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Shelton DA, Gefke I, Summers V, Kim YK, Yu H, Getz Y, Ferdous S, Donaldson K, Liao K, Papania JT, Chrenek MA, Boatright JH, Nickerson JM. Age-Related RPE changes in Wildtype C57BL/6J Mice between 2 and 32 Months. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.574142. [PMID: 38352604 PMCID: PMC10862734 DOI: 10.1101/2024.01.30.574142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Purpose This study provides a systematic evaluation of age-related changes in RPE cell structure and function using a morphometric approach. We aim to better capture nuanced predictive changes in cell heterogeneity that reflect loss of RPE integrity during normal aging. Using C57BL6/J mice ranging from P60-P730, we sought to evaluate how regional changes in RPE shape reflect incremental losses in RPE cell function with advancing age. We hypothesize that tracking global morphological changes in RPE is predictive of functional defects over time. Methods We tested three groups of C57BL/6J mice (young: P60-180; Middle-aged: P365-729; aged: 730+) for function and structural defects using electroretinograms, immunofluorescence, and phagocytosis assays. Results The largest changes in RPE morphology were evident between the young and aged groups, while the middle-aged group exhibited smaller but notable region-specific differences. We observed a 1.9-fold increase in cytoplasmic alpha-catenin expression specifically in the central-medial region of the eye between the young and aged group. There was an 8-fold increase in subretinal, IBA-1-positive immune cell recruitment and a significant decrease in visual function in aged mice compared to young mice. Functional defects in the RPE corroborated by changes in RPE phagocytotic capacity. Conclusions The marked increase of cytoplasmic alpha-catenin expression and subretinal immune cell deposition, and decreased visual output coincide with regional changes in RPE cell morphometrics when stratified by age. These cumulative changes in the RPE morphology showed predictive regional patterns of stress associated with loss of RPE integrity.
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Affiliation(s)
- Debresha A. Shelton
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Isabelle Gefke
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Vivian Summers
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Yong-Kyu Kim
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
- Department of Ophthalmology, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul, South Korea
| | - Hanyi Yu
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
- Department of Computer Science, Emory University, Atlanta, Georgia, United States
| | - Yana Getz
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Salma Ferdous
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Kevin Donaldson
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Kristie Liao
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Jack T. Papania
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Micah A. Chrenek
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
| | - Jeffrey H. Boatright
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
- Atlanta VA Center for Visual and Neurocognitive Rehabilitation, Decatur, Georgia, United States
| | - John M. Nickerson
- Department of Ophthalmology, Emory University, Atlanta, Georgia, United States
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2
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Nguyen T, Urrutia-Cabrera D, Wang L, Lees JG, Wang JH, Hung SS, Hewitt AW, Edwards TL, McLenachan S, Chen FK, Lim SY, Luu CD, Guymer R, Wong RC. Knockout of AMD-associated gene POLDIP2 reduces mitochondrial superoxide in human retinal pigment epithelial cells. Aging (Albany NY) 2023; 15:1713-1733. [PMID: 36795578 PMCID: PMC10085620 DOI: 10.18632/aging.204522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Genetic and epidemiologic studies have significantly advanced our understanding of the genetic factors contributing to age-related macular degeneration (AMD). In particular, recent expression quantitative trait loci (eQTL) studies have highlighted POLDIP2 as a significant gene that confers risk of developing AMD. However, the role of POLDIP2 in retinal cells such as retinal pigment epithelium (RPE) and how it contributes to AMD pathology are unknown. Here we report the generation of a stable human RPE cell line ARPE-19 with POLDIP2 knockout using CRISPR/Cas, providing an in vitro model to investigate the functions of POLDIP2. We conducted functional studies on the POLDIP2 knockout cell line and showed that it retained normal levels of cell proliferation, cell viability, phagocytosis and autophagy. Also, we performed RNA sequencing to profile the transcriptome of POLDIP2 knockout cells. Our results highlighted significant changes in genes involved in immune response, complement activation, oxidative damage and vascular development. We showed that loss of POLDIP2 caused a reduction in mitochondrial superoxide levels, which is consistent with the upregulation of the mitochondrial superoxide dismutase SOD2. In conclusion, this study demonstrates a novel link between POLDIP2 and SOD2 in ARPE-19, which supports a potential role of POLDIP2 in regulating oxidative stress in AMD pathology.
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Affiliation(s)
- Tu Nguyen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Urrutia-Cabrera
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Luozixian Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Jarmon G. Lees
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- Departments of Surgery and Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Sandy S.C. Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Alex W. Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Thomas L. Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Sam McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Fred K. Chen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Shiang Y. Lim
- O’Brien Institute Department, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- Departments of Surgery and Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Chi D. Luu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Robyn Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Raymond C.B. Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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3
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Development of a CRISPRi Human Retinal Pigmented Epithelium Model for Functional Study of Age-Related Macular Degeneration Genes. Int J Mol Sci 2023; 24:ijms24043417. [PMID: 36834828 PMCID: PMC9962760 DOI: 10.3390/ijms24043417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Age-related macular degeneration (AMD) is a blinding disease characterised by dysfunction of the retinal pigmented epithelium (RPE) which culminates in disruption or loss of the neurosensory retina. Genome-wide association studies have identified >60 genetic risk factors for AMD; however, the expression profile and functional role of many of these genes remain elusive in human RPE. To facilitate functional studies of AMD-associated genes, we developed a human RPE model with integrated CRISPR interference (CRISPRi) for gene repression by generating a stable ARPE19 cell line expressing dCas9-KRAB. We performed transcriptomic analysis of the human retina to prioritise AMD-associated genes and selected TMEM97 as a candidate gene for knockdown study. Using specific sgRNAs, we showed that knockdown of TMEM97 in ARPE19 reduced reactive oxygen species (ROS) levels and exerted a protective effect against oxidative stress-induced cell death. This work provides the first functional study of TMEM97 in RPE and supports a potential role of TMEM97 in AMD pathobiology. Our study highlights the potential for using CRISPRi to study AMD genetics, and the CRISPRi RPE platform generated here provided a useful in vitro tool for functional studies of AMD-associated genes.
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Hu Y, Qi S, Zhuang H, Zhuo Q, Liang Y, Kong H, Zhao C, Zhang S. Proteotranscriptomic analyses reveal distinct interferon-beta signaling pathways and therapeutic targets in choroidal neovascularization. Front Immunol 2023; 14:1163739. [PMID: 37025993 PMCID: PMC10071000 DOI: 10.3389/fimmu.2023.1163739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/28/2023] [Indexed: 04/08/2023] Open
Abstract
Aim To investigate the molecular mechanism underlying the onset of choroidal neovascularization (CNV). Methods Integrated transcriptomic and proteomic analyses of retinas in mice with laser-induced CNV were performed using RNA sequencing and tandem mass tag. In addition, the laser-treated mice received systemic interferon-β (IFN-β) therapy. Measurements of CNV lesions were acquired by the confocal analysis of stained choroidal flat mounts. The proportions of T helper 17 (Th17) cells were determined by flow cytometric analysis. Results A total of differentially expressed 186 genes (120 up-regulated and 66 down-regulated) and 104 proteins (73 up-regulated and 31 down-regulated) were identified. The gene ontology and KEGG pathway analyses indicated that CNV was mainly associated with immune and inflammatory responses, such as cellular response to IFN-β and Th17 cell differentiation. Moreover, the key nodes of the protein-protein interaction network mainly involved up-regulated proteins, including alpha A crystallin and fibroblast growth factor 2, and were verified by Western blotting. To confirm the changes in gene expression, real-time quantitative PCR was performed. Furthermore, levels of IFN-β in both the retina and plasma, as measured by enzyme-linked immunosorbent assay (ELISA), were significantly lower in the CNV group than in the control group. IFN-β treatment significantly reduced CNV lesion size and promoted the proliferation of Th17 cells in laser-treated mice. Conclusions This study demonstrates that the occurrence of CNV might be associated with the dysfunction of immune and inflammatory processes and that IFN-β could serve as a potential therapeutic target.
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Affiliation(s)
| | | | | | | | | | | | - Chen Zhao
- *Correspondence: Chen Zhao, ; Shujie Zhang,
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5
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Fehér J, Élő Á, István L, Nagy ZZ, Radák Z, Scuderi G, Artico M, Kovács I. Microbiota mitochondria disorders as hubs for early age-related macular degeneration. GeroScience 2022; 44:2623-2653. [PMID: 35978068 PMCID: PMC9385247 DOI: 10.1007/s11357-022-00620-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/01/2022] [Indexed: 01/07/2023] Open
Abstract
Age-related macular degeneration (AMD) is a progressive neurodegenerative disease affecting the central area (macula lutea) of the retina. Research on the pathogenic mechanism of AMD showed complex cellular contribution governed by such risk factors as aging, genetic predisposition, diet, and lifestyle. Recent studies suggested that microbiota is a transducer and a modifier of risk factors for neurodegenerative diseases, and mitochondria may be one of the intracellular targets of microbial signaling molecules. This review explores studies supporting a new concept on the contribution of microbiota-mitochondria disorders to AMD. We discuss metabolic, vascular, immune, and neuronal mechanism in AMD as well as key alterations of photoreceptor cells, retinal pigment epithelium (RPE), Bruch's membrane, choriocapillaris endothelial, immune, and neuronal cells. Special attention was paid to alterations of mitochondria contact sites (MCSs), an organelle network of mitochondria, endoplasmic reticulum, lipid droplets (LDs), and peroxisomes being documented based on our own electron microscopic findings from surgically removed human eyes. Morphometry of Bruch's membrane lipids and proteoglycans has also been performed in early AMD and aged controls. Microbial metabolites (short-chain fatty acids, polyphenols, and secondary bile acids) and microbial compounds (lipopolysaccharide, peptidoglycan, and bacterial DNA)-now called postbiotics-in addition to local effects on resident microbiota and mucous membrane, regulate systemic metabolic, vascular, immune, and neuronal mechanisms in normal conditions and in various common diseases. We also discuss their antioxidant, anti-inflammatory, and metabolic effects as well as experimental and clinical observations on regulating the main processes of photoreceptor renewal, mitophagy, and autophagy in early AMD. These findings support an emerging concept that microbiota-mitochondria disorders may be a crucial pathogenic mechanism of early AMD; and similarly, to other age-related neurodegenerative diseases, new treatment approaches should be targeted at these disorders.
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Affiliation(s)
- János Fehér
- PRIMAVERA Program, Nutripharma Hungaria Ltd., Budapest, Hungary
| | - Ágnes Élő
- grid.11804.3c0000 0001 0942 9821Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Lilla István
- grid.11804.3c0000 0001 0942 9821Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Zoltán Zsolt Nagy
- grid.11804.3c0000 0001 0942 9821Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Zsolt Radák
- grid.472475.70000 0000 9243 1481Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Gianluca Scuderi
- grid.7841.aOphthalmology Unit, NESMOS Department, Sant’Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Marco Artico
- grid.417007.5Department of Sensory Organs, “Sapienza” University of Rome, Roma, Italy
| | - Illés Kovács
- grid.11804.3c0000 0001 0942 9821Department of Ophthalmology, Semmelweis University, Budapest, Hungary ,grid.5386.8000000041936877XDepartment of Ophthalmology, Weill Cornell Medical College, New York City, NY USA
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6
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Mallik S, Grodstein F, Bennett DA, Vavvas DG, Lemos B. Novel Epigenetic Clock Biomarkers of Age-Related Macular Degeneration. Front Med (Lausanne) 2022; 9:856853. [PMID: 35783640 PMCID: PMC9244395 DOI: 10.3389/fmed.2022.856853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023] Open
Abstract
Age-Related Macular Degeneration (AMD) is a bilateral ocular condition resulting in irreversible vision impairment caused by the progressive loss of photoreceptors in the macula, a region at the center of the retina. The progressive loss of photoreceptor is a key feature of dry AMD but not always wet AMD, though both forms of AMD can lead to loss of vision. Regression-based biological age clocks are one of the most promising biomarkers of aging but have not yet been used in AMD. Here we conducted analyses to identify regression-based biological age clocks for the retina and explored their use in AMD using transcriptomic data consisting of a total of 453 retina samples including 105 Minnesota Grading System (MGS) level 1 samples, 175 MGS level 2, 112 MGS level 3 and 61 MGS level 4 samples, as well as 167 fibroblast samples. The clocks yielded good separation among AMD samples with increasing severity score viz., MGS1-4, regardless of whether clocks were trained in retina tissue, dermal fibroblasts, or in combined datasets. Clock application to cultured fibroblasts, embryonic stem cells, and induced Pluripotent Stem Cells (iPSCs) were consistent with age reprograming in iPSCs. Moreover, clock application to in vitro neuronal differentiation suggests broader applications. Interesting, many of the age clock genes identified include known targets mechanistically linked to AMD and aging, such as GDF11, C16ORF72, and FBN2. This study provides new observations for retina age clocks and suggests new applications for monitoring in vitro neuronal differentiation. These clocks could provide useful markers for AMD monitoring and possible intervention, as well as potential targets for in vitro screens.
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Affiliation(s)
- Saurav Mallik
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Fran Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - Demetrios G. Vavvas
- Ines and Frederick Yeatts Retina Research Laboratory, Retina Service, Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
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7
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Li J, Chen Y, Ouyang S, Ma J, Sun H, Luo L, Chen S, Liu Y. Generation and Staging of Human Retinal Organoids Based on Self-Formed Ectodermal Autonomous Multi-Zone System. Front Cell Dev Biol 2021; 9:732382. [PMID: 34631711 PMCID: PMC8493070 DOI: 10.3389/fcell.2021.732382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 01/12/2023] Open
Abstract
Methods for stem cell-derived, three-dimensional retinal organoids induction have been established and shown great potential for retinal development modeling and drug screening. Herein, we reported an exogenous-factors-free and robust method to generate retinal organoids based on “self-formed ectodermal autonomous multi-zone” (SEAM) system, a two-dimensional induction scheme that can synchronously generate multiple ocular cell lineages. Characterized by distinct morphological changes, the differentiation of the obtained retinal organoids could be staged into the early and late differentiation phases. During the early differentiation stage, retinal ganglion cells, cone photoreceptor cells (PRs), amacrine cells, and horizontal cells developed; whereas rod PRs, bipolar cells, and Müller glial cells were generated in the late differentiation phase, resembling early-phase and late-phase retinogenesis in vivo. Additionally, we modified the maintenance strategy for the retinal organoids and successfully promoted their long-term survival. Using 3D immunofluorescence image reconstruction and transmission electron microscopy, the substantial mature PRs with outer segment, inner segment and ribbon synapse were demonstrated. Besides, the retinal pigment epithelium (RPE) was induced with distinct boundary and the formation of ciliary margin was observed by co-suspending retina organoids with the zone containing RPE. The obtained RPE could be expanded and displayed similar marker expression, ultrastructural feature and functional phagocytosis to native RPE. Thus, this research described a simple and robust system which enabled generation of retina organoids with substantial mature PRs, RPE and the ciliary margin without the need of exogenous factors, providing a new platform for research of retinogenesis and retinal translational application.
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Affiliation(s)
- Jinyan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yijia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuai Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jingyu Ma
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Hui Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lixia Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuyi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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8
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Cavigelli S, Leips J, Jenny Xiang QY, Lemke D, Konow N. Next Steps in Integrative Biology: Mapping Interactive Processes Across Levels of Biological Organization. Integr Comp Biol 2021; 61:2066-2074. [PMID: 34259855 DOI: 10.1093/icb/icab161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 01/03/2023] Open
Abstract
Emergent biological processes result from complex interactions within and across levels of biological organization, ranging from molecular to environmental dynamics. Powerful theories, database tools, and modeling methods have been designed to characterize network connections within levels, such as those among genes, proteins, biochemicals, cells, organisms and species. Here, we propose that developing integrative models of organismal function in complex environments can be facilitated by taking advantage of these methods to identify key nodes of communication across levels of organization. Mapping key drivers or connections among levels of organization will provide data and leverage to model potential rule-sets by which organisms respond and adjust to perturbations at any level of biological organization.
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Affiliation(s)
- Sonia Cavigelli
- Department of Biobehavioral Health, Pennsylvania State University, University Park PA 16802
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore MD 21250
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695
| | - Dawn Lemke
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville AL 35811
| | - Nicolai Konow
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell MA 01854
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9
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Chuang YF, Wang PY, Kumar S, Lama S, Lin FL, Liu GS. Methods for in vitro CRISPR/CasRx-Mediated RNA Editing. Front Cell Dev Biol 2021; 9:667879. [PMID: 34178991 PMCID: PMC8226256 DOI: 10.3389/fcell.2021.667879] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
Specific changes in the genome have been accomplished by the revolutionary gene-editing tool known as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system. The advent of programmable RNA editing CRISPR/Cas nucleases has made this gene-editing tool safer and more precise. Specifically, CasRx, a family member of the Cas13d family, has shown great therapeutic potential. Here, we describe the in vitro methods of utilizing this powerful RNA editing platform and determine the RNA editing efficiencies for CasRx with different forms of guide RNAs (also known as gRNA or sgRNA).
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Affiliation(s)
- Yu-Fan Chuang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Peng-Yuan Wang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Satheesh Kumar
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Suraj Lama
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Fan-Li Lin
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
- Aier Eye Institute, Changsha, China
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