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Yao Y, Bin X, Xu Y, Chen S, Chen S, Yuan XL, Cao Y, Ng TK. Cellular senescence mediates retinal ganglion cell survival regulation post-optic nerve crush injury. Cell Prolif 2024:e13719. [PMID: 39021340 DOI: 10.1111/cpr.13719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/24/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
Traumatic optic neuropathy refers to optic nerve (ON) injury by trauma, including explosion and traffic accident. Retinal ganglion cell (RGC) death is the critical pathological cause of irreversible visual impairment and blindness in ON injury. We previously investigated the patterns of 11 modes of cell death in mouse retina post-ON injury. Here we aimed to identify additional signalling pathways regulating RGC survival in rodents post-ON injury. RNA sequencing analysis identified the upregulation of inflammation and cellular senescence-related genes in retina post-ON injury, which were confirmed by immunoblotting and immunofluorescence analyses. Increased expression of senescence-associated β-galactosidase (SA-βgal) in RGCs and activation of microglia were also found. Transforming growth factor-β receptor type II inhibitor (LY2109761) treatment suppressed p15Ink4b and p21Cip1 protein and SA-βgal expression and promoted RGC survival post-ON injury with decreasing the expression of cell death markers in retina. Consistently, senolytics (dasatinib and quercetin) treatments can promote RGC survival and alleviate the reduction of ganglion cell complex thickness and pattern electroretinography activity post-ON injury with reducing SA-βgal, p15Ink4b, p21Cip1, microglial activation and cell death marker expression. In summary, this study revealed the activation of cellular senescence in rodent retina post-ON injury and contribute to RGC survival regulation. Targeting cellular senescence can promote RGC survival after ON injury, suggesting a potential treatment strategy for traumatic optic neuropathy.
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Affiliation(s)
- Yao Yao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Xin Bin
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Yanxuan Xu
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Shaowan Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Si Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Yingjie Cao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
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2
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Zhou W, Cuomo ASE, Xue A, Kanai M, Chau G, Krishna C, Xavier RJ, MacArthur DG, Powell JE, Daly MJ, Neale BM. Efficient and accurate mixed model association tool for single-cell eQTL analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307317. [PMID: 38798318 PMCID: PMC11118640 DOI: 10.1101/2024.05.15.24307317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Understanding the genetic basis of gene expression can help us understand the molecular underpinnings of human traits and disease. Expression quantitative trait locus (eQTL) mapping can help in studying this relationship but have been shown to be very cell-type specific, motivating the use of single-cell RNA sequencing and single-cell eQTLs to obtain a more granular view of genetic regulation. Current methods for single-cell eQTL mapping either rely on the "pseudobulk" approach and traditional pipelines for bulk transcriptomics or do not scale well to large datasets. Here, we propose SAIGE-QTL, a robust and scalable tool that can directly map eQTLs using single-cell profiles without needing aggregation at the pseudobulk level. Additionally, SAIGE-QTL allows for testing the effects of less frequent/rare genetic variation through set-based tests, which is traditionally excluded from eQTL mapping studies. We evaluate the performance of SAIGE-QTL on both real and simulated data and demonstrate the improved power for eQTL mapping over existing pipelines.
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3
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Farbehi N, Neavin DR, Cuomo ASE, Studer L, MacArthur DG, Powell JE. Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases. Nat Genet 2024; 56:758-766. [PMID: 38741017 DOI: 10.1038/s41588-024-01731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/20/2024] [Indexed: 05/16/2024]
Abstract
Human pluripotent stem (hPS) cells can, in theory, be differentiated into any cell type, making them a powerful in vitro model for human biology. Recent technological advances have facilitated large-scale hPS cell studies that allow investigation of the genetic regulation of molecular phenotypes and their contribution to high-order phenotypes such as human disease. Integrating hPS cells with single-cell sequencing makes identifying context-dependent genetic effects during cell development or upon experimental manipulation possible. Here we discuss how the intersection of stem cell biology, population genetics and cellular genomics can help resolve the functional consequences of human genetic variation. We examine the critical challenges of integrating these fields and approaches to scaling them cost-effectively and practically. We highlight two areas of human biology that can particularly benefit from population-scale hPS cell studies, elucidating mechanisms underlying complex disease risk loci and evaluating relationships between common genetic variation and pharmacotherapeutic phenotypes.
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Affiliation(s)
- Nona Farbehi
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Drew R Neavin
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anna S E Cuomo
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Lorenz Studer
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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4
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King NE, Courtney JM, Brown LS, Fortune AJ, Blackburn NB, Fletcher JL, Cashion JM, Talbot J, Pébay A, Hewitt AW, Morris GP, Young KM, Cook AL, Sutherland BA. Induced pluripotent stem cell derived pericytes respond to mediators of proliferation and contractility. Stem Cell Res Ther 2024; 15:59. [PMID: 38433209 PMCID: PMC10910734 DOI: 10.1186/s13287-024-03671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Pericytes are multifunctional contractile cells that reside on capillaries. Pericytes are critical regulators of cerebral blood flow and blood-brain barrier function, and pericyte dysfunction may contribute to the pathophysiology of human neurological diseases including Alzheimers disease, multiple sclerosis, and stroke. Induced pluripotent stem cell (iPSC)-derived pericytes (iPericytes) are a promising tool for vascular research. However, it is unclear how iPericytes functionally compare to primary human brain vascular pericytes (HBVPs). METHODS We differentiated iPSCs into iPericytes of either the mesoderm or neural crest lineage using established protocols. We compared iPericyte and HBVP morphologies, quantified gene expression by qPCR and bulk RNA sequencing, and visualised pericyte protein markers by immunocytochemistry. To determine whether the gene expression of neural crest iPericytes, mesoderm iPericytes or HBVPs correlated with their functional characteristics in vitro, we quantified EdU incorporation following exposure to the key pericyte mitogen, platelet derived growth factor (PDGF)-BB and, contraction and relaxation in response to the vasoconstrictor endothelin-1 or vasodilator adenosine, respectively. RESULTS iPericytes were morphologically similar to HBVPs and expressed canonical pericyte markers. However, iPericytes had 1864 differentially expressed genes compared to HBVPs, while there were 797 genes differentially expressed between neural crest and mesoderm iPericytes. Consistent with the ability of HBVPs to respond to PDGF-BB signalling, PDGF-BB enhanced and a PDGF receptor-beta inhibitor impaired iPericyte proliferation. Administration of endothelin-1 led to iPericyte contraction and adenosine led to iPericyte relaxation, of a magnitude similar to the response evoked in HBVPs. We determined that neural crest iPericytes were less susceptible to PDGFR beta inhibition, but responded most robustly to vasoconstrictive mediators. CONCLUSIONS iPericytes express pericyte-associated genes and proteins and, exhibit an appropriate physiological response upon exposure to a key endogenous mitogen or vasoactive mediators. Therefore, the generation of functional iPericytes would be suitable for use in future investigations exploring pericyte function or dysfunction in neurological diseases.
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Affiliation(s)
- Natalie E King
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Jo-Maree Courtney
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Lachlan S Brown
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Alastair J Fortune
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Nicholas B Blackburn
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Jessica L Fletcher
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Jake M Cashion
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Jana Talbot
- Wicking Dementia Education and Research Centre, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Gary P Morris
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Kaylene M Young
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Anthony L Cook
- Wicking Dementia Education and Research Centre, College of Health and Medicine, University of Tasmania, Hobart, Australia
| | - Brad A Sutherland
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Level 4, Medical Sciences Precinct, 17 Liverpool St, Hobart, TAS, 7000, Australia.
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5
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Wang J, Gleeson PA, Fourriere L. Long-term live cell imaging during differentiation of human iPSC-derived neurons. STAR Protoc 2023; 4:102699. [PMID: 37938977 PMCID: PMC10665918 DOI: 10.1016/j.xpro.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Live-cell imaging is crucial to appreciate the dynamics and the complexity of cellular interaction processes. However, live-cell imaging of human neurons is challenging due to neuronal sensitivity. Here, we describe a long-term live-cell imaging protocol for neurons derived from human induced pluripotent stem cells. By using an IncuCyte live-cell imaging system, we have obtained information on neuronal dynamics during the different stages of neurogenesis. The protocol has also been developed to monitor the dynamics of the neuronal intracellular organelles. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Jingqi Wang
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul A Gleeson
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Lou Fourriere
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
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6
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Cuomo ASE, Nathan A, Raychaudhuri S, MacArthur DG, Powell JE. Single-cell genomics meets human genetics. Nat Rev Genet 2023; 24:535-549. [PMID: 37085594 PMCID: PMC10784789 DOI: 10.1038/s41576-023-00599-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 04/23/2023]
Abstract
Single-cell genomic technologies are revealing the cellular composition, identities and states in tissues at unprecedented resolution. They have now scaled to the point that it is possible to query samples at the population level, across thousands of individuals. Combining single-cell information with genotype data at this scale provides opportunities to link genetic variation to the cellular processes underpinning key aspects of human biology and disease. This strategy has potential implications for disease diagnosis, risk prediction and development of therapeutic solutions. But, effectively integrating large-scale single-cell genomic data, genetic variation and additional phenotypic data will require advances in data generation and analysis methods. As single-cell genetics begins to emerge as a field in its own right, we review its current state and the challenges and opportunities ahead.
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Affiliation(s)
- Anna S E Cuomo
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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7
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Wang J, Daniszewski M, Hao MM, Hernández D, Pébay A, Gleeson PA, Fourriere L. Organelle mapping in dendrites of human iPSC-derived neurons reveals dynamic functional dendritic Golgi structures. Cell Rep 2023; 42:112709. [PMID: 37393622 DOI: 10.1016/j.celrep.2023.112709] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023] Open
Abstract
Secretory pathways within dendrites of neurons have been proposed for local transport of newly synthesized proteins. However, little is known about the dynamics of the local secretory system and whether the organelles are transient or stable structures. Here, we quantify the spatial and dynamic behavior of dendritic Golgi and endosomes during differentiation of human neurons generated from induced pluripotent stem cells (iPSCs). In early neuronal development, before and during migration, the entire Golgi apparatus transiently translocates from the soma into dendrites. In mature neurons, dynamic Golgi elements, containing cis and trans cisternae, are transported from the soma along dendrites, in an actin-dependent process. Dendritic Golgi outposts are dynamic and display bidirectional movement. Similar structures were observed in cerebral organoids. Using the retention using selective hooks (RUSH) system, Golgi resident proteins are transported efficiently into Golgi outposts from the endoplasmic reticulum. This study reveals dynamic, functional Golgi structures in dendrites and a spatial map for investigating dendrite trafficking in human neurons.
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Affiliation(s)
- Jingqi Wang
- The Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Marlene M Hao
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul A Gleeson
- The Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Lou Fourriere
- The Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
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8
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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] [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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9
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Cheng L, Kuehn MH. Human Retinal Organoids in Therapeutic Discovery: A Review of Applications. Handb Exp Pharmacol 2023; 281:157-187. [PMID: 37608005 DOI: 10.1007/164_2023_691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Human embryonic stem cells (hESCs)- and induced pluripotent stem cells (hiPSCs)-derived retinal organoids (ROs) are three-dimensional laminar structures that recapitulate the developmental trajectory of the human retina. The ROs provide a fascinating tool for basic science research, eye disease modeling, treatment development, and biobanking for tissue/cell replacement. Here we review the previous studies that paved the way for RO technology, the two most widely accepted, standardized protocols to generate ROs, and the utilization of ROs in medical discovery. This review is conducted from the perspective of basic science research, transplantation for regenerative medicine, disease modeling, and therapeutic development for drug screening and gene therapy. ROs have opened avenues for new technologies such as assembloids, coculture with other organoids, vasculature or immune cells, microfluidic devices (organ-on-chip), extracellular vesicles for drug delivery, biomaterial engineering, advanced imaging techniques, and artificial intelligence (AI). Nevertheless, some shortcomings of ROs currently limit their translation for medical applications and pose a challenge for future research. Despite these limitations, ROs are a powerful tool for functional studies and therapeutic strategies for retinal diseases.
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Affiliation(s)
- Lin Cheng
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
- Center for the Prevention and Treatment of Visual Loss, Veterans Affairs Medical Center, Iowa City, IA, USA.
| | - Markus H Kuehn
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Center for the Prevention and Treatment of Visual Loss, Veterans Affairs Medical Center, Iowa City, IA, USA
- Institute for Vision Research, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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10
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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] [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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