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Nguyen T, Urrutia-Cabrera D, Wang L, Lees JG, Wang JH, Hung SS, Hewitt AW, Edwards TL, McLenachan S, Chen FK, Lim SY, Luu CD, Guymer R, Wong RC. Knockout of AMD-associated gene POLDIP2 reduces mitochondrial superoxide in human retinal pigment epithelial cells. Aging (Albany NY) 2023; 15:1713-1733. [PMID: 36795578 PMCID: PMC10085620 DOI: 10.18632/aging.204522] [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: 07/16/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Genetic and epidemiologic studies have significantly advanced our understanding of the genetic factors contributing to age-related macular degeneration (AMD). In particular, recent expression quantitative trait loci (eQTL) studies have highlighted POLDIP2 as a significant gene that confers risk of developing AMD. However, the role of POLDIP2 in retinal cells such as retinal pigment epithelium (RPE) and how it contributes to AMD pathology are unknown. Here we report the generation of a stable human RPE cell line ARPE-19 with POLDIP2 knockout using CRISPR/Cas, providing an in vitro model to investigate the functions of POLDIP2. We conducted functional studies on the POLDIP2 knockout cell line and showed that it retained normal levels of cell proliferation, cell viability, phagocytosis and autophagy. Also, we performed RNA sequencing to profile the transcriptome of POLDIP2 knockout cells. Our results highlighted significant changes in genes involved in immune response, complement activation, oxidative damage and vascular development. We showed that loss of POLDIP2 caused a reduction in mitochondrial superoxide levels, which is consistent with the upregulation of the mitochondrial superoxide dismutase SOD2. In conclusion, this study demonstrates a novel link between POLDIP2 and SOD2 in ARPE-19, which supports a potential role of POLDIP2 in regulating oxidative stress in AMD pathology.
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Affiliation(s)
- Tu Nguyen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Urrutia-Cabrera
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Luozixian Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Jarmon G. Lees
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- Departments of Surgery and Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Sandy S.C. Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Alex W. Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Thomas L. Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Sam McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Fred K. Chen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Shiang Y. Lim
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- Departments of Surgery and Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Chi D. Luu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Robyn Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Raymond C.B. Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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2
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Lyu Q, Gong S, Lees JG, Yin J, Yap LW, Kong AM, Shi Q, Fu R, Zhu Q, Dyer A, Dyson JM, Lim SY, Cheng W. A soft and ultrasensitive force sensing diaphragm for probing cardiac organoids instantaneously and wirelessly. Nat Commun 2022; 13:7259. [PMID: 36433978 PMCID: PMC9700778 DOI: 10.1038/s41467-022-34860-y] [Citation(s) in RCA: 10] [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: 06/10/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
Time-lapse mechanical properties of stem cell derived cardiac organoids are important biological cues for understanding contraction dynamics of human heart tissues, cardiovascular functions and diseases. However, it remains difficult to directly, instantaneously and accurately characterize such mechanical properties in real-time and in situ because cardiac organoids are topologically complex, three-dimensional soft tissues suspended in biological media, which creates a mismatch in mechanics and topology with state-of-the-art force sensors that are typically rigid, planar and bulky. Here, we present a soft resistive force-sensing diaphragm based on ultrasensitive resistive nanocracked platinum film, which can be integrated into an all-soft culture well via an oxygen plasma-enabled bonding process. We show that a reliable organoid-diaphragm contact can be established by an 'Atomic Force Microscope-like' engaging process. This allows for instantaneous detection of the organoids' minute contractile forces and beating patterns during electrical stimulation, resuscitation, drug dosing, tissue culture, and disease modelling.
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Affiliation(s)
- Quanxia Lyu
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Shu Gong
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Jarmon G. Lees
- grid.1073.50000 0004 0626 201XO’Brien Institute Department, St. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medicine and Surgery, University of Melbourne, Melbourne, VIC Australia
| | - Jialiang Yin
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Lim Wei Yap
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Anne M. Kong
- grid.1073.50000 0004 0626 201XO’Brien Institute Department, St. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
| | - Qianqian Shi
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Runfang Fu
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia
| | - Qiang Zhu
- grid.410660.5The Melbourne Centre for Nanofabrication, Clayton, VIC 3800 Australia
| | - Ash Dyer
- grid.410660.5The Melbourne Centre for Nanofabrication, Clayton, VIC 3800 Australia
| | - Jennifer M. Dyson
- Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Clayton, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Faculty of Engineering, Monash Institute of Medical Engineering (MIME), Monash University, Clayton, VIC 3800 Australia
| | - Shiang Y. Lim
- grid.1073.50000 0004 0626 201XO’Brien Institute Department, St. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medicine and Surgery, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Drug Discovery Biology, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia ,grid.419385.20000 0004 0620 9905National Heart Research Institute Singapore, National Heart Centre, Singapore, Singapore
| | - Wenlong Cheng
- grid.1002.30000 0004 1936 7857Department of Chemical & Biological Engineering, Monash University, Clayton, VIC 3800 Australia ,grid.410660.5The Melbourne Centre for Nanofabrication, Clayton, VIC 3800 Australia
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3
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Daniszewski M, Senabouth A, Liang HH, Han X, Lidgerwood GE, Hernández D, Sivakumaran P, Clarke JE, Lim SY, Lees JG, Rooney L, Gulluyan L, Souzeau E, Graham SL, Chan CL, Nguyen U, Farbehi N, Gnanasambandapillai V, McCloy RA, Clarke L, Kearns LS, Mackey DA, Craig JE, MacGregor S, Powell JE, Pébay A, Hewitt AW. Retinal ganglion cell-specific genetic regulation in primary open-angle glaucoma. Cell Genom 2022; 2:100142. [PMID: 36778138 PMCID: PMC9903700 DOI: 10.1016/j.xgen.2022.100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/19/2020] [Revised: 03/08/2021] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
To assess the transcriptomic profile of disease-specific cell populations, fibroblasts from patients with primary open-angle glaucoma (POAG) were reprogrammed into induced pluripotent stem cells (iPSCs) before being differentiated into retinal organoids and compared with those from healthy individuals. We performed single-cell RNA sequencing of a total of 247,520 cells and identified cluster-specific molecular signatures. Comparing the gene expression profile between cases and controls, we identified novel genetic associations for this blinding disease. Expression quantitative trait mapping identified a total of 4,443 significant loci across all cell types, 312 of which are specific to the retinal ganglion cell subpopulations, which ultimately degenerate in POAG. Transcriptome-wide association analysis identified genes at loci previously associated with POAG, and analysis, conditional on disease status, implicated 97 statistically significant retinal ganglion cell-specific expression quantitative trait loci. This work highlights the power of large-scale iPSC studies to uncover context-specific profiles for a genetically complex disease.
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Affiliation(s)
- Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anne Senabouth
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Helena H. Liang
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Jordan E. Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Shiang Y. Lim
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia
| | - Jarmon G. Lees
- O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia,Department of Medicine, St Vincent’s Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart L. Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Chia-Ling Chan
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Uyen Nguyen
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Nona Farbehi
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Rachael A. McCloy
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lisa S. Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - David A. Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Crawley, WA 6009, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Joseph E. Powell
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW 2052, Australia,Corresponding author
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,Corresponding author
| | - Alex W. Hewitt
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia,Corresponding author
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4
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Phang RJ, Ritchie RH, Hausenloy DJ, Lees JG, Lim SY. Cellular interplay between cardiomyocytes and non-myocytes in diabetic cardiomyopathy. Cardiovasc Res 2022; 119:668-690. [PMID: 35388880 PMCID: PMC10153440 DOI: 10.1093/cvr/cvac049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Received: 12/01/2021] [Revised: 02/16/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with Type 2 diabetes mellitus (T2DM) frequently exhibit a distinctive cardiac phenotype known as diabetic cardiomyopathy. Cardiac complications associated with T2DM include cardiac inflammation, hypertrophy, fibrosis and diastolic dysfunction in the early stages of the disease, which can progress to systolic dysfunction and heart failure. Effective therapeutic options for diabetic cardiomyopathy are limited and often have conflicting results. The lack of effective treatments for diabetic cardiomyopathy is due in part, to our poor understanding of the disease development and progression, as well as a lack of robust and valid preclinical human models that can accurately recapitulate the pathophysiology of the human heart. In addition to cardiomyocytes, the heart contains a heterogeneous population of non-myocytes including fibroblasts, vascular cells, autonomic neurons and immune cells. These cardiac non-myocytes play important roles in cardiac homeostasis and disease, yet the effect of hyperglycaemia and hyperlipidaemia on these cell types are often overlooked in preclinical models of diabetic cardiomyopathy. The advent of human induced pluripotent stem cells provides a new paradigm in which to model diabetic cardiomyopathy as they can be differentiated into all cell types in the human heart. This review will discuss the roles of cardiac non-myocytes and their dynamic intercellular interactions in the pathogenesis of diabetic cardiomyopathy. We will also discuss the use of sodium-glucose cotransporter 2 inhibitors as a therapy for diabetic cardiomyopathy and their known impacts on non-myocytes. These developments will no doubt facilitate the discovery of novel treatment targets for preventing the onset and progression of diabetic cardiomyopathy.
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Affiliation(s)
- Ren Jie Phang
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.,Departments of Surgery and Medicine, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rebecca H Ritchie
- School of Biosciences, Parkville, Victoria 3010, Australia.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.,Department of Pharmacology, Monash University, Clayton, Victoria 3800, Australia
| | - Derek J Hausenloy
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore.,The Hatter Cardiovascular Institute, University College London, London, UK.,Cardiovascular Research Center, College of Medical and Health Sciences, Asia University, Taichung City, Taiwan
| | - Jarmon G Lees
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.,Departments of Surgery and Medicine, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shiang Y Lim
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.,Departments of Surgery and Medicine, University of Melbourne, Parkville, Victoria 3010, Australia.,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
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5
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Kalkhoran SB, Kriston-Vizi J, Hernandez-Resendiz S, Crespo-Avilan GE, Rosdah AA, Lees JG, Costa JRSD, Ling NXY, Holien JK, Samangouei P, Chinda K, Yap EP, Riquelme JA, Ketteler R, Yellon DM, Lim SY, Hausenloy DJ. Hydralazine protects the heart against acute ischaemia/reperfusion injury by inhibiting Drp1-mediated mitochondrial fission. Cardiovasc Res 2022; 118:282-294. [PMID: 33386841 PMCID: PMC8752357 DOI: 10.1093/cvr/cvaa343] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/09/2020] [Indexed: 01/01/2023] Open
Abstract
AIMS Genetic and pharmacological inhibition of mitochondrial fission induced by acute myocardial ischaemia/reperfusion injury (IRI) has been shown to reduce myocardial infarct size. The clinically used anti-hypertensive and heart failure medication, hydralazine, is known to have anti-oxidant and anti-apoptotic effects. Here, we investigated whether hydralazine confers acute cardioprotection by inhibiting Drp1-mediated mitochondrial fission. METHODS AND RESULTS Pre-treatment with hydralazine was shown to inhibit both mitochondrial fission and mitochondrial membrane depolarisation induced by oxidative stress in HeLa cells. In mouse embryonic fibroblasts (MEFs), pre-treatment with hydralazine attenuated mitochondrial fission and cell death induced by oxidative stress, but this effect was absent in MEFs deficient in the mitochondrial fission protein, Drp1. Molecular docking and surface plasmon resonance studies demonstrated binding of hydralazine to the GTPase domain of the mitochondrial fission protein, Drp1 (KD 8.6±1.0 µM), and inhibition of Drp1 GTPase activity in a dose-dependent manner. In isolated adult murine cardiomyocytes subjected to simulated IRI, hydralazine inhibited mitochondrial fission, preserved mitochondrial fusion events, and reduced cardiomyocyte death (hydralazine 24.7±2.5% vs. control 34.1±1.5%, P=0.0012). In ex vivo perfused murine hearts subjected to acute IRI, pre-treatment with hydralazine reduced myocardial infarct size (as % left ventricle: hydralazine 29.6±6.5% vs. vehicle control 54.1±4.9%, P=0.0083), and in the murine heart subjected to in vivo IRI, the administration of hydralazine at reperfusion, decreased myocardial infarct size (as % area-at-risk: hydralazine 28.9±3.0% vs. vehicle control 58.2±3.8%, P<0.001). CONCLUSION We show that, in addition to its antioxidant and anti-apoptotic effects, hydralazine, confers acute cardioprotection by inhibiting IRI-induced mitochondrial fission, raising the possibility of repurposing hydralazine as a novel cardioprotective therapy for improving post-infarction outcomes.
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Affiliation(s)
- Siavash Beikoghli Kalkhoran
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College, 67 Chenies Mews, WC1E 6HX London, UK
- Cardiovascular and Metabolic Disorder Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
| | - Janos Kriston-Vizi
- MRC Laboratory for Molecular Cell Biology, University College, Gower St, Kings Cross, WC1E 6BT London, UK
| | - Sauri Hernandez-Resendiz
- Cardiovascular and Metabolic Disorder Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
| | - Gustavo E Crespo-Avilan
- Cardiovascular and Metabolic Disorder Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
- Department of Biochemistry, Medical Faculty, Justus Liebig-University, Ludwigstraße 23, 35390 Giessen, Germany
| | - Ayeshah A Rosdah
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, 9 Princes Street Fitzroy Victoria, 3065, Australia
- Faculty of Medicine, Universitas Sriwijaya, Palembang, Bukit Lama, Kec. Ilir Bar. I, Kota Palembang, 30139 Sumatera Selatan, Indonesia
- Department of Surgery and Medicine, University of Melbourne, Medical Building, Cnr Grattan Street & Royal Parade, 3010 Victoria, Australia
| | - Jarmon G Lees
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, 9 Princes Street Fitzroy Victoria, 3065, Australia
- Department of Surgery and Medicine, University of Melbourne, Medical Building, Cnr Grattan Street & Royal Parade, 3010 Victoria, Australia
| | | | - Naomi X Y Ling
- Metabolic Signalling Laboratory, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica K Holien
- Department of Surgery and Medicine, University of Melbourne, Medical Building, Cnr Grattan Street & Royal Parade, 3010 Victoria, Australia
- St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy Victoria, 3065, Australia
- ACRF Rational Drug Discovery Centre, St Vincent’s Institute of Medical Research, 9 Princes Street Fitzroy Victoria, 3065, Australia
| | - Parisa Samangouei
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College, 67 Chenies Mews, WC1E 6HX London, UK
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
| | - Kroekkiat Chinda
- Department of Physiology, Faculty of Medical Science, Naresuan University, Tha Pho, Mueang Phitsanulok, 65000, Thailand
| | - En Ping Yap
- Cardiovascular and Metabolic Disorder Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
| | - Jaime A Riquelme
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College, 67 Chenies Mews, WC1E 6HX London, UK
- Advanced Center for Chronic Disease (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College, Gower St, Kings Cross, WC1E 6BT London, UK
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College, 67 Chenies Mews, WC1E 6HX London, UK
| | - Shiang Y Lim
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, 9 Princes Street Fitzroy Victoria, 3065, Australia
- Department of Surgery and Medicine, University of Melbourne, Medical Building, Cnr Grattan Street & Royal Parade, 3010 Victoria, Australia
| | - Derek J Hausenloy
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College, 67 Chenies Mews, WC1E 6HX London, UK
- Cardiovascular and Metabolic Disorder Programme, Duke-NUS Medical School, 8 College Road, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre, 5 Hospital Drive, 169609, Singapore
- Yong Loo Lin School of Medicine, National University Singapore, 1E Kent Ridge Road, 119228, Singapore
- Cardiovascular Research Center, College of Medical and Health Sciences, Asia University, Lioufeng Rd., Wufeng, 41354 Taichung, Taiwan
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6
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Lees JG, Napierala M, Pébay A, Dottori M, Lim SY. Cellular pathophysiology of Friedreich's ataxia cardiomyopathy. Int J Cardiol 2022; 346:71-78. [PMID: 34798207 DOI: 10.1016/j.ijcard.2021.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Received: 07/13/2021] [Revised: 11/01/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022]
Abstract
Friedreich's ataxia (FRDA) is a hereditary neuromuscular disorder. Cardiomyopathy is the leading cause of premature death in FRDA. FRDA cardiomyopathy is a complex and progressive disease with no cure or treatment to slow its progression. At the cellular level, cardiomyocyte hypertrophy, apoptosis and fibrosis contribute to the cardiac pathology. However, the heart is composed of multiple cell types and several clinical studies have reported the involvement of cardiac non-myocytes such as vascular cells, autonomic neurons, and inflammatory cells in the pathogenesis of FRDA cardiomyopathy. In fact, several of the cardiac pathologies associated with FRDA including cardiomyocyte necrosis, fibrosis, and arrhythmia, could be contributed to by a diseased vasculature and autonomic dysfunction. Here, we review available evidence regarding the current understanding of cellular mechanisms for, and the involvement of, cardiac non-myocytes in the pathogenesis of FRDA cardiomyopathy.
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Affiliation(s)
- Jarmon G Lees
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mirella Dottori
- Illawarra Health and Medical Research Institute, School of Medicine, Molecular Horizons, University of Wollongong, New South Wales 2522, Australia; Department of Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Shiang Y Lim
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria 3010, Australia.
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7
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Abstract
PURPOSE OF REVIEW This study is aimed at reviewing the recent progress in Drp1 inhibition as a novel approach for reducing doxorubicin-induced cardiotoxicity and for improving cancer treatment. RECENT FINDINGS Anthracyclines (e.g. doxorubicin) are one of the most common and effective chemotherapeutic agents to treat a variety of cancers. However, the clinical usage of doxorubicin has been hampered by its severe cardiotoxic side effects leading to heart failure. Mitochondrial dysfunction is one of the major aetiologies of doxorubicin-induced cardiotoxicity. The morphology of mitochondria is highly dynamic, governed by two opposing processes known as fusion and fission, collectively known as mitochondrial dynamics. An imbalance in mitochondrial dynamics is often reported in tumourigenesis which can lead to adaptive and acquired resistance to chemotherapy. Drp1 is a key mitochondrial fission regulator, and emerging evidence has demonstrated that Drp1-mediated mitochondrial fission is upregulated in both cancer cells to their survival advantage and injured heart tissue in the setting of doxorubicin-induced cardiotoxicity. Effective treatment to prevent and mitigate doxorubicin-induced cardiotoxicity is currently not available. Recent advances in cardio-oncology have highlighted that Drp1 inhibition holds great potential as a targeted mitochondrial therapy for doxorubicin-induced cardiotoxicity.
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Affiliation(s)
- Yali Deng
- Department of Surgery and Medicine, University of Melbourne, Melbourne, Victoria Australia ,O’Brien Institute Department, St Vincent’s Institute of Medical Research, Fitzroy, Victoria Australia
| | - Doan T. M. Ngo
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, New Lambton Heights, New South Wales Australia
| | - Jessica K. Holien
- Department of Surgery and Medicine, University of Melbourne, Melbourne, Victoria Australia ,School of Science, STEM College, RMIT University, Melbourne, Victoria Australia
| | - Jarmon G. Lees
- Department of Surgery and Medicine, University of Melbourne, Melbourne, Victoria Australia ,O’Brien Institute Department, St Vincent’s Institute of Medical Research, Fitzroy, Victoria Australia
| | - Shiang Y. Lim
- Department of Surgery and Medicine, University of Melbourne, Melbourne, Victoria Australia ,O’Brien Institute Department, St Vincent’s Institute of Medical Research, Fitzroy, Victoria Australia ,Drug Discovery Biology, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, Victoria Australia ,National Heart Research Institute Singapore, National Heart Centre, Singapore, Singapore
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8
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Kompa AR, Greening DW, Kong AM, McMillan PJ, Fang H, Saxena R, Wong RCB, Lees JG, Sivakumaran P, Newcomb AE, Tannous BA, Kos C, Mariana L, Loudovaris T, Hausenloy DJ, Lim SY. Sustained subcutaneous delivery of secretome of human cardiac stem cells promotes cardiac repair following myocardial infarction. Cardiovasc Res 2021; 117:918-929. [PMID: 32251516 PMCID: PMC7898942 DOI: 10.1093/cvr/cvaa088] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/13/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
AIMS To establish pre-clinical proof of concept that sustained subcutaneous delivery of the secretome of human cardiac stem cells (CSCs) can be achieved in vivo to produce significant cardioreparative outcomes in the setting of myocardial infarction. METHODS AND RESULTS Rats were subjected to permanent ligation of left anterior descending coronary artery and randomized to receive subcutaneous implantation of TheraCyte devices containing either culture media as control or 1 × 106 human W8B2+ CSCs, immediately following myocardial ischaemia. At 4 weeks following myocardial infarction, rats treated with W8B2+ CSCs encapsulated within the TheraCyte device showed preserved left ventricular ejection fraction. The preservation of cardiac function was accompanied by reduced fibrotic scar tissue, interstitial fibrosis, cardiomyocyte hypertrophy, as well as increased myocardial vascular density. Histological analysis of the TheraCyte devices harvested at 4 weeks post-implantation demonstrated survival of human W8B2+ CSCs within the devices, and the outer membrane was highly vascularized by host blood vessels. Using CSCs expressing plasma membrane reporters, extracellular vesicles of W8B2+ CSCs were found to be transferred to the heart and other organs at 4 weeks post-implantation. Furthermore, mass spectrometry-based proteomic profiling of extracellular vesicles of W8B2+ CSCs identified proteins implicated in inflammation, immunoregulation, cell survival, angiogenesis, as well as tissue remodelling and fibrosis that could mediate the cardioreparative effects of secretome of human W8B2+ CSCs. CONCLUSIONS Subcutaneous implantation of TheraCyte devices encapsulating human W8B2+ CSCs attenuated adverse cardiac remodelling and preserved cardiac function following myocardial infarction. The TheraCyte device can be employed to deliver stem cells in a minimally invasive manner for effective secretome-based cardiac therapy.
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Affiliation(s)
- Andrew R Kompa
- Departments of Medicine and Surgery, University of Melbourne,
Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Centre of Cardiovascular
Research and Education in Therapeutics, Monash University, Melbourne, VIC,
Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute,
Melbourne, VIC, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular
Science, La Trobe University, Melbourne, VIC, Australia
| | - Anne M Kong
- O’Brien Institute Department, St Vincent’s Institute of Medical
Research, 9 Princes Street, Fitzroy, VIC 3065, Australia
| | - Paul J McMillan
- Department of Biochemistry and Molecular Biology, Biological Optical Microscopy
Platform, University of Melbourne, Melbourne, VIC, Australia
| | - Haoyun Fang
- Molecular Proteomics, Baker Heart and Diabetes Institute,
Melbourne, VIC, Australia
| | - Ritika Saxena
- O’Brien Institute Department, St Vincent’s Institute of Medical
Research, 9 Princes Street, Fitzroy, VIC 3065, Australia
- School of Life and Environmental Sciences, Faculty of Science, Deakin
University, Burwood, VIC, Australia
| | - Raymond C B Wong
- Departments of Medicine and Surgery, University of Melbourne,
Melbourne, VIC, Australia
- Cellular Reprogramming Unit, Centre for Eye Research Australia, Royal Victorian
Eye and Ear Hospital, East Melbourne, VIC, Australia
- Shenzhen Eye Hospital, Shenzhen University School of Medicine,
Shenzhen, China
| | - Jarmon G Lees
- Departments of Medicine and Surgery, University of Melbourne,
Melbourne, VIC, Australia
- O’Brien Institute Department, St Vincent’s Institute of Medical
Research, 9 Princes Street, Fitzroy, VIC 3065, Australia
| | - Priyadharshini Sivakumaran
- O’Brien Institute Department, St Vincent’s Institute of Medical
Research, 9 Princes Street, Fitzroy, VIC 3065, Australia
| | - Andrew E Newcomb
- Department of Cardiothoracic Surgery, St Vincent’s Hospital
Melbourne, Melbourne, VIC, Australia
| | - Bakhos A Tannous
- Department of Neurology and Pathology, Massachusetts General
Hospital, Charlestown, MA, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA,
USA
| | - Cameron Kos
- O'Brien Institute Department & Immunology & Diabetes Unit, St Vincent’s
Institute of Medical Research, VIC, Australia
| | - Lina Mariana
- O'Brien Institute Department & Immunology & Diabetes Unit, St Vincent’s
Institute of Medical Research, VIC, Australia
| | - Thomas Loudovaris
- O'Brien Institute Department & Immunology & Diabetes Unit, St Vincent’s
Institute of Medical Research, VIC, Australia
| | - Derek J Hausenloy
- Cardiovascular and Metabolic Disorders Program, Duke-National University of
Singapore Medical School, Singapore, Singapore
- National Heart Research Institute Singapore, National Heart
Centre, Singapore, Singapore
- The Hatter Cardiovascular Institute, University College London,
London, UK
- Cardiovascular Research Center, College of Medical and Health Sciences, Asia
University, Taichung, Taiwan
- Yong Loo Lin School of Medicine, National University Singapore,
Singapore, Singapore
| | - Shiang Y Lim
- Departments of Medicine and Surgery, University of Melbourne,
Melbourne, VIC, Australia
- O’Brien Institute Department, St Vincent’s Institute of Medical
Research, 9 Princes Street, Fitzroy, VIC 3065, Australia
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9
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Prakoso D, Lim SY, Erickson JR, Wallace RS, Lees JG, Tate M, Kiriazis H, Donner DG, Henstridge DC, Davey JR, Qian H, Deo M, Parry LJ, Davidoff AJ, Gregorevic P, Chatham JC, De Blasio MJ, Ritchie RH. Fine-tuning the cardiac O-GlcNAcylation regulatory enzymes governs the functional and structural phenotype of the diabetic heart. Cardiovasc Res 2021; 118:212-225. [PMID: 33576380 DOI: 10.1093/cvr/cvab043] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
AIMS The glucose-driven enzymatic modification of myocardial proteins by the sugar moiety, β-N-acetylglucosamine (O-GlcNAc), is increased in pre-clinical models of diabetes, implicating protein O-GlcNAc modification in diabetes-induced heart failure. Our aim was to specifically examine cardiac manipulation of the two regulatory enzymes of this process on the cardiac phenotype, in the presence and absence of diabetes, utilising cardiac-targeted recombinant-adeno-associated viral-vector-6 (rAAV6)-mediated gene delivery. METHODS AND RESULTS In human myocardium, total protein O-GlcNAc modification was elevated in diabetic relative to non-diabetic patients, and correlated with left ventricular (LV) dysfunction. The impact of rAAV6-delivered O-GlcNAc transferase (rAAV6-OGT, facilitating protein O-GlcNAcylation), O-GlcNAcase (rAAV6-OGA, facilitating de-O-GlcNAcylation) and empty vector (null) were determined in non-diabetic and diabetic mice. In non-diabetic mice, rAAV6-OGT was sufficient to impair LV diastolic function and induce maladaptive cardiac remodelling, including cardiac fibrosis and increased Myh-7 and Nppa pro-hypertrophic gene expression, recapitulating characteristics of diabetic cardiomyopathy. In contrast, rAAV6-OGA (but not rAAV6-OGT) rescued LV diastolic function and adverse cardiac remodelling in diabetic mice. Molecular insights implicated impaired cardiac PI3K(p110α)-Akt signalling as a potential contributing mechanism to the detrimental consequences of rAAV6-OGT in vivo. In contrast, rAAV6-OGA preserved PI3K(p110α)-Akt signalling in diabetic mouse myocardium in vivo and prevented high glucose-induced impairments in mitochondrial respiration in human cardiomyocytes in vitro. CONCLUSION Maladaptive protein O-GlcNAc modification is evident in human diabetic myocardium, and is a critical regulator of the diabetic heart phenotype. Selective targeting of cardiac protein O-GlcNAcylation to restore physiological O-GlcNAc balance may represent a novel therapeutic approach for diabetes-induced heart failure. TRANSLATIONAL PERSPECTIVE There remains a lack of effective clinical management of diabetes-induced cardiac dysfunction, even via conventional intensive glucose-lowering approaches. Here we reveal that the modification of myocardial proteins by O-GlcNAc, a glucose-driven process, is not only increased in human diabetic myocardium, but correlates with reduced cardiac function in affected patients. Moreover, manipulation of the two regulatory enzymes of this process exert opposing influences on the heart, whereby increasing O-GlcNAc transferase (OGT) is sufficient to replicate the cardiac phenotype of diabetes (in the absence of this disease), while increasing O-GlcNAc-ase (OGA) rescues diabetes-induced impairments in both cardiac dysfunction and remodelling. Cardiac O-GlcNAcylation thus represents a novel therapeutic target for diabetes-induced heart failure.
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Affiliation(s)
- Darnel Prakoso
- School of Biosciences, Parkville, Victoria, Australia, 3010.,Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia, 3052
| | - Shiang Y Lim
- O'Brien Institute Dept, St Vincent Institute of Medical Research, Fitzroy, Victoria, Australia, 3065
| | - Jeffrey R Erickson
- Dept of Physiology and HeartOtago, University of Otago, Dunedin, New Zealand, 9054
| | - Rachel S Wallace
- Dept of Physiology and HeartOtago, University of Otago, Dunedin, New Zealand, 9054
| | - Jarmon G Lees
- O'Brien Institute Dept, St Vincent Institute of Medical Research, Fitzroy, Victoria, Australia, 3065
| | - Mitchel Tate
- School of Biosciences, Parkville, Victoria, Australia, 3010.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia, 3052
| | - Helen Kiriazis
- School of Biosciences, Parkville, Victoria, Australia, 3010
| | | | - Darren C Henstridge
- School of Biosciences, Parkville, Victoria, Australia, 3010.,College of Health and Medicine, School of Health Sciences, University of Tasmania, Launceston, Australia, 7250
| | - Jonathan R Davey
- Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Hongwei Qian
- Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Minh Deo
- School of Biosciences, Parkville, Victoria, Australia, 3010.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia, 3052
| | - Laura J Parry
- Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Amy J Davidoff
- Dept of Biomedical Sciences, University of New England, Biddeford, Maine, USA, 04005
| | - Paul Gregorevic
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia, 3004.,Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010.,Depts of Biochemistry and Molecular Biology, Clayton, Victoria, Australia, 3800.,Dept of Neurology, The University of Washington, Seattle, Washington, USA, 98195
| | - John C Chatham
- Dept of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA 35924
| | - Miles J De Blasio
- School of Biosciences, Parkville, Victoria, Australia, 3010.,Centre for Muscle Research, Dept of Physiology, The University of Melbourne, Parkville, Victoria, Australia, 3010.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia, 3052.,Pharmacology, Monash University, Clayton, Victoria, Australia, 3800
| | - Rebecca H Ritchie
- School of Biosciences, Parkville, Victoria, Australia, 3010.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia, 3052.,Pharmacology, Monash University, Clayton, Victoria, Australia, 3800
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10
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Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen N, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM, Orengo CA. SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. Sci Rep 2020; 10:16471. [PMID: 33020502 PMCID: PMC7536205 DOI: 10.1038/s41598-020-71936-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [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: 06/09/2020] [Accepted: 08/17/2020] [Indexed: 01/04/2023] Open
Abstract
SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.
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Affiliation(s)
- S D Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - V P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - H M Scholes
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - P Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- Indian Institute of Science Education and Research, Pune, 411008, India
| | - L van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - C Rauer
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N L Dawson
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C S M Pang
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - M Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - I Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - S J L Edwards
- Department of Science and Technology Studies, University College London, London, WC1E 6BT, UK
| | - F Fraternali
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - J G Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 OBP, UK
| | - J M Santini
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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11
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Lewis TE, Sillitoe I, Lees JG. cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly. Bioinformatics 2020; 35:1766-1767. [PMID: 30295745 PMCID: PMC6513158 DOI: 10.1093/bioinformatics/bty863] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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] [Received: 07/07/2018] [Revised: 09/18/2018] [Accepted: 10/05/2018] [Indexed: 11/26/2022] Open
Abstract
Motivation Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory. Results We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large datasets. Availability and implementation CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- T E Lewis
- Department of Structural and Molecular Biology, UCL, Darwin Building, London, UK
| | - I Sillitoe
- Department of Structural and Molecular Biology, UCL, Darwin Building, London, UK
| | - J G Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
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12
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Lozano O, Silva-Platas C, Chapoy-Villanueva H, Pérez BE, Lees JG, Ramachandra CJA, Contreras-Torres FF, Lázaro-Alfaro A, Luna-Figueroa E, Bernal-Ramírez J, Gordillo-Galeano A, Benitez A, Oropeza-Almazán Y, Castillo EC, Koh PL, Hausenloy DJ, Lim SY, García-Rivas G. Amorphous SiO2 nanoparticles promote cardiac dysfunction via the opening of the mitochondrial permeability transition pore in rat heart and human cardiomyocytes. Part Fibre Toxicol 2020; 17:15. [PMID: 32381100 PMCID: PMC7206702 DOI: 10.1186/s12989-020-00346-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Background Silica nanoparticles (nanoSiO2) are promising systems that can deliver biologically active compounds to tissues such as the heart in a controllable manner. However, cardiac toxicity induced by nanoSiO2 has been recently related to abnormal calcium handling and energetic failure in cardiomyocytes. Moreover, the precise mechanisms underlying this energetic debacle remain unclear. In order to elucidate these mechanisms, this article explores the ex vivo heart function and mitochondria after exposure to nanoSiO2. Results The cumulative administration of nanoSiO2 reduced the mechanical performance index of the rat heart with a half-maximal inhibitory concentration (IC50) of 93 μg/mL, affecting the relaxation rate. In isolated mitochondria nanoSiO2 was found to be internalized, inhibiting oxidative phosphorylation and significantly reducing the mitochondrial membrane potential (ΔΨm). The mitochondrial permeability transition pore (mPTP) was also induced with an increasing dose of nanoSiO2 and partially recovered with, a potent blocker of the mPTP, Cyclosporine A (CsA). The activity of aconitase and thiol oxidation, in the adenine nucleotide translocase, were found to be reduced due to nanoSiO2 exposure, suggesting that nanoSiO2 induces the mPTP via thiol modification and ROS generation. In cardiac cells exposed to nanoSiO2, enhanced viability and reduction of H2O2 were observed after application of a specific mitochondrial antioxidant, MitoTEMPO. Concomitantly, CsA treatment in adult rat cardiac cells reduced the nanoSiO2-triggered cell death and recovered ATP production (from 32.4 to 65.4%). Additionally, we performed evaluation of the mitochondrial effect of nanoSiO2 in human cardiomyocytes. We observed a 40% inhibition of maximal oxygen consumption rate in mitochondria at 500 μg/mL. Under this condition we identified a remarkable diminution in the spare respiratory capacity. This data indicates that a reduction in the amount of extra ATP that can be produced by mitochondria during a sudden increase in energy demand. In human cardiomyocytes, increased LDH release and necrosis were found at increased doses of nanoSiO2, reaching 85 and 48%, respectively. Such deleterious effects were partially prevented by the application of CsA. Therefore, exposure to nanoSiO2 affects cardiac function via mitochondrial dysfunction through the opening of the mPTP. Conclusion The aforementioned effects can be partially avoided reducing ROS or retarding the opening of the mPTP. These novel strategies which resulted in cardioprotection could be considered as potential therapies to decrease the side effects of nanoSiO2 exposure.
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Affiliation(s)
- Omar Lozano
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico.,Tecnologico de Monterrey. Centro de Investigación Biomédica, Hospital Zambrano-Helión, San Pedro Garza-García, Mexico
| | - Christian Silva-Platas
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Héctor Chapoy-Villanueva
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Baruc E Pérez
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Jarmon G Lees
- Departments of Medicine and Surgery, University of Melbourne, Melbourne, Victoria, Australia.,O'Brien Institute Department, St Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
| | - Chrishan J A Ramachandra
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | | | - Anay Lázaro-Alfaro
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Estefanía Luna-Figueroa
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Judith Bernal-Ramírez
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | | | - Alfredo Benitez
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, USA
| | - Yuriana Oropeza-Almazán
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Elena C Castillo
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico
| | - Poh Ling Koh
- Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Derek J Hausenloy
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore.,The Hatter Cardiovascular Institute, University College London, London, UK.,Cardiovascular Research Center, College of Medical and Health Sciences, Asia University, Taichung City, Taiwan
| | - Shiang Y Lim
- Departments of Medicine and Surgery, University of Melbourne, Melbourne, Victoria, Australia.,O'Brien Institute Department, St Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
| | - Gerardo García-Rivas
- Tecnologico de Monterrey. Escuela Nacional de Medicina y Ciencias de la Salud, Cátedra de Cardiología y Medicina Vascular, Monterrey, Mexico. .,Tecnologico de Monterrey. Centro de Investigación Biomédica, Hospital Zambrano-Helión, San Pedro Garza-García, Mexico.
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13
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Lees JG, Gardner DK, Harvey AJ. Nicotinamide adenine dinucleotide induces a bivalent metabolism and maintains pluripotency in human embryonic stem cells. Stem Cells 2020; 38:624-638. [PMID: 32003519 DOI: 10.1002/stem.3152] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/27/2019] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+ ) and its precursor metabolites are emerging as important regulators of both cell metabolism and cell state. Interestingly, the role of NAD+ in human embryonic stem cell (hESC) metabolism and the regulation of pluripotent cell state is unresolved. Here we show that NAD+ simultaneously increases hESC mitochondrial oxidative metabolism and partially suppresses glycolysis and stimulates amino acid turnover, doubling the consumption of glutamine. Concurrent with this metabolic remodeling, NAD+ increases hESC pluripotent marker expression and proliferation, inhibits BMP4-induced differentiation and reduces global histone 3 lysine 27 trimethylation, plausibly inducing an intermediate naïve-to-primed bivalent metabolism and pluripotent state. Furthermore, maintenance of NAD+ recycling via malate aspartate shuttle activity is identified as an absolute requirement for hESC self-renewal, responsible for 80% of the oxidative capacity of hESC mitochondria. Our findings implicate NAD+ in the regulation of cell state, suggesting that the hESC pluripotent state is dependent upon cellular NAD+ .
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Affiliation(s)
- Jarmon G Lees
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine at St Vincent's Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
| | - David K Gardner
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandra J Harvey
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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14
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Kong AM, Yap KK, Lim SY, Marre D, Pébay A, Gerrand YW, Lees JG, Palmer JA, Morrison WA, Mitchell GM. Bio-engineering a tissue flap utilizing a porous scaffold incorporating a human induced pluripotent stem cell-derived endothelial cell capillary network connected to a vascular pedicle. Acta Biomater 2019; 94:281-294. [PMID: 31152943 DOI: 10.1016/j.actbio.2019.05.067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 10/31/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 01/18/2023]
Abstract
Tissue flaps are used to cover large/poorly healing wounds, but involve complex surgery and donor site morbidity. In this study a tissue flap is assembled using the mammalian body as a bioreactor to functionally connect an artery and vein to a human capillary network assembled from induced pluripotent stem cell-derived endothelial cells (hiPSC ECs). In vitro: Porous NovoSorb™ scaffolds (3 mm × 1.35 mm) were seeded with 200,000 hiPSC ECs ± 100,000 human vascular smooth muscle cells (hvSMC), and cultured for 1-3 days, with capillaries formed by 24 h which were CD31+, VE-Cadherin+, EphB4+, VEGFR2+ and Ki67+, whilst hvSMCs (calponin+) attached abluminally. In vivo: In SCID mice, bi-lateral epigastric vascular pedicles were isolated in a silicone chamber for a 3 week 'delay period' for pedicle capillary sprouting, then reopened, and two hiPSC EC ± hvSMCs seeded scaffolds transplanted over the pedicle. The chamber was either resealed (Group 1), or removed and surrounding tissue secured around the pedicle + scaffolds (Group 2), for 1 or 2 weeks. Human capillaries survived in vivo and were CD31+, VE-Cadherin+ and VEGFR2+. Human vSMCs remained attached, and host mesenchymal cells also attached abluminally. Systemically injected FITC-dextran present in human capillary lumens indicated inosculation to host capillaries. Human iPSC EC capillary morphometric parameters at one week in vivo were equal to or higher than the same parameters measured in human abdominal skin. This 'proof of concept' study has demonstrated that bio-engineering an autologous human tissue flap based on hiPSC EC could minimize the use of donor flaps and has potential applications for complex wound coverage. STATEMENT OF SIGNIFICANCE: Tissue flaps, used for surgical reconstruction of wounds, require complex surgery, often associated with morbidity. Bio-engineering a simpler alternative, we assembled a human induced pluripotent stem cell derived endothelial cell (hiPSC ECs) capillary network in a porous scaffold in vitro, which when transplanted over a mouse vascular pedicle in vivo formed a functional tissue flap with mouse blood flow in the human capillaries. Therefore it is feasible to form an autologous tissue flap derived from a hiPSC EC capillary network assembled in vitro, and functionally connect to a vascular pedicle in vivo that could be utilized in complex wound repair for chronic or acute wounds.
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Affiliation(s)
- Anne M Kong
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia
| | - Kiryu K Yap
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia; Univ. of Melbourne, Dept. of Surgery at St Vincent's Hospital, Melbourne, Australia; Department of Plastic and Reconstructive Surgery, St Vincent's Hospital, Melbourne, Australia
| | - Shiang Y Lim
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia; Univ. of Melbourne, Dept. of Surgery at St Vincent's Hospital, Melbourne, Australia
| | - Diego Marre
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia
| | - Alice Pébay
- Department of Surgery, The University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Victoria 3010, Australia
| | - Yi-Wen Gerrand
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia
| | - Jarmon G Lees
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia
| | - Jason A Palmer
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia
| | - Wayne A Morrison
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia; Univ. of Melbourne, Dept. of Surgery at St Vincent's Hospital, Melbourne, Australia; Faculty of Health Sciences, Australian Catholic University, Fitzroy, Melbourne, Australia; Department of Plastic and Reconstructive Surgery, St Vincent's Hospital, Melbourne, Australia
| | - Geraldine M Mitchell
- O'Brien Institute Dept. of St Vincent's Institute, Melbourne, Australia; Univ. of Melbourne, Dept. of Surgery at St Vincent's Hospital, Melbourne, Australia; Faculty of Health Sciences, Australian Catholic University, Fitzroy, Melbourne, Australia.
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15
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Lees JG, Gardner DK, Harvey AJ. Mitochondrial and glycolytic remodeling during nascent neural differentiation of human pluripotent stem cells. Development 2018; 145:dev.168997. [DOI: 10.1242/dev.168997] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022]
Abstract
As human pluripotent stem cells (hPSC) exit pluripotency, they reportedly switch from glycolytic energy production to primarily mitochondrial metabolism. Here we show that upon ectoderm differentiation to neural precursor cells (NPC), hPSC increase glycolytic rate, ultimately producing more carbon as lactate than consumed as glucose. However, glucose, lactate, and pyruvate utilization decrease to half their PSC levels by the NPC stage, establishing a more quiescent metabolic state. Furthermore, we characterize a metabolic exit event within the first 24 hours of differentiation, plausibly necessary to transition hPSC out of the pluripotent state. Contrary to the current thinking, mitochondrial mass does not increase during NPC induction. Instead, mitochondrial DNA copies and mitochondrial activity decrease suggesting that mitochondrial metabolism either requires suppression, or is not required, for nascent ectoderm differentiation. Our work, therefore, contrasts with the dogma that the hPSC state is primarily glycolytic, transitioning to an oxidative metabolism upon the loss of the pluripotent state. Instead, we show that a heightened glycolytic metabolism is acquired, indicating that metabolic modulation of both glycolysis and mitochondrial metabolism occurs during exit from pluripotency in hPSC.
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Affiliation(s)
- Jarmon G. Lees
- School of BioSciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - David K. Gardner
- School of BioSciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Alexandra J. Harvey
- School of BioSciences, University of Melbourne, Parkville 3010, Victoria, Australia
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16
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Lees JG, Rathjen J, Sheedy JR, Gardner DK, Harvey AJ. Distinct profiles of human embryonic stem cell metabolism and mitochondria identified by oxygen. Reproduction 2015; 150:367-82. [PMID: 26159831 DOI: 10.1530/rep-14-0633] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 07/09/2015] [Indexed: 12/20/2022]
Abstract
Oxygen is a powerful regulator of cell function and embryonic development. It has previously been determined that oxygen regulates human embryonic stem (hES) cell glycolytic and amino acid metabolism, but the effects on mitochondria are as yet unknown. Two hES cell lines (MEL1, MEL2) were analyzed to determine the role of 5% (physiological) and 20% (atmospheric) oxygen in regulating mitochondrial activity. In response to extended physiological oxygen culture, MEL2 hES cells displayed reduced mtDNA content, mitochondrial mass and expression of metabolic genes TFAM, NRF1, PPARa and MT-ND4. Furthermore, MEL2 hES cell glucose consumption, lactate production and amino acid turnover were elevated under physiological oxygen. In stark contrast, MEL1 hES cell amino acid and carbohydrate use and mitochondrial function were relatively unaltered in response to oxygen. Furthermore, differentiation kinetics were delayed in the MEL1 hES cell line following BMP4 treatment. Here we report the first incidence of metabolic dysfunction in a hES cell population, defined as a failure to respond to oxygen concentration through the modulation of metabolism, demonstrating that hES cells can be perturbed during culture despite exhibiting the defining characteristics of pluripotent cells. Collectively, these data reveal a central role for oxygen in the regulation of hES cell metabolism and mitochondrial function, whereby physiological oxygen promotes glucose flux and suppresses mitochondrial biogenesis and gene expression.
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Affiliation(s)
- Jarmon G Lees
- School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia
| | - Joy Rathjen
- School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia
| | - John R Sheedy
- School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia
| | - David K Gardner
- School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia
| | - Alexandra J Harvey
- School of BiosciencesUniversity of Melbourne, Parkville 3010, Victoria, AustraliaMenzies Institute of Medical ResearchUniversity of Tasmania, Hobart 7000, Tasmania, Australia
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Abstract
Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances in the field of high throughput experiments to determine protein interactions, the majority of associations remain unknown. Here we describe computational methods for significantly expanding protein association networks. We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use.
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Affiliation(s)
- J G Lees
- Research Department of Structural & Molecular Biology, University College London, London, UK.
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18
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Wien F, Miles AJ, Lees JG, Vrønning Hoffmann S, Wallace BA. VUV irradiation effects on proteins in high-flux synchrotron radiation circular dichroism spectroscopy. J Synchrotron Radiat 2005; 12:517-23. [PMID: 15968132 DOI: 10.1107/s0909049505006953] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Accepted: 03/04/2005] [Indexed: 05/03/2023]
Abstract
Synchrotron radiation circular dichroism (SRCD) spectroscopy is emerging as an important new tool in structural molecular biology. Previously we had shown that in lower-flux SRCD instruments, such as UV1 at ISA and beamline 3.1 at the SRS, vacuum ultraviolet (VUV) radiation damage to proteins was not evident after exposure over a period of hours. No effects were detected in either the protein primary or the secondary structures. However, with the development of high-flux beamlines, such as CD12 at the SRS, this issue has been revisited because of changes observed in the SRCD spectra of consecutive scans of protein samples obtained on this high-flux beamline. Experiments have been designed to distinguish between two different possible mechanisms: (i) photoionization causing free radicals or secondary electrons producing degradation of the protein, and (ii) local heating of the sample resulting in protein denaturation. The latter appears to be the principal source of the signal deterioration.
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Affiliation(s)
- F Wien
- Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
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Lees JG, Smith BR, Wien F, Miles AJ, Wallace BA. CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving. Anal Biochem 2005; 332:285-9. [PMID: 15325297 DOI: 10.1016/j.ab.2004.06.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Indexed: 11/22/2022]
Abstract
CDtool is a software package written to facilitate circular dichroism (CD) spectroscopic studies on both conventional lab-based instruments and synchrotron beamlines. It takes format-independent input data from any type of CD instrument, enables a wide range of standard and advanced processing methods, and, in a single user-friendly graphics-based package, takes raw data through the entire processing procedure and, importantly, uses data-mining techniques to retain in the final output all the information associated with the processing. It permits the facile comparison of data obtained from different instruments without the need for reformatting and displays it in graphical formats suitable for publication. It also includes the ability to automatically archive the processed data. This latter feature may be especially useful in light of recent funding institution directives with regard to data sharing and archiving and requirements for "good practice" and "traceability" within the pharmaceutical industry. In addition, CDtool includes a means of interfacing with protein data bank coordinate files and calculating secondary structures from them using alternate definitions and algorithms. This feature, along with a function that permits the facile production of new reference databases, enables the creation of specialized databases for secondary structural analyses of specific types of proteins. Thus the CDtool software not only enables rapid data processing and analyses but also includes many enhanced features not available in other CD data processing/analysis packages.
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Affiliation(s)
- J G Lees
- Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK
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Wallace BA, Lees JG, Orry AJW, Lobley A, Janes RW. Analyses of circular dichroism spectra of membrane proteins. Protein Sci 2003; 12:875-84. [PMID: 12649445 PMCID: PMC2323856 DOI: 10.1110/ps.0229603] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [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: 08/28/2002] [Revised: 12/19/2002] [Accepted: 12/19/2002] [Indexed: 10/27/2022]
Abstract
Circular dichroism (CD) spectroscopy is a valuable technique for the determination of protein secondary structures. Many linear and nonlinear algorithms have been developed for the empirical analysis of CD data, using reference databases derived from proteins of known structures. To date, the reference databases used by the various algorithms have all been derived from the spectra of soluble proteins. When applied to the analysis of soluble protein spectra, these methods generally produce calculated secondary structures that correspond well with crystallographic structures. In this study, however, it was shown that when applied to membrane protein spectra, the resulting calculations produce considerably poorer results. One source of this discrepancy may be the altered spectral peak positions (wavelength shifts) of membrane proteins due to the different dielectric of the membrane environment relative to that of water. These results have important consequences for studies that seek to use the existing soluble protein reference databases for the analyses of membrane proteins.
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Affiliation(s)
- B A Wallace
- Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK.
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21
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Adeagbo AS, Breen CA, Cutz E, Lees JG, Olley PM, Coceani F. Lamb ductus venosus: evidence of a cytochrome P-450 mechanism in its contractile tension. J Pharmacol Exp Ther 1990; 252:875-9. [PMID: 2313604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have recently shown that a cytochrome P-450-based mechanism is important for the generation of contractile tension by the ductus arteriosus and have now examined whether the same mechanism operates in the ductus venosus. Carbon monoxide (CO/O2 ratio, 0.27) and cytochrome P-450 inhibitors [metyrapone; 4-phenylimidazole; 14-isocyano, 15-(methoxymethyleneoxy)-5Z,8Z,11Z- eicosatrienoic acid; alpha-naphthoflavone] were tested in vitro on the ductus venosus sphincter from mature fetal lambs. Each preparation was precontracted with indomethacin (2.8 x 10(-6) M). Carbon monoxide completely relaxed the ductus, and its action was reversed by illumination with monochromatic light. Peak photocontraction occurred at 450 nm. With the exception of alpha-naphthoflavone, all cytochrome P-450 inhibitors were also relaxant agents. Alpha-naphthoflavone (the sole type I inhibitor tested) produced instead a modest contraction that was often transient. Relaxation brought about by both carbon monoxide and drugs was fully reversed by the thromboxane A2 analog 9,11-epithio-11,12-methano-thromboxane A2 and by excess potassium (55 mM). Carbon monoxide was equally effective in the intact ductus and the ductus denuded of endothelium, whereas cytochrome P-450 inhibitors were marginally less effective in the latter preparation. These findings indicate that the ductus venosus sphincter, like the ductus arteriosus, relies on an intramural cytochrome P-450 mechanism to develop its contractile tone. The actual constrictor remains to be characterized in both vessels.
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Affiliation(s)
- A S Adeagbo
- Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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Coceani F, Breen CA, Lees JG, Falck JR, Olley PM. Further evidence implicating a cytochrome P-450-mediated reaction in the contractile tension of the lamb ductus arteriosus. Circ Res 1988; 62:471-7. [PMID: 3124973 DOI: 10.1161/01.res.62.3.471] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [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] [Indexed: 01/04/2023]
Abstract
The authors have recently provided evidence implicating the cytochrome P-450 system in the generation of contractile tension of the ductus arteriosus. To confirm this possibility, carbon monoxide (CO/O2 ratio, 0.27) and cytochrome P-450 inhibitors [4-phenylimidazole; 14-isocyano,15-(methoxymethyleneoxy)-5Z,8Z,11 Z-eicosatrienoic acid; 9-hydroxyellipticine; alpha-naphthoflavone] were tested on the isolated ductus arteriosus from mature fetal lambs equilibrated at low (4-26 mm Hg) or high (229-694 mm Hg) O2 partial pressure (PO2). Carbon monoxide completely relaxed intact vessel wall preparations and preparations consisting of only the muscle. Carbon monoxide relaxation was reversed by illumination with monochromatic light and the peak for the photoactivated contraction occurred at 450 nm. 4-Phenylimidazole (100 and 1,000 microM) was also a relaxant agent, and its action was manifest at both low and high PO2. Unlike 4-phenylimidazole, the isonitrile compound (5 microM) and 9-hydroxyellipticine (10 and 100 microM) were relaxant only at low PO2 and were also less potent. At the same PO2, alpha-naphthoflavone (10 microM) barely reduced ductal tension. Treatment of the ductus with either a combination of superoxide dismutase (60 or 150 U/ml) and catalase (40 or 1,000 U/ml) or mannitol alone (80 mM) failed to alter the steady-state tone at low PO2 and the contractile response to O2. Arachidonic acid was tested on tissues pretreated with the dual cyclooxygenase and lipoxygenase inhibitor, BW755C (10 microM), and produced a weak relaxation at a concentration of 1 microM or higher. 5,6-Epoxytrienoic acid relaxed the untreated tissue, and its action was abolished by indomethacin (2.8 microM).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- F Coceani
- Research Institute, Hospital for Sick Children, Toronto, Canada
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23
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Lees JG. Legal issues in nursing. But I was just the supervisor. Focus Crit Care 1986; 13:33-4. [PMID: 3636234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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