1
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Westhaus A, Eamegdool SS, Fernando M, Fuller-Carter P, Brunet AA, Miller AL, Rashwan R, Knight M, Daniszewski M, Lidgerwood GE, Pébay A, Hewitt A, Santilli G, Thrasher AJ, Carvalho LS, Gonzalez-Cordero A, Jamieson RV, Lisowski L. AAV capsid bioengineering in primary human retina models. Sci Rep 2023; 13:21946. [PMID: 38081924 PMCID: PMC10713676 DOI: 10.1038/s41598-023-49112-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Adeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Genethon, Evry, France
| | - Steven S Eamegdool
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | | | - Alicia A Brunet
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Annie L Miller
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | | | - Maddison Knight
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Alex Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Livia S Carvalho
- Lions Eye Institute, Nedlands, Australia
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Stem Cell Medicine Group, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.
- Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia.
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland.
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2
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Hall J, Daniszewski M, Cheung S, Shobhana K, Kumar H, Liang HH, Beetham H, Cho E, Abbott C, Hewitt AW, Simpson KJ, Guymer RH, Paull D, Pébay A, Lidgerwood GE. A semi-automated pipeline for quantifying drusen-like deposits in human induced pluripotent stem cell-derived retinal pigment epithelium cells. SLAS Technol 2023:S2472-6303(23)00055-9. [PMID: 37657710 DOI: 10.1016/j.slast.2023.08.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Age-Related Macular Degeneration (AMD) is a highly prevalent form of retinal disease amongst Western communities over 50 years of age. A hallmark of AMD pathogenesis is the accumulation of drusen underneath the retinal pigment epithelium (RPE), a biological process also observable in vitro. The accumulation of drusen has been shown to predict the progression to advanced AMD, making accurate characterisation of drusen in vitro models valuable in disease modelling and drug development. More recently, deposits above the RPE in the subretinal space, called reticular pseudodrusen (RPD) have been recognized as a sub-phenotype of AMD. While in vitro imaging techniques allow for the immunostaining of drusen-like deposits, quantification of these deposits often requires slow, low throughput manual counting of images. This further lends itself to issues including sampling biases, while ignoring critical data parameters including volume and precise localization. To overcome these issues, we developed a semi-automated pipeline for quantifying the presence of drusen-like deposits in vitro, using RPE cultures derived from patient-specific induced pluripotent stem cells (iPSCs). Using high-throughput confocal microscopy, together with three-dimensional reconstruction, we developed an imaging and analysis pipeline that quantifies the number of drusen-like deposits, and accurately and reproducibly provides the location and composition of these deposits. Extending its utility, this pipeline can determine whether the drusen-like deposits locate to the apical or basal surface of RPE cells. Here, we validate the utility of this pipeline in the quantification of drusen-like deposits in six iPSCs lines derived from patients with AMD, following their differentiation into RPE cells. This pipeline provides a valuable tool for the in vitro modelling of AMD and other retinal disease, and is amenable to mid and high throughput screenings.
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Affiliation(s)
- Jenna Hall
- Department of Anatomy and Physiology, The University of Melbourne, VIC, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, VIC, Australia
| | - Shane Cheung
- Biological Optical Microscopy Platform, The University of Melbourne, VIC, Australia
| | - Kalyan Shobhana
- Biological Optical Microscopy Platform, The University of Melbourne, VIC, Australia
| | - Himeesh Kumar
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, Australia; Department of Surgery, Ophthalmology, The University of Melbourne, VIC, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, Australia
| | - Henry Beetham
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC, Australia; Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, VIC, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, The University of Melbourne, VIC, Australia
| | - Carla Abbott
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, Australia; Department of Surgery, Ophthalmology, The University of Melbourne, VIC, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, Australia; Department of Surgery, Ophthalmology, The University of Melbourne, VIC, Australia
| | - Kaylene J Simpson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC, Australia; Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, VIC, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, VIC, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, Australia; Department of Surgery, Ophthalmology, The University of Melbourne, VIC, Australia
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, New York, United States
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, VIC, Australia; Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, VIC, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, VIC, Australia.
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3
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Neavin DR, Steinmann AM, Farbehi N, Chiu HS, Daniszewski MS, Arora H, Bermudez Y, Moutinho C, Chan CL, Bax M, Tyebally M, Gnanasambandapillai V, Lam CE, Nguyen U, Hernández D, Lidgerwood GE, Graham RM, Hewitt AW, Pébay A, Palpant NJ, Powell JE. A village in a dish model system for population-scale hiPSC studies. Nat Commun 2023; 14:3240. [PMID: 37296104 PMCID: PMC10256711 DOI: 10.1038/s41467-023-38704-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 08/31/2021] [Accepted: 04/26/2023] [Indexed: 06/12/2023] Open
Abstract
The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and different conditions. Human induced pluripotent stem cells are uniquely suited to study these context-dependent effects but cell lines from hundreds or thousands of individuals are required. Village cultures, where multiple induced pluripotent stem lines are cultured and differentiated in a single dish, provide an elegant solution for scaling induced pluripotent stem experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned to an induced pluripotent stem line using single-cell sequencing and illustrating that the genetic, epigenetic or induced pluripotent stem line-specific effects explain a large percentage of gene expression variation for many genes. We demonstrate that village methods can effectively detect induced pluripotent stem line-specific effects, including sensitive dynamics of cell states.
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Affiliation(s)
- Drew R Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Angela M Steinmann
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Nona Farbehi
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Kensington, 2033, Sydney, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Maciej S Daniszewski
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Himanshi Arora
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Yasmin Bermudez
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Cátia Moutinho
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Monique Bax
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Mubarika Tyebally
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | | | - Chuan E Lam
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Uyen Nguyen
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Robert M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- St Vincent's Hospital, Darlinghurst, 2010, NSW, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
- Department of Surgery, Royal Melbourne Hospital, Anatomy and Neuroscience, the University of Melbourne, Melbourne, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia.
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, 2052, Sydney, Australia.
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4
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Hall JC, Paull D, Pébay A, Lidgerwood GE. Human pluripotent stem cells for the modelling of retinal pigment epithelium homeostasis and disease: A review. Clin Exp Ophthalmol 2022; 50:667-677. [PMID: 35739648 PMCID: PMC9546239 DOI: 10.1111/ceo.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 12/05/2022]
Abstract
Human pluripotent stem cells (hPSCs), which include induced pluripotent stem cells and embryonic stem cells, are powerful tools for studying human development, physiology and disease, including those affecting the retina. Cells from selected individuals, or specific genetic backgrounds, can be differentiated into distinct cell types allowing the modelling of diseases in a dish for therapeutic development. hPSC‐derived retinal cultures have already been used to successfully model retinal pigment epithelium (RPE) degeneration for various retinal diseases including monogenic conditions and complex disease such as age‐related macular degeneration. Here, we will review the current knowledge gained in understanding the molecular events involved in retinal disease using hPSC‐derived retinal models, in particular RPE models. We will provide examples of various conditions to illustrate the scope of applications associated with the use of hPSC‐derived RPE models.
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Affiliation(s)
- Jenna C Hall
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute New York New York USA
| | - Alice Pébay
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
- Department of Surgery, Royal Melbourne Hospital The University of Melbourne Parkville Victoria Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
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5
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Senabouth A, Daniszewski M, Lidgerwood GE, Liang HH, Hernández D, Mirzaei M, Keenan SN, Zhang R, Han X, Neavin D, Rooney L, Lopez Sanchez MIG, Gulluyan L, Paulo JA, Clarke L, Kearns LS, Gnanasambandapillai V, Chan CL, Nguyen U, Steinmann AM, McCloy RA, Farbehi N, Gupta VK, Mackey DA, Bylsma G, Verma N, MacGregor S, Watt MJ, Guymer RH, Powell JE, Hewitt AW, Pébay A. Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nat Commun 2022; 13:4233. [PMID: 35882847 PMCID: PMC9325891 DOI: 10.1038/s41467-022-31707-4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
There are currently no treatments for geographic atrophy, the advanced form of age-related macular degeneration. Hence, innovative studies are needed to model this condition and prevent or delay its progression. Induced pluripotent stem cells generated from patients with geographic atrophy and healthy individuals were differentiated to retinal pigment epithelium. Integrating transcriptional profiles of 127,659 retinal pigment epithelium cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identify 445 expression quantitative trait loci in cis that are asssociated with disease status and specific to retinal pigment epithelium subpopulations. Transcriptomics and proteomics approaches identify molecular pathways significantly upregulated in geographic atrophy, including in mitochondrial functions, metabolic pathways and extracellular cellular matrix reorganization. Five significant protein quantitative trait loci that regulate protein expression in the retinal pigment epithelium and in geographic atrophy are identified - two of which share variants with cis- expression quantitative trait loci, including proteins involved in mitochondrial biology and neurodegeneration. Investigation of mitochondrial metabolism confirms mitochondrial dysfunction as a core constitutive difference of the retinal pigment epithelium from patients with geographic atrophy. This study uncovers important differences in retinal pigment epithelium homeostasis associated with geographic atrophy.
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Affiliation(s)
- Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Helena H Liang
- 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
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Stacey N Keenan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ran Zhang
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - 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
| | | | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Uyen Nguyen
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Angela M Steinmann
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Rachael A McCloy
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Nona Farbehi
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Vivek K Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - David A Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Guy Bylsma
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Nitin Verma
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- School of Medicine, University of Tasmania, Hobart, TAS, 7005, Australia.
- Department of Surgery, Ophthalmology, Royal Victorian Eye and Ear Hospital, The University of Melbourne, East Melbourne, VIC, 3002, Australia.
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia.
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3010, Australia.
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6
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Wang JH, Lidgerwood GE, Daniszewski M, Hu ML, Roberts GE, Wong RCB, Hung SSC, McClements ME, Hewitt AW, Pébay A, Hickey DG, Edwards TL. AAV2-mediated gene therapy for Bietti crystalline dystrophy provides functional CYP4V2 in multiple relevant cell models. Sci Rep 2022; 12:9525. [PMID: 35680963 PMCID: PMC9184470 DOI: 10.1038/s41598-022-12210-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/06/2022] [Indexed: 12/23/2022] Open
Abstract
Bietti crystalline dystrophy (BCD) is an inherited retinal disease (IRD) caused by mutations in the CYP4V2 gene. It is a relatively common cause of IRD in east Asia. A number of features of this disease make it highly amenable to gene supplementation therapy. This study aims to validate a series of essential precursor in vitro experiments prior to developing a clinical gene therapy for BCD. We demonstrated that HEK293, ARPE19, and patient induced pluripotent stem cell (iPSC)-derived RPE cells transduced with AAV2 vectors encoding codon optimization of CYP4V2 (AAV2.coCYP4V2) resulted in elevated protein expression levels of CYP4V2 compared to those transduced with AAV2 vectors encoding wild type CYP4V2 (AAV2.wtCYP4V2), as assessed by immunocytochemistry and western blot. Similarly, we observed significantly increased CYP4V2 enzyme activity in cells transduced with AAV2.coCYP4V2 compared to those transduced with AAV2.wtCYP4V2. We also showed CYP4V2 expression in human RPE/choroid explants transduced with AAV2.coCYP4V2 compared to those transduced with AAV2.wtCYP4V2. These preclinical data support the further development of a gene supplementation therapy for a currently untreatable blinding condition—BCD. Codon-optimized CYP4V2 transgene was superior to wild type in terms of protein expression and enzyme activity. Ex vivo culture of human RPE cells provided an effective approach to test AAV-mediated transgene delivery.
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Affiliation(s)
- Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia.,Department of Anatomy and Physiology, The University of Melbourne, Parkville, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Australia
| | - Monica L Hu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Georgina E Roberts
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, VIC, Australia.,Shenzhen Eye Hospital, Shenzhen University School of Medicine, Shenzhen, China
| | - Sandy S C Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, VIC, Australia
| | - Michelle E McClements
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, UK
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia.,Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, VIC, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Australia.,Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, Australia
| | - Doron G Hickey
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Thomas L Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Level 7, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia. .,Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, VIC, Australia.
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7
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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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8
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Neavin D, Nguyen Q, Daniszewski MS, Liang HH, Chiu HS, Wee YK, Senabouth A, Lukowski SW, Crombie DE, Lidgerwood GE, Hernández D, Vickers JC, Cook AL, Palpant NJ, Pébay A, Hewitt AW, Powell JE. Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biol 2021; 22:76. [PMID: 33673841 PMCID: PMC7934233 DOI: 10.1186/s13059-021-02293-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. Gene expression plays a critical role in complex disease risk and therapeutic response. However, while the genetic background of reprogrammed cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells which would provide significant resolution. By integrating single cell RNA-sequencing (scRNA-seq) and population genetics, we apply a framework in which to evaluate cell type-specific effects of genetic variation on gene expression. RESULTS Here, we perform scRNA-seq on 64,018 fibroblasts from 79 donors and map expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generate scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type-specific eQTLs in iPSCs and show that the eQTLs in fibroblasts almost entirely disappear during reprogramming. CONCLUSIONS This work provides an atlas of how genetic variation influences gene expression across cell subtypes and provides evidence for patterns of genetic architecture that lead to cell type-specific eQTL effects.
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Affiliation(s)
- Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Maciej S Daniszewski
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yong Kiat Wee
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Duncan E Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Melbourne, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia.
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, Australia.
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9
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Lidgerwood GE, Senabouth A, Smith-Anttila CJA, Gnanasambandapillai V, Kaczorowski DC, Amann-Zalcenstein D, Fletcher EL, Naik SH, Hewitt AW, Powell JE, Pébay A. Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. Genomics Proteomics Bioinformatics 2020; 19:223-242. [PMID: 33307245 PMCID: PMC8602392 DOI: 10.1016/j.gpb.2020.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 11/14/2019] [Revised: 07/04/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native counterparts, we characterised the transcriptomic profiles of the hPSC-derived RPE cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single-cell RNA-sequencing of a total of 16,576 cells to assess the molecular changes of the RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial–mesenchymal transition, and with the maturing populations of the RPE observed with time in culture. Assessment of Gene Ontology pathways revealed that as the cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirms a maturing transcriptional profile of RPE cells in culture. These results suggest that long-term in vitro culture of RPE cells allows the modelling of specific phenotypes observed in native mature tissues. Our work highlights the transcriptional landscape of hPSC-derived RPE cells as they age in culture, which provides a reference for native and patient samples to be benchmarked against.
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Affiliation(s)
- Grace E Lidgerwood
- Department of Anatomy and Neuroscience, 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
| | - Casey J A Smith-Anttila
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Dominik C Kaczorowski
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Daniela Amann-Zalcenstein
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Erica L Fletcher
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shalin H Naik
- Single Cell Open Research Endeavour, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - 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
| | - 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, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alice Pébay
- Department of Anatomy and Neuroscience, 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.
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10
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Nguyen Tran MT, Mohd Khalid MKN, Wang Q, Walker JKR, Lidgerwood GE, Dilworth KL, Lisowski L, Pébay A, Hewitt AW. Engineering domain-inlaid SaCas9 adenine base editors with reduced RNA off-targets and increased on-target DNA editing. Nat Commun 2020; 11:4871. [PMID: 32978399 PMCID: PMC7519688 DOI: 10.1038/s41467-020-18715-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 04/08/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
Precision genome engineering has dramatically advanced with the development of CRISPR/Cas base editing systems that include cytosine base editors and adenine base editors (ABEs). Herein, we compare the editing profile of circularly permuted and domain-inlaid Cas9 base editors, and find that on-target editing is largely maintained following their intradomain insertion, but that structural permutation of the ABE can affect differing RNA off-target events. With this insight, structure-guided design was used to engineer an SaCas9 ABE variant (microABE I744) that has dramatically improved on-target editing efficiency and a reduced RNA-off target footprint compared to current N-terminal linked SaCas9 ABE variants. This represents one of the smallest AAV-deliverable Cas9-ABEs available, which has been optimized for robust on-target activity and RNA-fidelity based upon its stereochemistry. Off-target effects and the feasibility for AAV-mediated delivery are the major barriers impeding the clinical in vivo application of base editors. Here, the authors report the small size AAV-deliverable Cas9-ABE variant that has improved on-target editing efficiency and reduced RNA-off target footprint.
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Affiliation(s)
- Minh Thuan Nguyen Tran
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia.
| | | | - Qi Wang
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia
| | - Jacqueline K R Walker
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia
| | - Grace E Lidgerwood
- Department of Surgery, The University of Melbourne, Victoria, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Australia
| | - Kimberley L Dilworth
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
| | - Alice Pébay
- Department of Surgery, The University of Melbourne, Victoria, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Tasmania, Australia.,Centre for Eye Research Australia, The University of Melbourne, Victoria, Australia
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11
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Suzuki S, Shadforth AM, McLenachan S, Zhang D, Chen SC, Walshe J, Lidgerwood GE, Pébay A, Chirila TV, Chen FK, Harkin DG. Optimization of silk fibroin membranes for retinal implantation. Materials Science and Engineering: C 2019; 105:110131. [DOI: 10.1016/j.msec.2019.110131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/02/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022]
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12
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Lidgerwood GE, Hewitt AW, Pébay A. Human pluripotent stem cells for the modelling of diseases of the retina and optic nerve: toward a retina in a dish. Curr Opin Pharmacol 2019; 48:114-119. [PMID: 31590110 DOI: 10.1016/j.coph.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
Human pluripotent stem cells can be differentiated into specific, relevant cell types of interest including the cells of the retina and optic nerve. These cells can then be used to study fundamental biology as well as disease modelling and subsequent screening of potential treatments. Many models of differentiation and modelling have relied on two-dimensional monocultures of specific cell types, which are not representative of the complexity of the human retina and optic nerve. Hence, more complex models of the human retina and optic nerve are required. Three-dimensional organoids and emerging cell culture methods may provide more physiologically relevant models to study developmental biology and pathology of the retina and optic nerve.
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Affiliation(s)
- Grace E Lidgerwood
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Australia; Department of Surgery, The University of Melbourne, Parkville, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Alex W Hewitt
- Department of Surgery, The University of Melbourne, Parkville, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Alice Pébay
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Australia; Department of Surgery, The University of Melbourne, Parkville, Australia.
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13
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Lidgerwood GE, Pitson SM, Bonder C, Pébay A. Roles of lysophosphatidic acid and sphingosine-1-phosphate in stem cell biology. Prog Lipid Res 2018; 72:42-54. [PMID: 30196008 DOI: 10.1016/j.plipres.2018.09.001] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023]
Abstract
Stem cells are unique in their ability to self-renew and differentiate into various cell types. Because of these features, stem cells are key to the formation of organisms and play fundamental roles in tissue regeneration and repair. Mechanisms controlling their fate are thus fundamental to the development and homeostasis of tissues and organs. Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are bioactive phospholipids that play a wide range of roles in multiple cell types, during developmental and pathophysiological events. Considerable evidence now demonstrates the potent roles of LPA and S1P in the biology of pluripotent and adult stem cells, from maintenance to repair. Here we review their roles for each main category of stem cells and explore how those effects impact development and physiopathology.
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Affiliation(s)
- Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Claudine Bonder
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, Australia.
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14
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Daniszewski M, Nguyen Q, Chy HS, Singh V, Crombie DE, Kulkarni T, Liang HH, Sivakumaran P, Lidgerwood GE, Hernández D, Conquest A, Rooney LA, Chevalier S, Andersen SB, Senabouth A, Vickers JC, Mackey DA, Craig JE, Laslett AL, Hewitt AW, Powell JE, Pébay A. Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media. iScience 2018; 7:30-39. [PMID: 30267684 PMCID: PMC6135898 DOI: 10.1016/j.isci.2018.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 03/13/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 02/08/2023] Open
Abstract
We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.
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Affiliation(s)
- Maciej Daniszewski
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hun S Chy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Vikrant Singh
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Duncan E Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Tejal Kulkarni
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Alison Conquest
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Louise A Rooney
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Sophie Chevalier
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
| | - Stacey B Andersen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne Senabouth
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - James C Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
| | | | - Andrew L Laslett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia.
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Lidgerwood GE, Morris AJ, Conquest A, Daniszewski M, Rooney LA, Lim SY, Hernández D, Liang HH, Allen P, Connell PP, Guymer RH, Hewitt AW, Pébay A. Role of lysophosphatidic acid in the retinal pigment epithelium and photoreceptors. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:750-761. [DOI: 10.1016/j.bbalip.2018.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/12/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
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Lidgerwood GE, Lim SY, Crombie DE, Ali R, Gill KP, Hernández D, Kie J, Conquest A, Waugh HS, Wong RCB, Liang HH, Hewitt AW, Davidson KC, Pébay A. Defined Medium Conditions for the Induction and Expansion of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium. Stem Cell Rev Rep 2017; 12:179-88. [PMID: 26589197 DOI: 10.1007/s12015-015-9636-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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] [Indexed: 01/12/2023]
Abstract
We demonstrate that a combination of Noggin, Dickkopf-1, Insulin Growth Factor 1 and basic Fibroblast Growth Factor, promotes the differentiation of human pluripotent stem cells into retinal pigment epithelium (RPE) cells. We describe an efficient one-step approach that allows the generation of RPE cells from both human embryonic stem cells and human induced pluripotent stem cells within 40-60 days without the need for manual excision, floating aggregates or imbedded cysts. Compared to methods that rely on spontaneous differentiation, our protocol results in faster differentiation into RPE cells. This pro-retinal culture medium promotes the growth of functional RPE cells that exhibit key characteristics of the RPE including pigmentation, polygonal morphology, expression of mature RPE markers, electrophysiological membrane potential and the ability to phagocytose photoreceptor outer segments. This protocol can be adapted for feeder, feeder-free and serum-free conditions. This method thereby provides a rapid and simplified production of RPE cells for downstream applications such as disease modelling and drug screening.
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Affiliation(s)
- Grace E Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Shiang Y Lim
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Duncan E Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Ray Ali
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, TAS, Australia
| | - Katherine P Gill
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Damián Hernández
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Josh Kie
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, Australia
| | - Alison Conquest
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Hayley S Waugh
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Helena H Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, TAS, Australia
| | - Kathryn C Davidson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital; Ophthalmology, University of Melbourne, Department of Surgery, 32 Gisborne Street, East Melbourne, VIC, 3002, Australia.
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17
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Crombie DE, Daniszewski M, Liang HH, Kulkarni T, Li F, Lidgerwood GE, Conquest A, Hernández D, Hung SS, Gill KP, De Smit E, Kearns LS, Clarke L, Sluch VM, Chamling X, Zack DJ, Wong RCB, Hewitt AW, Pébay A. Development of a Modular Automated System for Maintenance and Differentiation of Adherent Human Pluripotent Stem Cells. SLAS Discov 2017; 22:1016-1025. [PMID: 28287872 DOI: 10.1177/2472555217696797] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) have tremendous potential for development of regenerative medicine, disease modeling, and drug discovery. However, the processes of reprogramming, maintenance, and differentiation are labor intensive and subject to intertechnician variability. To address these issues, we established and optimized protocols to allow for the automated maintenance of reprogrammed somatic cells into iPSCs to enable the large-scale culture and passaging of human pluripotent stem cells (PSCs) using a customized TECAN Freedom EVO. Generation of iPSCs was performed offline by nucleofection followed by selection of TRA-1-60-positive cells using a Miltenyi MultiMACS24 Separator. Pluripotency markers were assessed to confirm pluripotency of the generated iPSCs. Passaging was performed using an enzyme-free dissociation method. Proof of concept of differentiation was obtained by differentiating human PSCs into cells of the retinal lineage. Key advantages of this automated approach are the ability to increase sample size, reduce variability during reprogramming or differentiation, and enable medium- to high-throughput analysis of human PSCs and derivatives. These techniques will become increasingly important with the emergence of clinical trials using stem cells.
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Affiliation(s)
- Duncan E Crombie
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia.,Co-first authors
| | - Maciej Daniszewski
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia.,Co-first authors
| | - Helena H Liang
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Tejal Kulkarni
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Fan Li
- 2 School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,3 State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Grace E Lidgerwood
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Alison Conquest
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Damian Hernández
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Sandy S Hung
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Katherine P Gill
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Elisabeth De Smit
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Lisa S Kearns
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Linda Clarke
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Valentin M Sluch
- 4 Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xitiz Chamling
- 4 Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donald J Zack
- 4 Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,5 Departments of Neuroscience, Molecular Biology and Genetics, and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Raymond C B Wong
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia
| | - Alex W Hewitt
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia.,2 School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Co-senior authors
| | - Alice Pébay
- 1 Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Department of Ophthalmology, the University of Melbourne, East Melbourne, Victoria, Australia.,Co-senior authors
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Grubman A, Lidgerwood GE, Duncan C, Bica L, Tan JL, Parker SJ, Caragounis A, Meyerowitz J, Volitakis I, Moujalled D, Liddell JR, Hickey JL, Horne M, Longmuir S, Koistinaho J, Donnelly PS, Crouch PJ, Tammen I, White AR, Kanninen KM. Deregulation of subcellular biometal homeostasis through loss of the metal transporter, Zip7, in a childhood neurodegenerative disorder. Acta Neuropathol Commun 2014; 2:25. [PMID: 24581221 PMCID: PMC4029264 DOI: 10.1186/2051-5960-2-25] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/19/2014] [Indexed: 12/31/2022] Open
Abstract
Background Aberrant biometal metabolism is a key feature of neurodegenerative disorders including Alzheimer’s and Parkinson’s diseases. Metal modulating compounds are promising therapeutics for neurodegeneration, but their mechanism of action remains poorly understood. Neuronal ceroid lipofuscinoses (NCLs), caused by mutations in CLN genes, are fatal childhood neurodegenerative lysosomal storage diseases without a cure. We previously showed biometal accumulation in ovine and murine models of the CLN6 variant NCL, but the mechanism is unknown. This study extended the concept that alteration of biometal functions is involved in pathology in these disorders, and investigated molecular mechanisms underlying impaired biometal trafficking in CLN6 disease. Results We observed significant region-specific biometal accumulation and deregulation of metal trafficking pathways prior to disease onset in CLN6 affected sheep. Substantial progressive loss of the ER/Golgi-resident Zn transporter, Zip7, which colocalized with the disease-associated protein, CLN6, may contribute to the subcellular deregulation of biometal homeostasis in NCLs. Importantly, the metal-complex, ZnII(atsm), induced Zip7 upregulation, promoted Zn redistribution and restored Zn-dependent functions in primary mouse Cln6 deficient neurons and astrocytes. Conclusions This study demonstrates the central role of the metal transporter, Zip7, in the aberrant biometal metabolism of CLN6 variants of NCL and further highlights the key contribution of deregulated biometal trafficking to the pathology of neurodegenerative diseases. Importantly, our results suggest that ZnII(atsm) may be a candidate for therapeutic trials for NCLs.
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Moujalled D, James JL, Parker SJ, Lidgerwood GE, Duncan C, Meyerowitz J, Nonaka T, Hasegawa M, Kanninen KM, Grubman A, Liddell JR, Crouch PJ, White AR. Kinase Inhibitor Screening Identifies Cyclin-Dependent Kinases and Glycogen Synthase Kinase 3 as Potential Modulators of TDP-43 Cytosolic Accumulation during Cell Stress. PLoS One 2013; 8:e67433. [PMID: 23840699 PMCID: PMC3694067 DOI: 10.1371/journal.pone.0067433] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/21/2013] [Indexed: 12/13/2022] Open
Abstract
Abnormal processing of TAR DNA binding protein 43 (TDP-43) has been identified as a major factor in neuronal degeneration during amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration (FTLD). It is unclear how changes to TDP-43, including nuclear to cytosolic translocation and subsequent accumulation, are controlled in these diseases. TDP-43 is a member of the heterogeneous ribonucleoprotein (hnRNP) RNA binding protein family and is known to associate with cytosolic RNA stress granule proteins in ALS and FTLD. hnRNP trafficking and accumulation is controlled by the action of specific kinases including members of the mitogen-activated protein kinase (MAPK) pathway. However, little is known about how kinase pathways control TDP-43 movement and accumulation. In this study, we used an in vitro model of TDP-43-positve stress granule formation to screen for the effect of kinase inhibitors on TDP-43 accumulation. We found that while a number of kinase inhibitors, particularly of the MAPK pathways modulated both TDP-43 and the global stress granule marker, human antigen R (HuR), multiple inhibitors were more specific to TDP-43 accumulation, including inhibitors of cyclin-dependent kinases (CDKs) and glycogen synthase kinase 3 (GSK3). Close correlation was observed between effects of these inhibitors on TDP-43, hnRNP K and TIAR, but often with different effects on HuR accumulation. This may indicate a potential interaction between TDP-43, hnRNP K and TIAR. CDK inhibitors were also found to reverse pre-formed TDP-43-positive stress granules and both CDK and GSK3 inhibitors abrogated the accumulation of C-terminal TDP-43 (219–414) in transfected cells. Further studies are required to confirm the specific kinases involved and whether their action is through phosphorylation of the TDP-43 binding partner hnRNP K. This knowledge provides a valuable insight into the mechanisms controlling abnormal cytoplasmic TDP-43 accumulation and may herald new opportunities for kinase modulation-based therapeutic intervention in ALS and FTLD.
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Affiliation(s)
- Diane Moujalled
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Janine L. James
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Sarah J. Parker
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Grace E. Lidgerwood
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Clare Duncan
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Jodi Meyerowitz
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Takashi Nonaka
- Department of Neuropathology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Masato Hasegawa
- Department of Neuropathology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, Laboratory of Molecular Brain Research, University of Eastern Finland, Kuopio, Finland
| | - Alexandra Grubman
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Jeffrey R. Liddell
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Peter J. Crouch
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Anthony R. White
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
- * E-mail:
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20
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Kanninen KM, Grubman A, Caragounis A, Duncan C, Parker SJ, Lidgerwood GE, Volitakis I, Ganio G, Crouch PJ, White AR. Altered biometal homeostasis is associated with CLN6 mRNA loss in mouse neuronal ceroid lipofuscinosis. Biol Open 2013; 2:635-46. [PMID: 23789114 PMCID: PMC3683166 DOI: 10.1242/bio.20134804] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 03/15/2013] [Accepted: 04/23/2013] [Indexed: 12/21/2022] Open
Abstract
Neuronal ceroid lipofuscinoses, the most common fatal childhood neurodegenerative illnesses, share many features with more prevalent neurodegenerative diseases. Neuronal ceroid lipofuscinoses are caused by mutations in CLN genes. CLN6 encodes a transmembrane endoplasmic reticulum protein with no known function. We characterized the behavioural phenotype of spontaneous mutant mice modeling CLN6 disease, and demonstrate progressive motor and visual decline and reduced lifespan in these mice, consistent with symptoms observed in neuronal ceroid lipofuscinosis patients. Alterations to biometal homeostasis are known to play a critical role in pathology in Alzheimer's, Parkinson's, Huntington's and motor neuron diseases. We have previously shown accumulation of the biometals, zinc, copper, manganese and cobalt, in CLN6 Merino and South Hampshire sheep at the age of symptom onset. Here we determine the physiological and disease-associated expression of CLN6, demonstrating regional CLN6 transcript loss, and concurrent accumulation of the same biometals in the CNS and the heart of presymptomatic CLN6 mice. Furthermore, increased expression of the ER/Golgi-localized cation transporter protein, Zip7, was detected in cerebellar Purkinje cells and whole brain fractions. Purkinje cells not only control motor function, an early symptomatic change in the CLN6 mice, but also display prominent neuropathological changes in mouse models and patients with different forms of neuronal ceroid lipofuscinoses. Whole brain fractionation analysis revealed biometal accumulation in fractions expressing markers for ER, Golgi, endosomes and lysosomes of CLN6 brains. These data are consistent with a link between CLN6 expression and biometal homeostasis in CLN6 disease, and provide further support for altered cation transporter regulation as a key factor in neurodegeneration.
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Affiliation(s)
- Katja M Kanninen
- Department of Pathology, The University of Melbourne , Parkville, Victoria 3010 , Australia ; Present address: AI Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
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Duncan C, Bica L, Crouch PJ, Caragounis A, Lidgerwood GE, Parker SJ, Meyerowitz J, Volitakis I, Liddell JR, Raghupathi R, Paterson BM, Duffield MD, Cappai R, Donnelly PS, Grubman A, Camakaris J, Keating DJ, White AR. Copper modulates the large dense core vesicle secretory pathway in PC12 cells. Metallomics 2013; 5:700-14. [DOI: 10.1039/c3mt20231c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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