modulates renal sodium excretion and blood pressure. Here, we demonstrate the ability of the hGRK4γ(142V) to increase the expression and activity of the AT1R. We show that hGRK4γ(142V) phosphorylates histone deacetylase type 1 and promotes its nuclear export to the cytoplasm, resulting in increased AT1R expression and greater pressor response to angiotensin II. AT1R blockade and the deletion of the Agtr1a gene normalize the hypertension in hGRK4γ(142V) mice. These findings illustrate the unique role of GRK4 by targeting receptors with opposite physiological activity for the same goal of maintaining blood pressure homeostasis, and thus making the GRK4 a relevant therapeutic target to control blood pressure.
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Affiliation(s)
- Zheng Wang
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Chunyu Zeng
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Van Anthony M Villar
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Shi-You Chen
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Prasad Konkalmatt
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Xiaoyan Wang
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Laureano D Asico
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - John E Jones
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Yu Yang
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Hironobu Sanada
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Robin A Felder
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Gilbert M Eisner
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Matthew R Weir
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Ines Armando
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Pedro A Jose
- From the Division of Pediatric Nephrology, Department of Pediatrics, Georgetown University of School of Medicine, Washington, DC (Z.W.); Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China (C.Z.); Chongqing Institute of Cardiology, Chongqing, P.R. China; Division of Nephrology, Department of Medicine (V.A.M.V., X.W., L.D.A., J.E.J., Y.Y., M.R.W., I.A., P.A.J.) and Department of Physiology (P.A.J.), University of Maryland School of Medicine, Baltimore, MD; Department of Physiology and Pharmacology, University of Georgia, Athens, GA (S.-Y.C.); Division of Health Science Research, Fukushima Welfare Federation of Agricultural Cooperatives, Fukushima, Japan (H.S.); Department of Pathology, The University of Virginia Health Sciences Center, Charlottesville (R.A.F.); Department of Medicine, Georgetown University Medical Center, Washington, DC (G.M.E.); Division of Renal Diseases and Hypertension, Department of Medicine (P.A.J.) and Department of Physiology (P.A.J.), The George Washington University School of Medicine and Health Sciences, Washington, DC.
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Brum AM, van de Peppel J, van der Leije CS, Schreuders-Koedam M, Eijken M, van der Eerden BCJ, van Leeuwen JPTM. Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway. Proc Natl Acad Sci U S A 2015; 112:12711-6. [PMID: 26420877 PMCID: PMC4611615 DOI: 10.1073/pnas.1501597112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. In this study, we have identified pathways that stimulate differentiation of bone forming osteoblasts from human mesenchymal stromal cells (hMSCs). Gene expression profiling was performed in hMSCs differentiated toward osteoblasts (at 6 h). Significantly regulated genes were analyzed in silico, and the Connectivity Map (CMap) was used to identify candidate bone stimulatory compounds. The signature of parbendazole matches the expression changes observed for osteogenic hMSCs. Parbendazole stimulates osteoblast differentiation as indicated by increased alkaline phosphatase activity, mineralization, and up-regulation of bone marker genes (alkaline phosphatase/ALPL, osteopontin/SPP1, and bone sialoprotein II/IBSP) in a subset of the hMSC population resistant to the apoptotic effects of parbendazole. These osteogenic effects are independent of glucocorticoids because parbendazole does not up-regulate glucocorticoid receptor (GR) target genes and is not inhibited by the GR antagonist mifepristone. Parbendazole causes profound cytoskeletal changes including degradation of microtubules and increased focal adhesions. Stabilization of microtubules by pretreatment with Taxol inhibits osteoblast differentiation. Parbendazole up-regulates bone morphogenetic protein 2 (BMP-2) gene expression and activity. Cotreatment with the BMP-2 antagonist DMH1 limits, but does not block, parbendazole-induced mineralization. Using the CMap we have identified a previously unidentified lineage-specific, bone anabolic compound, parbendazole, which induces osteogenic differentiation through a combination of cytoskeletal changes and increased BMP-2 activity.
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Affiliation(s)
- Andrea M Brum
- Department of Internal Medicine, Erasmus MC, 3015 CN Rotterdam, The Netherlands
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Hayashi K, Sasamura H, Nakamura M, Sakamaki Y, Azegami T, Oguchi H, Tokuyama H, Wakino S, Hayashi K, Itoh H. Renin-angiotensin blockade resets podocyte epigenome through Kruppel-like Factor 4 and attenuates proteinuria. Kidney Int 2015; 88:745-53. [PMID: 26108068 DOI: 10.1038/ki.2015.178] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/21/2015] [Accepted: 04/16/2015] [Indexed: 02/07/2023]
Abstract
Proteinuria is a central component of chronic kidney disease and an independent risk factor for cardiovascular disease. Kidney podocytes have an essential role as a filtration barrier against proteinuria. Kruppel-like Factor 4 (KLF4) is expressed in podocytes and decreased in glomerular diseases leading to methylation of the nephrin promoter, decreased nephrin expression and proteinuria. Treatment with an angiotensin receptor blocker (ARB) reduced methylation of the nephrin promoter in murine glomeruli of an adriamycin nephropathy model with recovery of KLF4 expression and a decrease in albuminuria. In podocyte-specific KLF4 knockout mice, the effect of ARB on albuminuria and the nephrin promoter methylation was attenuated. In cultured human podocytes, angiotensin II reduced KLF4 expression and caused methylation of the nephrin promoter with decreased nephrin expression. In patients, nephrin promoter methylation was increased in proteinuric kidney diseases with decreased KLF4 and nephrin expression. KLF4 expression in ARB-treated patients was higher in patients with than without ARB treatment. Thus, angiotensin II can modulate epigenetic regulation in podocytes and ARB inhibits these actions in part via KLF4 in proteinuric kidney diseases. This study provides a new concept that renin-angiotensin system blockade can exert therapeutic effects through epigenetic modulation of the kidney gene expression.
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Affiliation(s)
- Kaori Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroyuki Sasamura
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Mari Nakamura
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Yusuke Sakamaki
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Tatsuhiko Azegami
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hideyo Oguchi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hirobumi Tokuyama
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Shu Wakino
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Koichi Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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Recent developments in epigenetics of acute and chronic kidney diseases. Kidney Int 2015; 88:250-61. [PMID: 25993323 PMCID: PMC4522401 DOI: 10.1038/ki.2015.148] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/22/2015] [Accepted: 03/30/2015] [Indexed: 12/25/2022]
Abstract
The growing epidemic of obesity and diabetes, the aging population as well as prevalence of drug abuse has led to significant increases in the rates of the closely associated acute and chronic kidney diseases, including diabetic nephropathy. Furthermore, evidence shows that parental behavior and diet can affect the phenotype of subsequent generations via epigenetic transmission mechanisms. These data suggest a strong influence of the environment on disease susceptibility and that, apart from genetic susceptibility, epigenetic mechanisms need to be evaluated to gain critical new information about kidney diseases. Epigenetics is the study of processes that control gene expression and phenotype without alterations in the underlying DNA sequence. Epigenetic modifications, including cytosine DNA methylation and covalent post translational modifications of histones in chromatin are part of the epigenome, the interface between the stable genome and the variable environment. This dynamic epigenetic layer responds to external environmental cues to influence the expression of genes associated with disease states. The field of epigenetics has seen remarkable growth in the past few years with significant advances in basic biology, contributions to human disease, as well as epigenomics technologies. Further understanding of how the renal cell epigenome is altered by metabolic and other stimuli can yield novel new insights into the pathogenesis of kidney diseases. In this review, we have discussed the current knowledge on the role of epigenetic mechanisms (primarily DNA me and histone modifications) in acute and chronic kidney diseases, and their translational potential to identify much needed new therapies.
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Liu N, Zhuang S. Treatment of chronic kidney diseases with histone deacetylase inhibitors. Front Physiol 2015; 6:121. [PMID: 25972812 PMCID: PMC4411966 DOI: 10.3389/fphys.2015.00121] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/02/2015] [Indexed: 01/30/2023] Open
Abstract
Histone deacetylases (HDACs) induce deacetylation of both histone and non-histone proteins and play a critical role in the modulation of physiological and pathological gene expression. Pharmacological inhibition of HDAC has been reported to attenuate progression of renal fibrogenesis in obstructed kidney and reduce cyst formation in polycystic kidney disease. HDAC inhibitors (HDACis) are also able to ameliorate renal lesions in diabetes nephropathy, lupus nephritis, aristolochic acid nephropathy, and transplant nephropathy. The beneficial effects of HDACis are associated with their anti-fibrosis, anti-inflammation, and immunosuppressant effects. In this review, we summarize recent advances on the treatment of various chronic kidney diseases with HDACis in pre-clinical models.
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Affiliation(s)
- Na Liu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine Shanghai, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine Shanghai, China ; Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University Providence, RI, USA
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Hayashi K, Itoh H. Transcription Factors and Epigenetic Modulation: Its Therapeutic Implication in Chronic Kidney Disease. Arch Immunol Ther Exp (Warsz) 2014; 63:193-6. [DOI: 10.1007/s00005-014-0326-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/18/2014] [Indexed: 11/24/2022]
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Grzasko N, Morawska M, Hus M. Optimizing the treatment of patients with multiple myeloma and renal impairment. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2014; 15:187-98. [PMID: 25458082 DOI: 10.1016/j.clml.2014.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
Renal impairment is a common complication of multiple myeloma. It is found in about 20% to 25% of patients at diagnosis and in ≤ 50% at some point during the disease course. The presence of renal insufficiency diminishes patients' quality of life and has been associated with increased mortality, although the outcomes of patients after successful induction therapy have been comparable to those with normal renal function. Therefore, the treatment of patients with multiple myeloma and renal impairment is a major challenge and should aim to achieve remission in a large proportion of patients. New drugs introduced to treat multiple myeloma during the past decade have an established place in the treatment of patients with renal failure. Bortezomib appears to be most beneficial in this setting and, combined with other drugs, provides a chance for rapid remission and related improvement of renal function. Immunomodulatory drugs such as thalidomide and lenalidomide have also been used successfully in patients with renal insufficiency, although for the latter drug appropriate dose adjustments are necessary. The presence of renal failure is not a contraindication to autologous bone marrow transplantation in patients eligible for this procedure. Among the classic cytotoxic agents, bendamustine, in particular, should be considered for patients with renal insufficiency. Appropriate supportive care is also extremely important in the treatment of patients with multiple myeloma and renal failure. It can include plasmapheresis and removal of free light chains with high cut-off hemodialysis, adapted dosages of bisphosphonates, and avoidance of drugs and conditions that can impair renal function.
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Affiliation(s)
- Norbert Grzasko
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland.
| | - Marta Morawska
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Marek Hus
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
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Smyth LJ, Duffy S, Maxwell AP, McKnight AJ. Genetic and epigenetic factors influencing chronic kidney disease. Am J Physiol Renal Physiol 2014; 307:F757-76. [PMID: 25080522 DOI: 10.1152/ajprenal.00306.2014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chronic kidney disease (CKD) has become a serious public health problem because of its associated morbidity, premature mortality, and attendant healthcare costs. The rising number of persons with CKD is linked with the aging population structure and an increased prevalence of diabetes, hypertension, and obesity. There is an inherited risk associated with developing CKD, as evidenced by familial clustering and differing prevalence rates across ethnic groups. Previous studies to determine the inherited risk factors for CKD rarely identified genetic variants that were robustly replicated. However, improvements in genotyping technologies and analytic methods are now helping to identify promising genetic loci aided by international collaboration and multiconsortia efforts. More recently, epigenetic modifications have been proposed to play a role in both the inherited susceptibility to CKD and, importantly, to explain how the environment dynamically interacts with the genome to alter an individual's disease risk. Genome-wide, epigenome-wide, and whole transcriptome studies have been performed, and optimal approaches for integrative analysis are being developed. This review summarizes recent research and the current status of genetic and epigenetic risk factors influencing CKD using population-based information.
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Affiliation(s)
- L J Smyth
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - S Duffy
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - A P Maxwell
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - A J McKnight
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
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The molecular phenotype of endocapillary proliferation: novel therapeutic targets for IgA nephropathy. PLoS One 2014; 9:e103413. [PMID: 25133636 PMCID: PMC4136785 DOI: 10.1371/journal.pone.0103413] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/29/2014] [Indexed: 12/13/2022] Open
Abstract
IgA nephropathy (IgAN) is a clinically and pathologically heterogeneous disease. Endocapillary proliferation is associated with higher risk of progressive disease, and clinical studies suggest that corticosteroids mitigate this risk. However, corticosteroids are associated with protean cellular effects and significant toxicity. Furthermore the precise mechanism by which they modulate kidney injury in IgAN is not well delineated. To better understand molecular pathways involved in the development of endocapillary proliferation and to identify novel specific therapeutic targets, we evaluated the glomerular transcriptome of microdissected kidney biopsies from 22 patients with IgAN. Endocapillary proliferation was defined according to the Oxford scoring system independently by 3 nephropathologists. We analyzed mRNA expression using microarrays and identified transcripts differentially expressed in patients with endocapillary proliferation compared to IgAN without endocapillary lesions. Next, we employed both transcription factor analysis and in silico drug screening and confirmed that the endocapillary proliferation transcriptome is significantly enriched with pathways that can be impacted by corticosteroids. With this approach we also identified novel therapeutic targets and bioactive small molecules that may be considered for therapeutic trials for the treatment of IgAN, including resveratrol and hydroquinine. In summary, we have defined the distinct molecular profile of a pathologic phenotype associated with progressive renal insufficiency in IgAN. Exploration of the pathways associated with endocapillary proliferation confirms a molecular basis for the clinical effectiveness of corticosteroids in this subgroup of IgAN, and elucidates new therapeutic strategies for IgAN.
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Novitskaya T, McDermott L, Zhang KX, Chiba T, Paueksakon P, Hukriede NA, de Caestecker MP. A PTBA small molecule enhances recovery and reduces postinjury fibrosis after aristolochic acid-induced kidney injury. Am J Physiol Renal Physiol 2013; 306:F496-504. [PMID: 24370591 DOI: 10.1152/ajprenal.00534.2013] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Phenylthiobutanoic acids (PTBAs) are a new class of histone deacetylase (HDAC) inhibitors that accelerate recovery and reduce postinjury fibrosis after ischemia-reperfusion-induced acute kidney injury. However, unlike the more common scenario in which patients present with protracted and less clearly defined onset of renal injury, this model of acute kidney injury gives rise to a clearly defined injury that begins to resolve over a short period of time. In these studies, we show for the first time that treatment with the PTBA analog methyl-4-(phenylthio)butanoate (M4PTB) accelerates recovery and reduces postinjury fibrosis in a progressive model of acute kidney injury and renal fibrosis that occurs after aristolochic acid injection in mice. These effects are apparent when M4PTB treatment is delayed 4 days after the initiating injury and are associated with increased proliferation and decreased G2/M arrest of regenerating renal tubular epithelial cells. In addition, there is reduced peritubular macrophage infiltration and decreased expression of the macrophage chemokines CX3Cl1 and CCL2. Since macrophage infiltration plays a role in promoting kidney injury, and since renal tubular epithelial cells show defective repair and a marked increase in maladaptive G2/M arrest after aristolochic acid injury, these findings suggest M4PTB may be particularly beneficial in reducing injury and enhancing intrinsic cellular repair even when administered days after aristolochic acid ingestion.
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Affiliation(s)
- Tatiana Novitskaya
- Vanderbilt Univ. Medical Center, Dept. of Medicine, Div. of Nephrology, S3223 Medical Center North, 1161 21st Ave. South, Nashville, TN 37232.
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Montero-Melendez T, Perretti M. Connections in pharmacology: innovation serving translational medicine. Drug Discov Today 2013; 19:820-3. [PMID: 24316023 DOI: 10.1016/j.drudis.2013.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/04/2013] [Accepted: 11/28/2013] [Indexed: 10/25/2022]
Abstract
There is a paucity of molecules that progress through the drug development pipeline, making the drug discovery process expensive and frustrating. Innovative approaches to drug development are therefore required to maximise opportunities. Strategies such as the Connectivity Map (CMap), which compares >7000 gene expression signatures generated from more than 1000 drugs, can produce associations between currently unrelated therapeutics, unveiling new mechanisms of action and favouring drug repositioning. Here, we discuss these opportunities that could aid the drug development process and propose rigorous publication of 'omics data with open access and data sharing. We, pharmacologists of the third millennium, must aim towards maximising knowledge in an unbiased and cost-effective manner, to deliver new drugs for the global benefit of patients.
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Affiliation(s)
- Trinidad Montero-Melendez
- The William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Mauro Perretti
- The William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Legouis D, Hertig A. La marque des histones dans l’insuffisance rénale aiguë. Nephrol Ther 2013; 9:518-20. [DOI: 10.1016/j.nephro.2013.07.367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/21/2013] [Indexed: 11/29/2022]
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Abstract
Our understanding of the pathogenesis of most primary glomerular diseases, including IgA nephropathy, membranous nephropathy and focal segmental glomerulosclerosis, is limited. Advances in molecular technology now permit genome-wide, high-throughput characterization of genes and gene products from biological samples. Comprehensive examinations of the genome, transcriptome, proteome and metabolome (collectively known as omics analyses), have been applied to the study of IgA nephropathy, membranous nephropathy and focal segmental glomerulosclerosis in both animal models and human patients. However, most omics studies of primary glomerular diseases, with the exception of large genomic studies, have been limited by inadequate sample sizes and the lack of kidney-specific data sets derived from kidney biopsy samples. Collaborative efforts to develop a standardized approach for prospective recruitment of patients, scheduled monitoring of clinical outcomes, and protocols for sampling of kidney tissues will be instrumental in uncovering the mechanisms that drive these diseases. Integration of molecular data sets with the results of clinical and histopathological studies will ultimately enable these diseases to be characterized in a comprehensive and systematic manner, and is expected to improve the diagnosis and treatment of these diseases.
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