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Rafehi H, Bennett MF, Bahlo M. Detection and discovery of repeat expansions in ataxia enabled by next-generation sequencing: present and future. Emerg Top Life Sci 2023; 7:349-359. [PMID: 37733280 PMCID: PMC10754322 DOI: 10.1042/etls20230018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Hereditary cerebellar ataxias are a heterogenous group of progressive neurological disorders that are disproportionately caused by repeat expansions (REs) of short tandem repeats (STRs). Genetic diagnosis for RE disorders such as ataxias are difficult as the current gold standard for diagnosis is repeat-primed PCR assays or Southern blots, neither of which are scalable nor readily available for all STR loci. In the last five years, significant advances have been made in our ability to detect STRs and REs in short-read sequencing data, especially whole-genome sequencing. Given the increasing reliance of genomics in diagnosis of rare diseases, the use of established RE detection pipelines for RE disorders is now a highly feasible and practical first-step alternative to molecular testing methods. In addition, many new pathogenic REs have been discovered in recent years by utilising WGS data. Collectively, genomes are an important resource/platform for further advancements in both the discovery and diagnosis of REs that cause ataxia and will lead to much needed improvement in diagnostic rates for patients with hereditary ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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2
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Fearnley LG, Rafehi H, Bennett MF, Bahlo M. Exploring THAP11 Repeat Expansion beyond Chinese-Ancestry Cohorts: An Examination of 1000 Genomes and UK Biobank Data. Mov Disord 2023; 38:2320-2322. [PMID: 38113319 PMCID: PMC10946534 DOI: 10.1002/mds.29636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Liam G. Fearnley
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Bruce Lefroy Centre for Genetic Health ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Haloom Rafehi
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Bruce Lefroy Centre for Genetic Health ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Mark F. Bennett
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
- Epilepsy Research Centre, Department of MedicineUniversity of Melbourne, Austin HealthHeidelbergVictoriaAustralia
| | - Melanie Bahlo
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
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3
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Karagiannis TC, Wall M, Ververis K, Pitsillou E, Tortorella SM, Wood PA, Rafehi H, Khurana I, Maxwell SS, Hung A, Vongsvivut J, El-Osta A. Characterization of K562 cells: uncovering novel chromosomes, assessing transferrin receptor expression, and probing pharmacological therapies. Cell Mol Life Sci 2023; 80:248. [PMID: 37578596 DOI: 10.1007/s00018-023-04905-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Human erythroleukemic K562 cells represent the prototypical cell culture model of chronic myeloid leukemia (CML). The cells are pseudo-triploid and positive for the Philadelphia chromosome. Therefore, K562 cells have been widely used for investigating the BCR/ABL1 oncogene and the tyrosine kinase inhibitor, imatinib-mesylate. Further, K562 cells overexpress transferrin receptors (TfR) and have been used as a model for targeting cytotoxic therapies, via receptor-mediated endocytosis. Here, we have characterized K562 cells focusing on the karyotype of cells in prolonged culture, regulation of expression of TfR in wildtype (WT) and doxorubicin-resistant cells, and responses to histone deacetylase inhibition (HDACi). Karyotype analysis indicates novel chromosomes and gene expression analysis suggests a shift of cultured K562 cells away from patient-derived leukemic cells. We confirm the high expression of TfR on K562 cells using immunofluorescence and cell-surface receptor binding radioassays. Importantly, high TfR expression is observed in patient-derived cells, and we highlight the persistent expression of TfR following doxorubicin acquired resistance. Epigenetic analysis indicates that permissive histone acetylation and methylation at the promoter region regulates the transcription of TfR in K562 cells. Finally, we show relatively high expression of HDAC enzymes in K562 cells and demonstrate the chemotoxic effects of HDACi, using the FDA-approved hydroxamic acid, vorinostat. Together with a description of morphology, infrared spectral analysis, and examination of metabolic properties, we provide a comprehensive characterization of K562 cells. Overall, K562 cell culture systems remain widely used for the investigation of novel therapeutics for CML, which is particularly important in cases of imatinib-mesylate resistance.
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MESH Headings
- Humans
- Imatinib Mesylate/pharmacology
- Imatinib Mesylate/therapeutic use
- K562 Cells
- Fusion Proteins, bcr-abl/genetics
- Transferrin
- Pyrimidines/pharmacology
- Drug Resistance, Neoplasm/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Histone Deacetylases/metabolism
- Doxorubicin/pharmacology
- Doxorubicin/therapeutic use
- Receptors, Transferrin/genetics
- Chromosomes/metabolism
- Mesylates/pharmacology
- Apoptosis
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Affiliation(s)
- Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia.
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Epigenomic in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia.
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, Fitzroy, VIC, 3065, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Katherine Ververis
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Stephanie M Tortorella
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter A Wood
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia
| | - Haloom Rafehi
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
| | - Scott S Maxwell
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | | | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30‑32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KH, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA27B/ATX-FGF14. Am J Hum Genet 2023; 110:1018. [PMID: 37267898 DOI: 10.1016/j.ajhg.2023.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
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Khurana I, Kaipananickal H, Maxwell S, Birkelund S, Syreeni A, Forsblom C, Okabe J, Ziemann M, Kaspi A, Rafehi H, Jørgensen A, Al-Hasani K, Thomas MC, Jiang G, Luk AO, Lee HM, Huang Y, Thewjitcharoen Y, Nakasatien S, Himathongkam T, Fogarty C, Njeim R, Eid A, Hansen TW, Tofte N, Ottesen EC, Ma RC, Chan JC, Cooper ME, Rossing P, Groop PH, El-Osta A. Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes. J Clin Invest 2023; 133:160959. [PMID: 36633903 PMCID: PMC9927943 DOI: 10.1172/jci160959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Diabetic nephropathy (DN) is a polygenic disorder with few risk variants showing robust replication in large-scale genome-wide association studies. To understand the role of DNA methylation, it is important to have the prevailing genomic view to distinguish key sequence elements that influence gene expression. This is particularly challenging for DN because genome-wide methylation patterns are poorly defined. While methylation is known to alter gene expression, the importance of this causal relationship is obscured by array-based technologies since coverage outside promoter regions is low. To overcome these challenges, we performed methylation sequencing using leukocytes derived from participants of the Finnish Diabetic Nephropathy (FinnDiane) type 1 diabetes (T1D) study (n = 39) that was subsequently replicated in a larger validation cohort (n = 296). Gene body-related regions made up more than 60% of the methylation differences and emphasized the importance of methylation sequencing. We observed differentially methylated genes associated with DN in 3 independent T1D registries originating from Denmark (n = 445), Hong Kong (n = 107), and Thailand (n = 130). Reduced DNA methylation at CTCF and Pol2B sites was tightly connected with DN pathways that include insulin signaling, lipid metabolism, and fibrosis. To define the pathophysiological significance of these population findings, methylation indices were assessed in human renal cells such as podocytes and proximal convoluted tubule cells. The expression of core genes was associated with reduced methylation, elevated CTCF and Pol2B binding, and the activation of insulin-signaling phosphoproteins in hyperglycemic cells. These experimental observations also closely parallel methylation-mediated regulation in human macrophages and vascular endothelial cells.
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Affiliation(s)
- Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Scott Maxwell
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sørine Birkelund
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Anne Jørgensen
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Keith Al-Hasani
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Merlin C. Thomas
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | | | - Andrea O.Y. Luk
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Heung Man Lee
- Department of Medicine and Therapeutics,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | | | | | - Christopher Fogarty
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rachel Njeim
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Assaad Eid
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Nete Tofte
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Ronald C.W. Ma
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Juliana C.N. Chan
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark E. Cooper
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Herlev, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KHC, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA50/ATX-FGF14. Am J Hum Genet 2023; 110:105-119. [PMID: 36493768 PMCID: PMC9892775 DOI: 10.1016/j.ajhg.2022.11.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
Adult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified an intronic (GAA) repeat expansion in fibroblast growth factor 14 (FGF14). Genetic analysis of 95 Australian individuals with adult-onset ataxia identified four (4.2%) with (GAA)>300 and a further nine individuals with (GAA)>250. PCR and long-read sequence analysis revealed these were pure (GAA) repeats. In comparison, no control subjects had (GAA)>300 and only 2/311 control individuals (0.6%) had a pure (GAA)>250. In a German validation cohort, 9/104 (8.7%) of affected individuals had (GAA)>335 and a further six had (GAA)>250, whereas 10/190 (5.3%) control subjects had (GAA)>250 but none were (GAA)>335. The combined data suggest (GAA)>335 are disease causing and fully penetrant (p = 6.0 × 10-8, OR = 72 [95% CI = 4.3-1,227]), while (GAA)>250 is likely pathogenic with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with variable features including vestibular impairment, hyper-reflexia, and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2 = 0.44, p = 0.00045, slope = -0.12) and identification of a shared haplotype in a minority of individuals suggests that the expansion can be inherited or generated de novo during meiotic division. This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansions via model-free, genome-wide analysis and identifies SCA50/ATX-FGF14 as a frequent cause of adult-onset ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Read
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - David J. Szmulewicz
- Cerebellar Ataxia Clinic, Eye and Ear Hospital, Melbourne, VIC, Australia,The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kayli C. Davies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam G. Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam Scott
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Mark F. Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathie J. Ngo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Luke Chen
- Alfred Hospital, Department of Neurology, Melbourne, VIC, Australia
| | - Mathew J. Wallis
- Clinical Genetics Service, Austin Health, Melbourne, VIC, Australia,Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Kishore R. Kumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord, NSW, Australia,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kathy HC. Wu
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Clinical Genomics, St Vincent’s Hospital, Darlinghurst, NSW, Australia,Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,School of Medicine, University of Notre Dame, Sydney, NSW, Australia
| | - Susan E. Tomlinson
- School of Medicine, University of Notre Dame, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Stephen Tisch
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Abhishek Malhotra
- Department of Neuroscience, University Hospital Geelong, Geelong, VIC, Australia
| | - Matthew Lee-Archer
- Launceston General Hospital, Tasmanian Health Service, Launceston, TAS, Australia
| | | | | | - Leslie J. Roberts
- Department of Neurology and Neurological Research, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Brent L. Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA,Departments of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Martin B. Delatycki
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Corresponding author
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7
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Rosenbohm A, Pott H, Thomsen M, Rafehi H, Kaya S, Szymczak S, Volk AE, Mueller K, Silveira I, Weishaupt JH, Tönnies H, Seibler P, Zschiedrich K, Schaake S, Westenberger A, Zühlke C, Depienne C, Trinh J, Ludolph AC, Klein C, Bahlo M, Lohmann K. Familial Cerebellar Ataxia and Amyotrophic Lateral Sclerosis/Frontotemporal Dementia with DAB1 and C9ORF72 Repeat Expansions: An 18-Year Study. Mov Disord 2022; 37:2427-2439. [PMID: 36148898 PMCID: PMC10900262 DOI: 10.1002/mds.29221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Coding and noncoding repeat expansions are an important cause of neurodegenerative diseases. OBJECTIVE This study determined the clinical and genetic features of a large German family that has been followed for almost 2 decades with an autosomal dominantly inherited spinocerebellar ataxia (SCA) and independent co-occurrence of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). METHODS We carried out clinical examinations and telephone interviews, reviewed medical records, and performed magnetic resonance imaging and positron emission tomography scans of all available family members. Comprehensive genetic investigations included linkage analysis, short-read genome sequencing, long-read sequencing, repeat-primed polymerase chain reaction, and Southern blotting. RESULTS The family comprises 118 members across seven generations, 30 of whom were definitely and five possibly affected. In this family, two different pathogenic mutations were found, a heterozygous repeat expansion in C9ORF72 in four patients with ALS/FTD and a heterozygous repeat expansion in DAB1 in at least nine patients with SCA, leading to a diagnosis of DAB1-related ataxia (ATX-DAB1; SCA37). One patient was affected by ALS and SCA and carried both repeat expansions. The repeat in DAB1 had the same configuration but was larger than those previously described ([ATTTT]≈75 [ATTTC]≈40-100 [ATTTT]≈415 ). Clinical features in patients with SCA included spinocerebellar symptoms, sometimes accompanied by additional ophthalmoplegia, vertical nystagmus, tremor, sensory deficits, and dystonia. After several decades, some of these patients suffered from cognitive decline and one from additional nonprogressive lower motor neuron affection. CONCLUSION We demonstrate genetic and clinical findings during an 18-year period in a unique family carrying two different pathogenic repeat expansions, providing novel insights into their genotypic and phenotypic spectrums. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Hendrik Pott
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Mirja Thomsen
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Haloom Rafehi
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Sabine Kaya
- Institute of Human GeneticsUniversity Hospital EssenEssenGermany
| | - Silke Szymczak
- Insitute of Medical Biometry and StatisticsUniversity of LübeckLübeckGermany
| | - Alexander E. Volk
- Institute of Human GeneticsUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | | | - Isabel Silveira
- i3S‐Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
| | - Jochen H. Weishaupt
- Division of Neurodegeneration, Neurology DepartmentUniversity Medicine Mannheim, Heidelberg UniversityMannheimGermany
| | - Holger Tönnies
- Institute of Human GeneticsChristian‐Albrechts‐UniversityKielGermany
| | - Philip Seibler
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Susen Schaake
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | | | | | - Joanne Trinh
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Albert C. Ludolph
- Department of NeurologyUniversity of UlmUlmGermany
- German Center for Neurodegenerative Diseases, Site UlmUlmGermany
| | | | - Melanie Bahlo
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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8
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Barbier M, Bahlo M, Pennisi A, Jacoupy M, Tankard RM, Ewenczyk C, Davies KC, Lino-Coulon P, Colace C, Rafehi H, Auger N, Ansell BRE, van der Stelt I, Howell KB, Coutelier M, Amor DJ, Mundwiller E, Guillot-Noël L, Storey E, Gardner RJM, Wallis MJ, Brusco A, Corti O, Rötig A, Leventer RJ, Brice A, Delatycki MB, Stevanin G, Lockhart PJ, Durr A. Heterozygous PNPT1 variants cause spinocerebellar ataxia type 25. Ann Neurol 2022; 92:122-137. [PMID: 35411967 DOI: 10.1002/ana.26366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Dominant spinocerebellar ataxias (SCA) are characterized by genetic heterogeneity. Some mapped and named loci remain without a causal gene identified. Here we applied next generation sequencing (NGS) to uncover the genetic etiology of the SCA25 locus. METHODS Whole-exome and whole-genome sequencing were performed in families linked to SCA25, including the French family in which the SCA25 locus was originally mapped. Whole exome sequence data was interrogated in a cohort of 796 ataxia patients of unknown aetiology. RESULTS The SCA25 phenotype spans a slowly evolving sensory and cerebellar ataxia, in most cases attributed to ganglionopathy. A pathogenic variant causing exon skipping was identified in the gene encoding Polyribonucleotide Nucleotidyltransferase PNPase 1 (PNPT1) located in the SCA25 linkage interval. A second splice variant in PNPT1 was detected in a large Australian family with a dominant ataxia also mapping to SCA25. An additional nonsense variant was detected in an unrelated individual with ataxia. Both nonsense and splice heterozygous variants result in premature stop codons, all located in the S1-domain of PNPase. In addition, an elevated type I interferon response was observed in blood from all affected heterozygous carriers tested. PNPase notably prevents the abnormal accumulation of double-stranded mtRNAs in the mitochondria and leakage into the cytoplasm, associated with triggering a type I interferon response. INTERPRETATION This study identifies PNPT1 as a new SCA gene, responsible for SCA25, and highlights biological links between alterations of mtRNA trafficking, interferonopathies and ataxia. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mathieu Barbier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alessandra Pennisi
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Maxime Jacoupy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Rick M Tankard
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Claire Ewenczyk
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Patricia Lino-Coulon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Claire Colace
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Nicolas Auger
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Ivo van der Stelt
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Donders Centre for Neuroscience, Faculty of Science, Radboud University, The Netherlands
| | - Katherine B Howell
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Marie Coutelier
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - David J Amor
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Emeline Mundwiller
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Lena Guillot-Noël
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Elsdon Storey
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | | | - Mathew J Wallis
- Clinical Genetics Service, Austin Health, Melbourne, Australia; Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Agnès Rötig
- Necker Hospital, APHP, Reference Center for Mitochondrial Diseases, Genetics Department, Institut Imagine, University of Paris, Paris, France.,Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Victorian Clinical Genetics Service, Melbourne, 3052, Australia
| | - Giovanni Stevanin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France.,Paris Sciences Lettres Research University, EPHE, Paris, France
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexandra Durr
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
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9
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Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat 2022; 43:16-29. [PMID: 34633740 PMCID: PMC8720068 DOI: 10.1002/humu.24289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 11/06/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disorders with an estimated heritability of >60%. Family-based genetic studies of ASD have generally focused on multiple small kindreds, searching for de novo variants of major effect. We hypothesized that molecular genetic analysis of large multiplex families would enable the identification of variants of milder effects. We studied a large multigenerational family of European ancestry with multiple family members affected with ASD or the broader autism phenotype (BAP). We identified a rare heterozygous variant in the gene encoding 1,4-ɑ-glucan branching enzyme 1 (GBE1) that was present in seven of seven individuals with ASD, nine of ten individuals with the BAP, and none of four tested unaffected individuals. We genotyped a community-acquired cohort of 389 individuals with ASD and identified three additional probands. Cascade analysis demonstrated that the variant was present in 11 of 13 individuals with familial ASD/BAP and neither of the two tested unaffected individuals in these three families, also of European ancestry. The variant was not enriched in the combined UK10K ASD cohorts of European ancestry but heterozygous GBE1 deletion was overrepresented in large ASD cohorts, collectively suggesting an association between GBE1 and ASD.
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Affiliation(s)
- Miriam Fanjul-Fernández
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute Victoria, Parkville, Victoria, Australia
- Royal Children’s Hospital Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Barwon Health, Geelong, Victoria, Australia
| | - Peter Hickey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Kiymet Bozaoglu
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cherie C Green
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - Audrey Rattray
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Savannah Young
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dana Alhuzaimi
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Vesna Lukic
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Tanya Vick
- Barwon Health, Geelong, Victoria, Australia
| | | | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington, USA
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah J Wilson
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul J Lockhart
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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10
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Sim CB, Phipson B, Ziemann M, Rafehi H, Mills RJ, Watt KI, Abu-Bonsrah KD, Kalathur RK, Voges HK, Dinh DT, ter Huurne M, Vivien CJ, Kaspi A, Kaipananickal H, Hidalgo A, Delbridge LM, Robker RL, Gregorevic P, dos Remedios CG, Lal S, Piers AT, Konstantinov IE, Elliott DA, El-Osta A, Oshlack A, Hudson JE, Porrello ER. Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor. Circulation 2021; 143:1614-1628. [PMID: 33682422 PMCID: PMC8055196 DOI: 10.1161/circulationaha.120.051921] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Despite in-depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals governing postnatal maturation of the human heart. METHODS Single-nucleus RNA sequencing of 54 140 nuclei from 9 human donors was used to profile transcriptional changes in diverse cardiac cell types during maturation from fetal stages to adulthood. Bulk RNA sequencing and the Assay for Transposase-Accessible Chromatin using sequencing were used to further validate transcriptional changes and to profile alterations in the chromatin accessibility landscape in purified cardiomyocyte nuclei from 21 human donors. Functional validation studies of sex steroids implicated in cardiac maturation were performed in human pluripotent stem cell-derived cardiac organoids and mice. RESULTS Our data identify the progesterone receptor as a key mediator of sex-dependent transcriptional programs during cardiomyocyte maturation. Functional validation studies in human cardiac organoids and mice demonstrate that the progesterone receptor drives sex-specific metabolic programs and maturation of cardiac contractile properties. CONCLUSIONS These data provide a blueprint for understanding human heart maturation in both sexes and reveal an important role for the progesterone receptor in human heart development.
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Affiliation(s)
- Choon Boon Sim
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Belinda Phipson
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre (B.P., A.O.), University of Melbourne, Victoria, Australia
| | - Mark Ziemann
- Department of Diabetes, Central Clinical School, Alfred Centre, Monash University, Melbourne, Victoria, Australia (M.Z., H.R., A.K., H.K., A.E.-O.)
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia (M.Z.)
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Haloom Rafehi
- Department of Diabetes, Central Clinical School, Alfred Centre, Monash University, Melbourne, Victoria, Australia (M.Z., H.R., A.K., H.K., A.E.-O.)
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Richard J. Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia (R.J.M., J.E.H.)
| | - Kevin I. Watt
- Peter MacCallum Cancer Centre (B.P., A.O.), University of Melbourne, Victoria, Australia
- Centre for Muscle Research (K.I.W., P.G., E.R.P.), University of Melbourne, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Kwaku D. Abu-Bonsrah
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- School of Biomedical Sciences, and Department of Paediatrics (K.D.A.-B., H.K.V., A.H., I.E.K., D.A.E.), University of Melbourne, Victoria, Australia
| | - Ravi K.R. Kalathur
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Holly K. Voges
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- School of Biomedical Sciences, and Department of Paediatrics (K.D.A.-B., H.K.V., A.H., I.E.K., D.A.E.), University of Melbourne, Victoria, Australia
| | - Doan T. Dinh
- Robinson Research Institute, The University of Adelaide, South Australia, Australia (D.T.D., R.L.R.)
| | - Menno ter Huurne
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Celine J. Vivien
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Antony Kaspi
- Department of Diabetes, Central Clinical School, Alfred Centre, Monash University, Melbourne, Victoria, Australia (M.Z., H.R., A.K., H.K., A.E.-O.)
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Harikrishnan Kaipananickal
- Department of Diabetes, Central Clinical School, Alfred Centre, Monash University, Melbourne, Victoria, Australia (M.Z., H.R., A.K., H.K., A.E.-O.)
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Alejandro Hidalgo
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- School of Biomedical Sciences, and Department of Paediatrics (K.D.A.-B., H.K.V., A.H., I.E.K., D.A.E.), University of Melbourne, Victoria, Australia
| | - Leanne M.D. Delbridge
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Anatomy and Physiology (K.I.W., L.M.D.D., P.G., E.R.P.), University of Melbourne, Victoria, Australia
| | - Rebecca L. Robker
- Robinson Research Institute, The University of Adelaide, South Australia, Australia (D.T.D., R.L.R.)
| | - Paul Gregorevic
- Department of Anatomy and Physiology (K.I.W., L.M.D.D., P.G., E.R.P.), University of Melbourne, Victoria, Australia
- Centre for Muscle Research (K.I.W., P.G., E.R.P.), University of Melbourne, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
| | - Cristobal G. dos Remedios
- School of Medical Sciences, The University of Sydney, New South Wales, Australia (C.G.d.R., S.L.)
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia (C.G.d.R.)
| | - Sean Lal
- School of Medical Sciences, The University of Sydney, New South Wales, Australia (C.G.d.R., S.L.)
| | - Adam T. Piers
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Igor E. Konstantinov
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Cardiac Surgery (I.E.K.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- School of Biomedical Sciences, and Department of Paediatrics (K.D.A.-B., H.K.V., A.H., I.E.K., D.A.E.), University of Melbourne, Victoria, Australia
| | - David A. Elliott
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- School of Biomedical Sciences, and Department of Paediatrics (K.D.A.-B., H.K.V., A.H., I.E.K., D.A.E.), University of Melbourne, Victoria, Australia
| | - Assam El-Osta
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Alicia Oshlack
- Department of Diabetes, Central Clinical School, Alfred Centre, Monash University, Melbourne, Victoria, Australia (M.Z., H.R., A.K., H.K., A.E.-O.)
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., H.R., K.I.W., A.K., H.K., P.G., A.E.-O.)
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, and The Chinese University of Hong Kong, China (A.E.-O.)
| | - James E. Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia (R.J.M., J.E.H.)
- Centre for Cardiac and Vascular Biology, School of Biomedical Sciences, The University of Queensland, Brisbane, Australia (J.E.H., E.R.P.)
| | - Enzo R. Porrello
- Murdoch Children’s Research Institute (C.B.S., B.P., K.D.A.-B., R.K.R.K., H.K.V., M.t.H., C.J.V., A.H., A.T.P., I.E.K., D.A.E., A.O., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (C.B.S., K.D.A.-B., R.K.R.K., M.t.H., C.J.V., L.M.D.D., A.T.P., I.E.K., D.A.E., E.R.P.), The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Anatomy and Physiology (K.I.W., L.M.D.D., P.G., E.R.P.), University of Melbourne, Victoria, Australia
- Centre for Muscle Research (K.I.W., P.G., E.R.P.), University of Melbourne, Victoria, Australia
- Centre for Cardiac and Vascular Biology, School of Biomedical Sciences, The University of Queensland, Brisbane, Australia (J.E.H., E.R.P.)
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11
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Brohus M, Arsov T, Wallace DA, Jensen HH, Nyegaard M, Crotti L, Adamski M, Zhang Y, Field MA, Athanasopoulos V, Baró I, Ribeiro de Oliveira-Mendes BB, Redon R, Charpentier F, Raju H, DiSilvestre D, Wei J, Wang R, Rafehi H, Kaspi A, Bahlo M, Dick IE, Chen SRW, Cook MC, Vinuesa CG, Overgaard MT, Schwartz PJ. Infanticide vs. inherited cardiac arrhythmias. Europace 2020; 23:441-450. [PMID: 33200177 PMCID: PMC7947592 DOI: 10.1093/europace/euaa272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/28/2023] Open
Abstract
AIMS In 2003, an Australian woman was convicted by a jury of smothering and killing her four children over a 10-year period. Each child died suddenly and unexpectedly during a sleep period, at ages ranging from 19 days to 18 months. In 2019 we were asked to investigate if a genetic cause could explain the children's deaths as part of an inquiry into the mother's convictions. METHODS AND RESULTS Whole genomes or exomes of the mother and her four children were sequenced. Functional analysis of a novel CALM2 variant was performed by measuring Ca2+-binding affinity, interaction with calcium channels and channel function. We found two children had a novel calmodulin variant (CALM2 G114R) that was inherited maternally. Three genes (CALM1-3) encode identical calmodulin proteins. A variant in the corresponding residue of CALM3 (G114W) was recently reported in a child who died suddenly at age 4 and a sibling who suffered a cardiac arrest at age 5. We show that CALM2 G114R impairs calmodulin's ability to bind calcium and regulate two pivotal calcium channels (CaV1.2 and RyR2) involved in cardiac excitation contraction coupling. The deleterious effects of G114R are similar to those produced by G114W and N98S, which are considered arrhythmogenic and cause sudden cardiac death in children. CONCLUSION A novel functional calmodulin variant (G114R) predicted to cause idiopathic ventricular fibrillation, catecholaminergic polymorphic ventricular tachycardia, or mild long QT syndrome was present in two children. A fatal arrhythmic event may have been triggered by their intercurrent infections. Thus, calmodulinopathy emerges as a reasonable explanation for a natural cause of their deaths.
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Affiliation(s)
- Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Todor Arsov
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David A Wallace
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia
| | - Helene Halkjær Jensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Lia Crotti
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin, Via Pier Lombardo, 22, 20135 Milan, Italy,Department of Cardiovascular, Neural and Metabolic Sciences, Istituto Auxologico Italiano, IRCCS, San Luca Hospital, Milan, Italy,Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marcin Adamski
- Biology Teaching and Learning Centre, Research School of Biology and John Curtin School of Medical Research, The Australian National University, Canberra, Acton 2601, Australia
| | - Yafei Zhang
- NGS Team, Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Acton 2601, Australia
| | - Matt A Field
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia
| | - Isabelle Baró
- Université de Nantes, CNRS, INSERM, L’institut du Thorax, F-44000 Nantes, France
| | | | - Richard Redon
- Université de Nantes, CNRS, INSERM, L’institut du Thorax, F-44000 Nantes, France
| | - Flavien Charpentier
- Université de Nantes, CNRS, INSERM, L’institut du Thorax, F-44000 Nantes, France
| | - Hariharan Raju
- Cardiology Department, Faculty of Medicine, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Deborah DiSilvestre
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jinhong Wei
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ruiwu Wang
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia,Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Antony Kaspi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia,Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia,Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Ivy E Dick
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sui Rong Wayne Chen
- Department of Physiology and Pharmacology, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease, Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, Acton 2601, Australia,Corresponding authors. +39 0255000408/9. E-mail address: (P.J.S.); Tel +45 9940 8525. E-mail address: (M.T.O.); Tel +61 432130556. E-mail address: (C.G.V.)
| | - Michael Toft Overgaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark,Corresponding authors. +39 0255000408/9. E-mail address: (P.J.S.); Tel +45 9940 8525. E-mail address: (M.T.O.); Tel +61 432130556. E-mail address: (C.G.V.)
| | - Peter J Schwartz
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin, Via Pier Lombardo, 22, 20135 Milan, Italy,Corresponding authors. +39 0255000408/9. E-mail address: (P.J.S.); Tel +45 9940 8525. E-mail address: (M.T.O.); Tel +61 432130556. E-mail address: (C.G.V.)
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12
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Rafehi H, Szmulewicz DJ, Pope K, Wallis M, Christodoulou J, White SM, Delatycki MB, Lockhart PJ, Bahlo M. Rapid Diagnosis of Spinocerebellar Ataxia 36 in a Three-Generation Family Using Short-Read Whole-Genome Sequencing Data. Mov Disord 2020; 35:1675-1679. [PMID: 32407596 DOI: 10.1002/mds.28105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinocerebellar ataxias are often caused by expansions of short tandem repeats. Recent methodological advances have made repeat expansion (RE) detection with whole-genome sequencing (WGS) feasible. OBJECTIVES The objective of this study was to determine the genetic basis of ataxia in a multigenerational Australian pedigree with autosomal-dominant inheritance. METHODS AND RESULTS WGS was performed on 3 affected relatives. The sequence data were screened for known pathogenic REs using 2 RE detection tools: exSTRa and ExpansionHunter. This screen provided a clear and rapid diagnosis (<5 days from receiving the sequencing data) of spinocerebellar ataxia 36, a rare form of ataxia caused by an intronic GGCCTG RE in NOP56. CONCLUSIONS The diagnosis of rare ataxias caused by REs is highly feasible and cost-effective with WGS. We propose that WGS could potentially be implemented as the frontline, cost-effective methodology for the molecular testing of individuals with a clinical diagnosis of ataxia. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Haloom Rafehi
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.,Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - David J Szmulewicz
- Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, Victoria, Australia.,Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, Victoria, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Tasmania, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Susan M White
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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13
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Bennett MF, Oliver KL, Regan BM, Bellows ST, Schneider AL, Rafehi H, Sikta N, Crompton DE, Coleman M, Hildebrand MS, Corbett MA, Kroes T, Gecz J, Scheffer IE, Berkovic SF, Bahlo M. Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families. Eur J Hum Genet 2020; 28:973-978. [PMID: 32203200 DOI: 10.1038/s41431-020-0606-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/05/2020] [Accepted: 03/03/2020] [Indexed: 11/09/2022] Open
Abstract
Familial adult myoclonic epilepsy 1 (FAME1), first recognised in Japanese families, was recently shown to be caused by a TTTCA repeat insertion in intron 4 of SAMD12 on chromosome 8. We performed whole genome sequencing on two families with FAME, one of Sri Lankan origin and the other of Indian origin, and identified a TTTCA repeat insertion in SAMD12 in both families. Haplotype analysis revealed that both families shared the same core ancestral haplotype reported in Japanese and Chinese families with FAME1. Mutation dating, based on the length of shared haplotypes, estimated the age of the ancestral haplotype to be ~670 generations, or 17,000 years old. Our data extend the geographic range of this repeat expansion to Southern Asia and potentially implicate an even broader regional distribution given the age of the variant. This finding suggests patients of Asian ancestry with suspected FAME should be screened for the SAMD12 TTTCA expansion.
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Affiliation(s)
- Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia.,Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Karen L Oliver
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Brigid M Regan
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Susannah T Bellows
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia.,Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Neblina Sikta
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Douglas E Crompton
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia.,Neurology Department, Northern Health, Melbourne, VIC, 3076, Australia
| | - Matthew Coleman
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, 3052, Australia
| | - Mark A Corbett
- Robinson Research Institute & Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Thessa Kroes
- Robinson Research Institute & Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Robinson Research Institute & Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, VIC, 3052, Australia.,The Florey Institute, Parkville, VIC, 3052, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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14
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Florian RT, Kraft F, Leitão E, Kaya S, Klebe S, Magnin E, van Rootselaar AF, Buratti J, Kühnel T, Schröder C, Giesselmann S, Tschernoster N, Altmueller J, Lamiral A, Keren B, Nava C, Bouteiller D, Forlani S, Jornea L, Kubica R, Ye T, Plassard D, Jost B, Meyer V, Deleuze JF, Delpu Y, Avarello MDM, Vijfhuizen LS, Rudolf G, Hirsch E, Kroes T, Reif PS, Rosenow F, Ganos C, Vidailhet M, Thivard L, Mathieu A, Bourgeron T, Kurth I, Rafehi H, Steenpass L, Horsthemke B, LeGuern E, Klein KM, Labauge P, Bennett MF, Bahlo M, Gecz J, Corbett MA, Tijssen MAJ, van den Maagdenberg AMJM, Depienne C. Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3. Nat Commun 2019; 10:4919. [PMID: 31664039 PMCID: PMC6820781 DOI: 10.1038/s41467-019-12763-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022] Open
Abstract
Familial Adult Myoclonic Epilepsy (FAME) is a genetically heterogeneous disorder characterized by cortical tremor and seizures. Intronic TTTTA/TTTCA repeat expansions in SAMD12 (FAME1) are the main cause of FAME in Asia. Using genome sequencing and repeat-primed PCR, we identify another site of this repeat expansion, in MARCH6 (FAME3) in four European families. Analysis of single DNA molecules with nanopore sequencing and molecular combing show that expansions range from 3.3 to 14 kb on average. However, we observe considerable variability in expansion length and structure, supporting the existence of multiple expansion configurations in blood cells and fibroblasts of the same individual. Moreover, the largest expansions are associated with micro-rearrangements occurring near the expansion in 20% of cells. This study provides further evidence that FAME is caused by intronic TTTTA/TTTCA expansions in distinct genes and reveals that expansions exhibit an unexpectedly high somatic instability that can ultimately result in genomic rearrangements.
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Affiliation(s)
- Rahel T Florian
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stephan Klebe
- Department of Neurology, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eloi Magnin
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Anne-Fleur van Rootselaar
- Departments of Neurology and Clinical Neurophysiology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Sebastian Giesselmann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Nikolai Tschernoster
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, 50931, Cologne, Germany
| | - Anaide Lamiral
- Department of Neurology, CHU Jean Minjoz, 25000, Besançon, France
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Caroline Nava
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Sylvie Forlani
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Ludmila Jornea
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Regina Kubica
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Tao Ye
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Damien Plassard
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Bernard Jost
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Yannick Delpu
- Genomic Vision, 80 Rue des Meuniers, 92220, Bagneux, France
| | | | - Lisanne S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Gabrielle Rudolf
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Edouard Hirsch
- Department of Neurology-centre de référence des epilepsies rares, University Hospital of Strasbourg, 1 Avenue Molière, 67200, Strasbourg, France
| | - Thessa Kroes
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Philipp S Reif
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
| | - Christos Ganos
- Department of Neurology, Charité University Medicine Berlin, 10117, Berlin, Germany
| | - Marie Vidailhet
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Lionel Thivard
- APHP, Hôpital Pitié-Salpêtrière, Département de Neurologie, 75013, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Pasteur Institute, UMR3571 CNRS, Université de Paris, 75015, Paris, France
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, 52062, Aachen, Germany
| | - Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Eric LeGuern
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Karl Martin Klein
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University and LOEWE Center for Personalized Translational Epilepsy Research (CePTER), 60323, Frankfurt am Main, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, 35037, Marburg, Germany
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Pierre Labauge
- Department of Neurology, Gui de Chauliac University Hospital, 34295, Montpellier, France
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Jozef Gecz
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
- South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Mark A Corbett
- School of Biological Sciences, School of Medicine and Robinson Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Marina A J Tijssen
- Department of Neurology, University Medical Center Groningen, University of Groningen, 9700, AB, Groningen, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany.
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France.
- IGBMC, CNRS UMR 7104/INSERM U1258/Université de Strasbourg, 1 Rue Laurent Fries, 67400, Illkirch-Graffenstaden, France.
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15
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Rafehi H, Szmulewicz DJ, Bennett MF, Sobreira NLM, Pope K, Smith KR, Gillies G, Diakumis P, Dolzhenko E, Eberle MA, Barcina MG, Breen DP, Chancellor AM, Cremer PD, Delatycki MB, Fogel BL, Hackett A, Halmagyi GM, Kapetanovic S, Lang A, Mossman S, Mu W, Patrikios P, Perlman SL, Rosemergy I, Storey E, Watson SRD, Wilson MA, Zee DS, Valle D, Amor DJ, Bahlo M, Lockhart PJ. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS. Am J Hum Genet 2019; 105:151-165. [PMID: 31230722 PMCID: PMC6612533 DOI: 10.1016/j.ajhg.2019.05.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/21/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - David J Szmulewicz
- Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC 3004, Australia; Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg, VIC 3084, Australia
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Katherine R Smith
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Egor Dolzhenko
- Illumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA
| | | | - María García Barcina
- Genetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain
| | - David P Breen
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, Scotland
| | - Andrew M Chancellor
- Department of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand
| | - Phillip D Cremer
- University of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Brent L Fogel
- Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia
| | - G Michael Halmagyi
- Neurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Solange Kapetanovic
- Servicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain
| | - Anthony Lang
- Edmond J. Safra Program in Parkinson disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada; Department of Medicine, Division of Neurology, University Health Network and the University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington 6021, New Zealand
| | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Susan L Perlman
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ian Rosemergy
- Department of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand
| | - Elsdon Storey
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shaun R D Watson
- Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Michael A Wilson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - David S Zee
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David J Amor
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia.
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16
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Stephenson SEM, Djaldetti R, Rafehi H, Wilson GR, Gillies G, Bahlo M, Lockhart PJ. Familial early onset Parkinson's disease caused by a homozygous frameshift variant in PARK7: Clinical features and literature update. Parkinsonism Relat Disord 2019; 64:308-311. [DOI: 10.1016/j.parkreldis.2019.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022]
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Abstract
Although methyl CpG binding domain protein-2 (MeCP2) is commonly understood to function as a silencing factor at methylated DNA sequences, recent studies also show that MeCP2 can bind unmethylated sequences and coordinate gene activation. MeCP2 displays broad binding patterns throughout the genome, with high expression levels similar to histone H1 in neurons. Despite its significant presence in the brain, only subtle gene expression changes occur in the absence of MeCP2. This may reflect a more complex regulatory mechanism of MeCP2 to complement chromatin binding. Using an RNA immunoprecipitation of native chromatin technique, we identify MeCP2 interacting microRNAs in mouse primary cortical neurons. In addition, comparison with mRNA sequencing data from Mecp2-null mice suggests that differentially expressed genes may indeed be targeted by MeCP2-interacting microRNAs. These findings highlight the MeCP2 interaction with microRNAs that may modulate its binding with chromatin and regulate gene expression.
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Affiliation(s)
- Abdul Waheed Khan
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia.,c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia
| | - Mark Ziemann
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Haloom Rafehi
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Scott Maxwell
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Giuseppe D Ciccotosto
- c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia.,d Bio21 Molecular science and Biotechnology Institute , Victoria , Australia
| | - Assam El-Osta
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia.,c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia.,e Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital , The Chinese University of Hong Kong , Hong Kong SAR
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18
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Rafehi H, Kaspi A, Ziemann M, Okabe J, Karagiannis TC, El-Osta A. Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. Epigenetics 2018; 12:991-1003. [PMID: 28886276 DOI: 10.1080/15592294.2017.1371892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Given the skyrocketing costs to develop new drugs, repositioning of approved drugs, such as histone deacetylase (HDAC) inhibitors, may be a promising strategy to develop novel therapies. However, a gap exists in the understanding and advancement of these agents to meaningful translation for which new indications may emerge. To address this, we performed systems-level analyses of 33 independent HDAC inhibitor microarray studies. Based on network analysis, we identified enrichment for pathways implicated in metabolic syndrome and diabetes (insulin receptor signaling, lipid metabolism, immunity and trafficking). Integration with ENCODE ChIP-seq datasets identified suppression of EP300 target genes implicated in diabetes. Experimental validation indicates reversal of diabetes-associated EP300 target genes in primary vascular endothelial cells derived from a diabetic individual following inhibition of HDACs (by SAHA), EP300, or EP300 knockdown. Our computational systems biology approach provides an adaptable framework for the prediction of novel therapeutics for existing disease.
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Affiliation(s)
- Haloom Rafehi
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Antony Kaspi
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Mark Ziemann
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Jun Okabe
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Tom C Karagiannis
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia.,b Department of Pathology, The University of Melbourne , Parkville , Victoria , Australia
| | - Assam El-Osta
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia.,b Department of Pathology, The University of Melbourne , Parkville , Victoria , Australia.,c Faculty of Medicine, Nursing and Health Sciences, Department of Diabetes, Monash University , Melbourne , Victoria , Australia.,d Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong , Hong Kong SAR
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Nguyen MN, Ziemann M, Kiriazis H, Su Y, Thomas Z, Lu Q, Donner DG, Zhao WB, Rafehi H, Sadoshima J, McMullen JR, El-Osta A, Du XJ. Galectin-3 deficiency ameliorates fibrosis and remodeling in dilated cardiomyopathy mice with enhanced Mst1 signaling. Am J Physiol Heart Circ Physiol 2018; 316:H45-H60. [PMID: 30387702 DOI: 10.1152/ajpheart.00609.2018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dilated cardiomyopathy (DCM) is a major cause of heart failure without effective therapy. Fibrogenesis plays a key role in the development of DCM, but little is known of the expression of the profibrotic factor galectin-3 (Gal-3) and its role in DCM pathophysiology. In a mouse DCM model with transgenic (TG) overexpression of mammalian sterile 20-like kinase 1 (Mst1), we studied Gal-3 expression and effects of the Gal-3 inhibitor modified citrus pectin (MCP) or Gal-3 gene knockout (KO). Gal-3 deletion in TG mice (TG/KO) was achieved by crossbreeding Mst1-TG mice with Gal-3 KO mice. The DCM phenotype was assessed by echocardiography and micromanometry. Cardiac expression of Gal-3 and fibrosis were determined. The cardiac transcriptome was profiled by RNA sequencing. Mst1-TG mice at 3-8 mo of age exhibited upregulated expression of Gal-3 by ~40-fold. TG mice had dilatation of cardiac chambers, suppressed left ventricular (LV) ejection fraction, poor LV contractility and relaxation, a threefold increase in LV collagen content, and upregulated fibrotic genes. Four-month treatment with MCP showed no beneficial effects. Gal-3 deletion in Mst1-TG mice attenuated chamber dilatation, organ congestion, and fibrogenesis. RNA sequencing identified profound disturbances by Mst1 overexpression in the cardiac transcriptome, which largely remained in TG/KO hearts. Gal-3 deletion in Mst1-TG mice, however, partially reversed the dysregulated transcriptional signaling involving extracellular matrix remodeling and collagen formation. We conclude that cardiac Mst1 activation leads to marked Gal-3 upregulation and transcriptome disturbances in the heart. Gal-3 deficiency attenuated cardiac remodeling and fibrotic signaling. NEW & NOTEWORTHY We found in a transgenic mouse dilated cardiomyopathy (DCM) model a pronounced upregulation of galectin-3 in cardiomyocytes. Galectin-3 gene deletion reduced cardiac fibrosis and fibrotic gene profiles and ameliorated cardiac remodeling and dysfunction. These benefits of galectin-3 deletion were in contrast to the lack of effect of treatment with the galectin-3 inhibitor modified citrus pectin. Our study suggests that suppression of galectin-3 mRNA expression could be used to treat DCM with high cardiac galectin-3 content.
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Affiliation(s)
- My-Nhan Nguyen
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia
| | - Mark Ziemann
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia
| | - Helen Kiriazis
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Yidan Su
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Zara Thomas
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Qun Lu
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Health Science Center, Xian Jiaotong University , Xian , People's Republic of China
| | - Daniel G Donner
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Wei-Bo Zhao
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Haloom Rafehi
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School , Newark, New Jersey
| | - Julie R McMullen
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia
| | - Assam El-Osta
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia.,Prince of Wales Hospital, The Chinese University of Hong Kong , Shatin, Hong Kong Special Administrative Region , People's Republic of China
| | - Xiao-Jun Du
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia.,Health Science Center, Xian Jiaotong University , Xian , People's Republic of China
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20
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Du XJ, Nguyen MN, Ziemann M, Kiriazis H, Su Y, Rafehi H, Donner D, Zhao WB, Dart AM, Sadoshima J, McMullen JR, El-Osta A. P941Galectin-3 deficiency ameliorates cardiac fibrosis and remodelling in transgenic mice with dilated cardiomyopathy. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy564.p941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- X.-J Du
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - M N Nguyen
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - M Ziemann
- Monash University, Department of Diabetes, Melbourne, Australia
| | - H Kiriazis
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - Y Su
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - H Rafehi
- Monash University, Department of Diabetes, Melbourne, Australia
| | - D Donner
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - W B Zhao
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - A M Dart
- The Alfred Hospital, Alfred Heart Centre, Melbourne, Australia
| | - J Sadoshima
- New Jersey Medical School, Department of Cell Biology and Molecular Medicine Rutgers, New Jersey, United States of America
| | - J R McMullen
- Baker IDI Heart and Diabetes Institute, Experimental Cardiology, Melbourne, Australia
| | - A El-Osta
- Monash University, Department of Diabetes, Melbourne, Australia
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21
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Quaife-Ryan GA, Sim CB, Ziemann M, Kaspi A, Rafehi H, Ramialison M, El-Osta A, Hudson JE, Porrello ER. Multicellular Transcriptional Analysis of Mammalian Heart Regeneration. Circulation 2017; 136:1123-1139. [PMID: 28733351 PMCID: PMC5598916 DOI: 10.1161/circulationaha.117.028252] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus nonregenerative (adult) state for the first time. METHODS Cardiomyocytes, fibroblasts, leukocytes, and endothelial cells from infarcted and noninfarcted neonatal (P1) and adult (P56) mouse hearts were isolated by enzymatic dissociation and fluorescence-activated cell sorting at day 3 following surgery. RNA sequencing was performed on these cell populations to generate the transcriptome of the major cardiac cell populations during cardiac development, repair, and regeneration. To complement our transcriptomic data, we also surveyed the epigenetic landscape of cardiomyocytes during postnatal maturation by performing deep sequencing of accessible chromatin regions by using the Assay for Transposase-Accessible Chromatin from purified mouse cardiomyocyte nuclei (P1, P14, and P56). RESULTS Profiling of cardiomyocyte and nonmyocyte transcriptional programs uncovered several injury-responsive genes across regenerative and nonregenerative time points. However, the majority of transcriptional changes in all cardiac cell types resulted from developmental maturation from neonatal stages to adulthood rather than activation of a distinct regeneration-specific gene program. Furthermore, adult leukocytes and fibroblasts were characterized by the expression of a proliferative gene expression network following infarction, which mirrored the neonatal state. In contrast, cardiomyocytes failed to reactivate the neonatal proliferative network following infarction, which was associated with loss of chromatin accessibility around cell cycle genes during postnatal maturation. CONCLUSIONS This work provides a comprehensive framework and transcriptional resource of multiple cardiac cell populations during cardiac development, repair, and regeneration. Our findings define a regulatory program underpinning the neonatal regenerative state and identify alterations in the chromatin landscape that could limit reinduction of the regenerative program in adult cardiomyocytes.
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Affiliation(s)
- Gregory A Quaife-Ryan
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Choon Boon Sim
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Mark Ziemann
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Antony Kaspi
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Haloom Rafehi
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Mirana Ramialison
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - Assam El-Osta
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.)
| | - James E Hudson
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.).
| | - Enzo R Porrello
- From School of Biomedical Sciences, University of Queensland, Brisbane, Australia (G.A.Q.-R., C.B.S., J.E.H., E.R.P.); Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Central Clinical School, Monash University, Melbourne, Victoria, Australia (M.Z., A.K., H.R., A.E.-O.); Australian Regenerative Medicine Institute, EMBL-Australia Collaborating Group, Systems Biology Institute Australia, Monash University, Melbourne, Victoria (M.R.); Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, Chinese University of Hong Kong (A.E.-O.); Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia (E.R.P.); and Department of Physiology, School of Biomedical Sciences, University of Melbourne, Victoria, Australia (E.R.P.).
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Rafehi H, Karagiannis TC, El-Osta A. Pharmacological Histone Deacetylation Distinguishes Transcriptional Regulators. Curr Top Med Chem 2017; 17:1611-1622. [PMID: 27823568 DOI: 10.2174/1568026617666161104104341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/14/2016] [Accepted: 06/19/2016] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Histone deacetylase (HDAC) enzymes control the acetylation status of transcription factors that regulate chromatin structure and gene function. The transcriptional regulatory factors that distinguish histone acetylation and deacetylation patterns by pharmacological HDAC inhibition (HDACi) have not yet been studied. METHODS We analysed sequencing datasets derived from human aortic endothelial cells (HAECs) stimulated with the HDAC inhibitors, Trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA). We integrated gene expression and histone acetylation profiles with the transcription factor binding site (TFBS) database derived from the Encyclopedia of DNA Elements (ENCODE) project. RESULTS Overall, TFBS signatures observed in SAHA and TSA stimulated cells were analogous. Histone acetylation was observed at transcription factor binding sites of target genes associated with the silencing factors NRSF, EZH2 and SUZ12. Histone deacetylation was a prominent property of HDACi and correlated with changes in the expression of genes regulated by proteins in transcriptional control such as histone acetyltransferase P300 and lysine demethylase JARID1A, as well as the regulatory factors cMYC, YY1 and STAT family proteins. CONCLUSION We identified several transcription factors and coregulators implicated in the regulation of histone modification at target genes mediated by pharmacological HDAC inhibition.
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Affiliation(s)
- Haloom Rafehi
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC, Australia
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23
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Khan AW, Ziemann M, Corcoran SJ, K N H, Okabe J, Rafehi H, Maxwell SS, Esler MD, El-Osta A. NET silencing by let-7i in postural tachycardia syndrome. JCI Insight 2017; 2:e90183. [PMID: 28352654 DOI: 10.1172/jci.insight.90183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
While strongly implicated in postural tachycardia syndrome (POTS), considerable controversy exists regarding norepinephrine transporter (NET) loss of function. POTS is characterized by the clinical symptoms of orthostatic intolerance, lightheadedness, tachycardia, and syncope or near syncope with upright posture. Abnormal sympathetic nervous system activity is typical, of a type which suggests dysfunction of the NET, with evidence that the gene responsible is under tight epigenetic control. Using RNA of isolated chromatin combined with massive parallel sequencing (RICh-seq) we show that let-7i miRNA suppresses NET by methyl-CpG-binding protein 2 (MeCP2). Vorinostat restores epigenetic control and NET expression in leukocytes derived from POTS participants.
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Affiliation(s)
- Abdul Waheed Khan
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Ziemann
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Susan J Corcoran
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Harikrishnan K N
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jun Okabe
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Scott S Maxwell
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Murray D Esler
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Assam El-Osta
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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24
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Abstract
Many epigenetic-based therapeutics, including drugs such as histone deacetylase inhibitors, are now used in the clinic or are undergoing advanced clinical trials. The study of chromatin-modifying proteins has benefited from the rapid advances in high-throughput sequencing methods, the organized efforts of major consortiums and by individual groups to profile human epigenomes in diverse tissues and cell types. However, while such initiatives have carefully characterized healthy human tissue, disease epigenomes and drug-epigenome interactions remain very poorly understood. Reviewed here is how high-throughput sequencing improves our understanding of chromatin regulator proteins and the potential implications for the study of human disease and drug development and discovery.
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Affiliation(s)
- Haloom Rafehi
- a Epigenetics in Human Health and Disease Laboratory , Baker IDI Heart and Diabetes Institute , Melbourne , Victoria , Australia
| | - Abdul Waheed Khan
- a Epigenetics in Human Health and Disease Laboratory , Baker IDI Heart and Diabetes Institute , Melbourne , Victoria , Australia.,b Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia
| | - Assam El-Osta
- a Epigenetics in Human Health and Disease Laboratory , Baker IDI Heart and Diabetes Institute , Melbourne , Victoria , Australia.,b Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia.,c Faculty of Medicine , Monash University , Melbourne , Victoria , Australia
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25
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Rodd AL, Ververis K, Sayakkarage D, Khan AW, Rafehi H, Ziemann M, Loveridge SJ, Lazarus R, Kerr C, Lockett T, El-Osta A, Karagiannis TC, Bennett LE. RNA sequencing supports distinct reactive oxygen species-mediated pathways of apoptosis by high and low size mass fractions of Bay leaf (Lauris nobilis) in HT-29 cells. Food Funct 2015; 6:2507-24. [PMID: 26114728 DOI: 10.1039/c5fo00467e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Anti-proliferative and pro-apoptotic effects of Bay leaf (Laurus nobilis) in mammalian cancer and HT-29 adenocarcinoma cells have been previously attributed to effects of polyphenolic and essential oil chemical species. Recently, we demonstrated differentiated growth-regulating effects of high (HFBL) versus low molecular mass (LFBL) aqueous fractions of bay leaf and now confirm by comparative effects on gene expression, that HFBL and LFBL suppress HT-29 growth by distinct mechanisms. Induction of intra-cellular lesions including DNA strand breakage by extra-cellular HFBL, invoked the hypothesis that iron-mediated reactive oxygen species with capacity to penetrate cell membrane, were responsible for HFBL-mediated effects, supported by equivalent effects of HFBL in combination with γ radiation. Activities of HFBL and LFBL were interpreted to reflect differentiated responses to iron-mediated reactive oxygen species (ROS), occurring either outside or inside cells. In the presence of LFBL, apoptotic death was relatively delayed compared with HFBL. ROS production by LFBL mediated p53-dependent apoptosis and recovery was suppressed by promoting G1/S phase arrest and failure of cellular tight junctions. In comparison, intra-cellular anti-oxidant protection exerted by LFBL was absent for extra-cellular HFBL (likely polysaccharide-rich), which potentiated more rapid apoptosis by producing DNA double strand breaks. Differentiated effects on expression of genes regulating ROS defense and chromatic condensation by LFBL versus HFBL, were observed. The results support ferrous iron in cell culture systems and potentially in vivo, can invoke different extra-cellular versus intra-cellular ROS-mediated chemistries, that may be regulated by exogenous, including dietary species.
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Affiliation(s)
- Annabelle L Rodd
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
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26
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Ooi JYY, Tuano NK, Rafehi H, Gao XM, Ziemann M, Du XJ, El-Osta A. HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes. Epigenetics 2015; 10:418-30. [PMID: 25941940 DOI: 10.1080/15592294.2015.1024406] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Pharmacological histone deacetylase (HDAC) inhibitors attenuate pathological cardiac remodeling and hypertrophic gene expression; yet, the direct histone targets remain poorly characterized. Since the inhibition of HDAC activity is associated with suppressing hypertrophy, we hypothesized histone acetylation would target genes implicated in cardiac remodeling. Trichostatin A (TSA) regulates cardiac gene expression and attenuates transverse aortic constriction (TAC) induced hypertrophy. We used chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq) to map, for the first time, genome-wide histone acetylation changes in a preclinical model of pathological cardiac hypertrophy and attenuation of pathogenesis with TSA. Pressure overload-induced cardiac hypertrophy was associated with histone acetylation of genes implicated in cardiac contraction, collagen deposition, inflammation, and extracellular matrix identified by ChIP-seq. Gene set enrichment analysis identified NF-kappa B (NF-κB) transcription factor activation with load induced hypertrophy. Increased histone acetylation was observed on the promoters of NFκB target genes (Icam1, Vcam1, Il21r, Il6ra, Ticam2, Cxcl10) consistent with gene activation in the hypertrophied heart. Surprisingly, TSA attenuated pressure overload-induced cardiac hypertrophy and the suppression of NFκB target genes by broad histone deacetylation. Our results suggest a mechanism for cardioprotection subject to histone deacetylation as a previously unknown target, implicating the importance of inflammation by pharmacological HDAC inhibition. The results of this study provides a framework for HDAC inhibitor function in the heart and argues the long held views of acetylation is subject to more flexibility than previously thought.
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Key Words
- ANP, Atrial natriuretic peptide
- BNP, Brain natriuretic peptide
- BW, Body Weight
- ChIP, Chromatin Immunoprecipitation
- Ct, threshold cycle number
- Cxcl10, Chemokine (C-X-C Motif) ligand 10
- ENCODE, Encyclopedia of DNA Elements Consortium
- FDR, False Discovery Rate
- FS, Fractional Shortening
- GAIIx, Genome Analyzer IIx
- HDAC inhibitor
- HDAC, Histone deacetylase
- Icam1, Intercellular adhesion molecule 1
- Il21r, Interleukin-21 receptor
- Il6ra, Interleukin-6 receptor
- LV, Left Ventricle
- LVDd, Left Ventricular Diastolic Dimension
- LVH, Left Ventricle Hypertrophy
- MACs, Model-based Analysis of ChIP-seq
- NES, normalized enrichment score
- NFκB, Nuclear factor of kappa light polypeptide gene enhancer in B-cells
- NGS, Next Generation Sequencing
- SEM, Standard Error of the Mean
- Serca2a, Sarcoplasmic reticulum Ca2+ ATPase
- TAC veh, TAC vehicle
- TAC, Transverse Aortic Constriction
- TF, transcription factor
- TL, Tibia Length
- TSA, Trichostatin A
- TSS, Transcription Start Site
- Ticam2, Toll-like receptor adaptor molecule 2
- Traf3, TNF receptor-associated factor 3
- UTR, Untranslated region
- Vcam1, Vascular cell adhesion molecule 1
- cDNA, complementary DNA
- cardiac hypertrophy
- chromatin
- epigenetics
- histone acetylation
- next generation sequencing
- α/βMHC, Alpha/Beta myosin heavy chain
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Affiliation(s)
- Jenny Y Y Ooi
- a Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute ; Melbourne , Victoria , Australia
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27
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Rafehi H, Balcerczyk A, Lunke S, Kaspi A, Ziemann M, Kn H, Okabe J, Khurana I, Ooi J, Khan AW, Du XJ, Chang L, Haviv I, Keating ST, Karagiannis TC, El-Osta A. Vascular histone deacetylation by pharmacological HDAC inhibition. Genome Res 2014; 24:1271-84. [PMID: 24732587 PMCID: PMC4120081 DOI: 10.1101/gr.168781.113] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
HDAC inhibitors can regulate gene expression by post-translational modification of histone as well as nonhistone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action. However, little is known of the extent of genome-wide changes in cells stimulated by the hydroxamic acids, TSA and SAHA. In this article, we map vascular chromatin modifications including histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation-mediated gene expression is often associated with modification of other lysine residues, we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). RNA sequencing indicates the differential expression of ∼30% of genes, with almost equal numbers being up- and down-regulated. We observed broad deacetylation and gene expression changes conferred by TSA and SAHA mediated by the loss of EP300/CREBBP binding at multiple gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation by pharmacological HDAC inhibition.
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Affiliation(s)
- Haloom Rafehi
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aneta Balcerczyk
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Sebastian Lunke
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Antony Kaspi
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Mark Ziemann
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Harikrishnan Kn
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Jun Okabe
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; Faculty of Medicine, Monash University, Victoria 3800, Australia
| | - Ishant Khurana
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Jenny Ooi
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Abdul Waheed Khan
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Xiao-Jun Du
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; Faculty of Medicine, Monash University, Victoria 3800, Australia
| | - Lisa Chang
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Izhak Haviv
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Samuel T Keating
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Tom C Karagiannis
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Assam El-Osta
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia; Department of Pathology, The University of Melbourne, Parkville, Victoria 3010, Australia; Faculty of Medicine, Monash University, Victoria 3800, Australia
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28
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Rafehi H, El-Osta A, Karagiannis TC. Epigenetic mechanisms in the pathogenesis of diabetic foot ulcers. J Diabetes Complications 2012; 26:554-61. [PMID: 22739801 DOI: 10.1016/j.jdiacomp.2012.05.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 05/03/2012] [Accepted: 05/22/2012] [Indexed: 12/14/2022]
Abstract
The incidence of diabetes mellitus, a chronic metabolic disease associated with both predisposing genetic and environmental factors, is increasing globally. As a result, it is expected that there will also be an increasing incidence of diabetic complications which arise as a result of poor glycemic control. Complications include cardiovascular diseases, nephropathy, retinopathy and diabetic foot ulcers. The findings of several major clinical trials have identified that diabetic complications may arise even after many years of proper glycemic control. This has led to the concept of persistent epigenetic changes. Various epigenetic mechanisms have been identified as important contributors to the pathogenesis of diabetes and diabetic complications. The aim of this review is to provide an overview of the pathobiology of type 2 diabetes with an emphasis on complications, particularly diabetic foot ulcers. An overview of epigenetic mechanisms is provided and the focus is on the emerging evidence for aberrant epigenetic mechanisms in diabetic foot ulcers.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
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29
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Abstract
Olive oil, an oil rich in monounsaturated fatty acids (MUFCs) and minor constituents including phenolic compounds, is a major component of the Mediterranean diet. The potential health benefits of the Mediterranean diet were highlighted by the seminal Seven Countries Study, and more contemporary research has identified olive oil as a major element responsible for these effects. It is emerging that the phenolic compounds are the most likely candidates accounting for the cardioprotective and cancer preventative effects of extra virgin olive oil (EVOO). In particular, the phenolic compound, hydroxytyrosol has been identified as one of the most potent antioxidants found in olive oil. This review will briefly consider historical aspects of olive oil research and the biological properties of phenolic compounds in olive oil will be discussed. The focus of the discussion will be related to the mechanisms of action of hydroxytyrosol. Studies have demonstrated that hydroxytyrosol induces apoptosis and cell cycle arrest in cancer cells. Further, research has shown that hydroxytyrosol can prevent cardiovascular disease by reducing the expression of adhesion molecules on endothelial cells and preventing the oxidation of low-density lipoprotein (LDL). The molecular mechanisms accounting for these effects are reviewed.
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Affiliation(s)
- Haloom Rafehi
- Department of Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, 75 Commercial Road, Melbourne, Victoria, Australia
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30
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Kaspi A, Ziemann M, Rafehi H, Lazarus R, El-Osta A. A pipeline for the identification and characterization of chromatin modifications derived from ChIP-Seq datasets. Biochimie 2012; 94:2353-9. [PMID: 22705386 DOI: 10.1016/j.biochi.2012.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/04/2012] [Indexed: 11/16/2022]
Abstract
The advent of massive parallel sequencing of immunopurified chromatin and its determinants has provided new avenues for researchers to map epigenome-wide changes and there is tremendous interest to uncover regulatory signatures to understand fundamental questions associated with chromatin structure and function. Indeed, the rapid development of large genome annotation projects has seen a resurgence in chromatin immunoprecipitation (ChIP) based protocols which are used to distinguish protein interactions coupled with large scale sequencing (Seq) to precisely map epigenome-wide interactions. Despite some of the great advances in our understanding of chromatin modifying complexes and their determinants, the development of ChIP-Seq technologies also pose specific demands on the integration of data for visualization, manipulation and analysis. In this article we discuss some of the considerations for experimental design planning, quality control, and bioinformatic analysis. The key aspects of post sequencing analysis are the identification of regions of interest, differentiation between biological conditions and the characterization of sequence differences for chromatin modifications. We provide an overview of best-practise approaches with background information and considerations of integrative analysis from ChIP-Seq experiments.
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Affiliation(s)
- Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
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31
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Abstract
Obesity levels have increased significantly in the past five decades and are predicted to continue rising, resulting in important health implications. In particular, this has translated to an increase in the occurrence of type II diabetes mellitus (T2D). To alleviate associated problems, certain nutraceuticals have been considered as potential adjuncts or alternatives to conventional prescription drugs. Cinnamon, a commonly consumed spice originating from South East Asia, is currently being investigated as a potential preventative supplement and treatment for insulin resistance, metabolic syndrome and T2D. Extensive in vitro evidence has shown that cinnamon may improve insulin resistance by preventing and reversing impairments in insulin signalling in skeletal muscle. In adipose tissue, it has been shown that cinnamon increases the expression of peroxisome proliferator-activated receptors including, PPARγ. This is comparable to the action of commonly used thiazolinediones, which are PPAR agonists. Studies have also shown that cinnamon has potent anti-inflammatory properties. However, numerous human clinical trials with cinnamon have been conducted with varying findings. While some studies have showed no beneficial effect, others have indicated improvements in cholesterol levels, systolic blood pressure, insulin sensitivity and postprandial glucose levels with cinnamon. However, the only measurement consistently improved by cinnamon consumption is fasting glucose levels. While it is still premature to suggest the use of cinnamon supplementation based on the evidence, further investigation into mechanisms of action is warranted. Apart from further characterization of genetic and epigenetic changes in model systems, systematic large-scale clinical trials are required. In this study, we discuss the mechanisms of action of cinnamon in the context of T2D and we highlight some of the associated controversies.
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Affiliation(s)
- H Rafehi
- Epigenomic Medicine Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
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Rafehi H, Ververis K, Balcerczyk A, Ziemann M, Ooi J, Hu S, Kwa FAA, Loveridge SJ, Georgiadis GT, El-Osta A, Karagiannis TC. Investigation of the biological properties of Cinnulin PF in the context of diabetes: mechanistic insights by genome-wide mRNA-Seq analysis. Pathobiol Aging Age Relat Dis 2012; 2:PBA-2-11905. [PMID: 22953038 PMCID: PMC3417697 DOI: 10.3402/pba.v2i0.11905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/17/2012] [Accepted: 02/01/2012] [Indexed: 01/20/2023]
Abstract
The accumulating evidence of the beneficial effects of cinnamon (Cinnamomum burmanni) in type-2 diabetes, a chronic age-associated disease, has prompted the commercialisation of various supplemental forms of the spice. One such supplement, Cinnulin PF®, represents the water soluble fraction containing relatively high levels of the double-linked procyanidin type-A polymers of flavanoids. The overall aim of this study was to utilize genome-wide mRNA-Seq analysis to characterise the changes in gene expression caused by Cinnulin PF in immortalised human keratinocytes and microvascular endothelial cells, which are relevant with respect to diabetic complications. In summary, our findings provide insights into the mechanisms of action of Cinnulin PF in diabetes and diabetic complications. More generally, we identify relevant candidate genes which could provide the basis for further investigation.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC., Australia
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33
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Rafehi H, Smith AJ, Balcerczyk A, Ziemann M, Ooi J, Loveridge SJ, Baker EK, El-Osta A, Karagiannis TC. Investigation into the biological properties of the olive polyphenol, hydroxytyrosol: mechanistic insights by genome-wide mRNA-Seq analysis. Genes Nutr 2011; 7:343-55. [PMID: 21953375 DOI: 10.1007/s12263-011-0249-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/13/2011] [Indexed: 02/06/2023]
Abstract
The medicinal properties of the leaves and fruit of Olea Europaea (olive tree) have been known since antiquity. Numerous contemporary studies have linked the Mediterranean diet with increased health. In particular, consumption of olive oil has been associated with a decreased risk of cardiovascular disease and certain cancers. Increasingly, there has been an interest in the biological properties of polyphenols, which are minor constituents of olive oil. For example, hydroxytyrosol has been shown to be a potent antioxidant and has anti-atherogenic and anti-cancer properties. The overall aim of this study was to provide insights into the molecular mechanisms of action of hydroxytyrosol using genome-wide mRNA-Seq. Initial experiments were aimed at assessing cytotoxicity, apoptosis and cell cycle effects of hydroxytyrosol in various cell lines. The findings indicated a dose-dependent reduction in cell viability in human erythroleukemic K562 and human keratinocytes. When comparing the viability in parental CEM-CCRF and R100 cells (which overexpress the P-glycoprotein pump), it was determined that the R100 cells were more resistant to effects of hydroxytyrosol suggesting efflux by the multi-drug resistance pump. By comparing the uptake of Hoechst 33342 in the two cell lines that had been pretreated with hydroxytyrosol, it was determined that the polyphenol may have P-glycoprotein-modulating activity. Further, initial studies indicated modest radioprotective effects of relatively low doses of hydroxytyrosol in human keratinocytes. Analysis of mRNA sequencing data identified that treatment of keratinocytes with 20 μM hydroxytyrosol results in the upregulation of numerous antioxidant proteins and enzymes, including heme oxygenase-1 (15.46-fold upregulation), glutaredoxin (1.65) and glutathione peroxidase (1.53). This may account for the radioprotective activity of the compound, and reduction in oxidative stress suggests a mechanism for chemoprevention of cancer by hydroxytyrosol. Alteration in the expression of transcription factors may also contribute to the anti-cancer effects described in numerous studies. These include changes in the expression of STAT3, STAT6, SMAD7 and ETS-1. The telomerase subunit TERT was also found to be downregulated in K562 cells. Overall, our findings provide insights into the mechanisms of action of hydroxytyrosol, and more generally, we identify potential gene candidates for further exploration.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, 75 Commercial Road, Melbourne, VIC, Australia
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Abstract
The clonogenic (or colony forming) assay has been established for more than 50 years; the original paper describing the technique was published in 1956. Apart from documenting the method, the initial landmark study generated the first radiation-dose response curve for X-ray irradiated mammalian (HeLa) cells in culture. Basically, the clonogenic assay enables an assessment of the differences in reproductive viability (capacity of cells to produce progeny; i.e. a single cell to form a colony of 50 or more cells) between control untreated cells and cells that have undergone various treatments such as exposure to ionising radiation, various chemical compounds (e.g. cytotoxic agents) or in other cases genetic manipulation. The assay has become the most widely accepted technique in radiation biology and has been widely used for evaluating the radiation sensitivity of different cell lines. Further, the clonogenic assay is commonly used for monitoring the efficacy of radiation modifying compounds and for determining the effects of cytotoxic agents and other anti-cancer therapeutics on colony forming ability, in different cell lines. A typical clonogenic survival experiment using adherent cells lines involves three distinct components, 1) treatment of the cell monolayer in tissue culture flasks, 2) preparation of single cell suspensions and plating an appropriate number of cells in petri dishes and 3) fixing and staining colonies following a relevant incubation period, which could range from 1-3 weeks, depending on the cell line. Here we demonstrate the general procedure for performing the clonogenic assay with adherent cell lines with the use of an immortalized human keratinocyte cell line (FEP-1811). Also, our aims are to describe common features of clonogenic assays including calculation of the plating efficiency and survival fractions after exposure of cells to radiation, and to exemplify modification of radiation-response with the use of a natural antioxidant formulation.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, BakerIDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct
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Abstract
The prevalence of the chronic metabolic disorder, diabetes mellitus, is expected to increase in the coming years and worldwide pandemic levels are predicted. Inevitably, this will be accompanied by an increase in the prevalence of diabetic complications, including diabetic foot ulcers. At present, treatment options for diabetic foot ulcers are in many cases insufficient, and progression of the condition results in the requirement for limb amputation in a proportion of patients. To improve therapy, an increase in our understanding of the pathobiology of diabetic complications such as impaired wound healing is necessary. In this review, recent advances in molecular aspects of normal and impaired diabetic wound healing are discussed. Furthermore, investigations of the role of epigenetic processes in the pathogenesis of impaired diabetic wound healing are now emerging. Indeed, epigenetic changes have already been identified as key factors in diabetes and related complications and these are overviewed in this review.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
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