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Qiu GH, Fu M, Zheng X, Huang C. Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases. Biol Rev Camb Philos Soc 2024. [PMID: 39327815 DOI: 10.1111/brv.13151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
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Affiliation(s)
- Guo-Hua Qiu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Mingjun Fu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Xintian Zheng
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Cuiqin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
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Herrera I, Fernandes JAL, Shir-Mohammadi K, Levesque J, Mattar P. Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration. Cell Death Dis 2023; 14:701. [PMID: 37880237 PMCID: PMC10600220 DOI: 10.1038/s41419-023-06224-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: 01/26/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Neurodegenerative diseases are accompanied by dynamic changes in gene expression, including the upregulation of hallmark stress-responsive genes. While the transcriptional pathways that impart adaptive and maladaptive gene expression signatures have been the focus of intense study, the role of higher order nuclear organization in this process is less clear. Here, we examine the role of the nuclear lamina in genome organization during the degeneration of rod photoreceptors. Two proteins had previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods. Here, we show that in the rd1 model of retinitis pigmentosa, LA ectopically upregulates in rod photoreceptors at the onset of degeneration. LA upregulation correlated with increased heterochromatin tethering at the nuclear periphery in rd1 rods, suggesting that LA reorganizes the nucleus. To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has relatively minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr both lead to marked increases in genome accessibility. Novel ATAC-seq peaks tended to be associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that heterochromatin tethering primes the photoreceptor genome to respond to stress.
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Affiliation(s)
- Ivana Herrera
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - José Alex Lourenço Fernandes
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Khatereh Shir-Mohammadi
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Jasmine Levesque
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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Grigoryan EN. Impact of Microgravity and Other Spaceflight Factors on Retina of Vertebrates and Humans In Vivo and In Vitro. Life (Basel) 2023; 13:1263. [PMID: 37374046 PMCID: PMC10305389 DOI: 10.3390/life13061263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Spaceflight (SF) increases the risk of developmental, regenerative, and physiological disorders in animals and humans. Astronauts, besides bone loss, muscle atrophy, and cardiovascular and immune system alterations, undergo ocular disorders affecting posterior eye tissues, including the retina. Few studies revealed abnormalities in the development and changes in the regeneration of eye tissues in lower vertebrates after SF and simulated microgravity. Under microgravity conditions, mammals show disturbances in the retinal vascular system and increased risk of oxidative stress that can lead to cell death in the retina. Animal studies provided evidence of gene expression changes associated with cellular stress, inflammation, and aberrant signaling pathways. Experiments using retinal cells in microgravity-modeling systems in vitro additionally indicated micro-g-induced changes at the molecular level. Here, we provide an overview of the literature and the authors' own data to assess the predictive value of structural and functional alterations for developing countermeasures and mitigating the SF effects on the human retina. Further emphasis is given to the importance of animal studies on the retina and other eye tissues in vivo and retinal cells in vitro aboard spacecraft for understanding alterations in the vertebrate visual system in response to stress caused by gravity variations.
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Affiliation(s)
- Eleonora N Grigoryan
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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Xu N, Liu Y, Nai S, Tao Y, Ding Y, Jia L, Geng Q, Li J, Bai Y, Wei GH, Dong MQ, Luo L, Zhao M, Xu X, Li XX, Li J, Huang L. UBE3D Is Involved in Blue Light-Induced Retinal Damage by Regulating Double-Strand Break Repair. Invest Ophthalmol Vis Sci 2022; 63:7. [PMID: 36094642 PMCID: PMC9482326 DOI: 10.1167/iovs.63.10.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is currently the leading cause of blindness worldwide. Previously, we identified ubiquitin-protein ligase E3D (UBE3D) as an AMD-associated protein for East Asian populations, and here we further demonstrate that UBE3D could be associated with DNA damage response. Methods The established I-SceI-inducible GFP reporter system was used to explore the effect of UBE3D on homologous recombination. Immunoprecipitation-mass spectrometry (MS) was used to explore potential UBE3D-interacting proteins and validated with coimmunoprecipitation assays and the pulldown assays. Micrococcal nuclease (MNase) assays were used to investigate the function of UBE3D on heterochromatin de-condensation upon DNA damage. An aged mouse model of blue light-induced eye damage was constructed, and electroretinography (ERG) and optical coherence tomography (OCT) were performed to compare the differences between wild-type and UBE3D+/- mice. Results First, we show that GFP-UBE3D is recruited to damage sites by PCNA, through a PCNA-interacting protein (PIP) box. Furthermore, UBE3D interacts with KAP1 via R377R378 and oxidation of the AMD-associated V379M mutation abolishes KAP1-UBE3D binding. By MNase assays, UBE3D depletion reduces the chromatin relaxation levels upon DNA damage. In addition, UBE3D depletion renders less KAP1 recruitment. Compared with wild type, blue light induces less damage in UBE3D+/- mice as measured by ERG and OCT, consistent with our biochemical results. Conclusions Hence, we propose that one potential mechanism that UBE3D-V379M contributes to AMD pathogenesis might be via defective DNA damage repair linked with oxidative stress and our results offered a potential direction for the treatment of AMD.
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Affiliation(s)
- Ningda Xu
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Yue Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Shanshan Nai
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Chaoyang District, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Lemei Jia
- National Institute of Biological Sciences, Beijing, China
| | - Qizhi Geng
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Jie Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Yujing Bai
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Linyi Luo
- Department of Ophthalmology and Visual Sciences, Affiliated Dongguan Hospital, Southern Medical University, Guangdong, China
| | - Mingwei Zhao
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiao-Xin Li
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
- Department of Ophthalmology, Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing, China
| | - Lvzhen Huang
- Department of Ophthalmology, Eye Diseases and Optometry Institute, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, College of Optometry, Peking University Health Science Center, Peking University People's Hospital Beijing, China
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Müller B, Serafin F, Laucke LL, Rheinhard W, Wimmer T, Stieger K. Characterization of Double-Strand Break Repair Protein Ku80 Location Within the Murine Retina. Invest Ophthalmol Vis Sci 2022; 63:22. [PMID: 35737378 PMCID: PMC9233284 DOI: 10.1167/iovs.63.6.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To characterize the spatial distribution of the DNA-double strand break-repair protein Ku80 in the murine retina. Even though robust data exist on the complexity of DNA repair mechanisms in dividing cells in vitro, almost nothing is known about it in post-mitotic neurons or photoreceptors (PRs). This knowledge is an important prerequisite for in vivo therapeutic approaches by genome editing in retina and PRs. Recently, it was shown that mouse rod PRs are incapable of repairing double-strand breaks induced by radiation. Material and Methods Retinae from wild-type, rd10, and RPGR-KI mouse lines were obtained and stained with antibodies against Ku80, and cellular markers CtBP2, beta-Dystropglycan, Lamin B, and peanut agglutinin. Organotypic explant cultures were generated and maintained for up to 10 days. Laser microdissection was performed to obtain photoreceptor nuclei, and Ku80 expression was compared to whole retina by real-time PCR (RT-PCR). Results Strong Ku80 immunoreactivity was observed in rod but not cone photoreceptor terminals localized in the outer plexiform layer of the retina in all three mouse lines. During retinal explant culture, we observed that Ku80-positive globules translocate into the heterochromatin region of nuclei in the outer nuclear layer (ONL). By quantitative PCR, we showed upregulation of relative Ku80 expression in the ONL during wild-type retinal explant culture. Discussion The unexpected localization of Ku80 to murine rod terminals indicates another tissue-specific modification to the canonical DNA repair mechanisms and warrants further investigation.
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Affiliation(s)
- Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Franziska Serafin
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Leonie Luise Laucke
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Wilhelm Rheinhard
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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Ke Q, Gong L, Zhu X, Qi R, Zou M, Chen B, Liu W, Huang S, Liu Y, Li DWC. Multinucleated Retinal Pigment Epithelial Cells Adapt to Vision and Exhibit Increased DNA Damage Response. Cells 2022; 11:cells11091552. [PMID: 35563857 PMCID: PMC9103592 DOI: 10.3390/cells11091552] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Multinucleated retinal pigment epithelium (RPE) cells have been reported in humans and other mammals. Rodents have an extremely high percentage of multinucleated cells (more than 80%). Both mouse and human multinucleated RPE cells exhibit specific regional distributions that are potentially correlated with photoreceptor density. However, detailed investigations of multinucleated RPE in different species and their behavior after DNA damage are missing. Here, we compared the composition of multinucleated RPE cells in nocturnal and diurnal animals that possess distinct rod and cone proportions. We further investigated the reactive oxygen species (ROS) production and DNA damage response in mouse mononucleated and multinucleated RPE cells and determined the effect of p53 dosage on the DNA damage response in these cells. Our results revealed an unrealized association between multinucleated RPE cells and nocturnal vision. In addition, we found multinucleated RPE cells exhibited increased ROS production and DNA damage after X-ray irradiation. Furthermore, haploinsufficiency of p53 led to increased DNA damage frequency after irradiation, and mononucleated RPE cells were more sensitive to a change in p53 dosage. In conclusion, this study provides novel information on in vivo PRE topography and the DNA damage response, which may reflect specific requirements for vision adaption and macular function.
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Frohns A, Stojanovic M, Barisani-Asenbauer T, Kuratli J, Borel N, Inic-Kanada A. Effects of water-filtered infrared A and visible light (wIRA/VIS) radiation on heat- and stress-responsive proteins in the retina and cornea of guinea pigs. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 224:112306. [PMID: 34562830 DOI: 10.1016/j.jphotobiol.2021.112306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/27/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Water-filtered infrared A and visible light (wIRA/VIS), shown to reduce chlamydial infections in vitro and in vivo, might represent an innovative therapeutic approach against trachoma, a neglected tropical disease caused by ocular infection with the bacterium C. trachomatis. In this in vivo study, we assessed the impact of wIRA radiation in combination with VIS (wavelength range 595-1400 nm, intensity 2100 W/m2) on the retina and cornea in a guinea pig animal model of inclusion conjunctivitis. We investigated the effects 19 days after wIRA/VIS irradiation by comparing a single and double wIRA/VIS treatment with a sham control. By immunolabeling and western blot analyses of critical heat- and stress-responsive proteins, we could not detect wIRA/VIS-induced changes in their expression pattern. Also, immunolabeling of specific retinal marker proteins revealed no changes in their expression pattern caused by the treatment. Our preclinical study suggests wIRA/VIS as a promising and safe therapeutic tool to treat ocular chlamydial infections.
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Affiliation(s)
| | | | - Talin Barisani-Asenbauer
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Jasmin Kuratli
- Institute of Veterinary Pathology, (IVPZ) and Center for Applied Biotechnology and Molecular Medicine (CABMM), Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Borel
- Institute of Veterinary Pathology, (IVPZ) and Center for Applied Biotechnology and Molecular Medicine (CABMM), Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Aleksandra Inic-Kanada
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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Campello L, Singh N, Advani J, Mondal AK, Corso-Díaz X, Swaroop A. Aging of the Retina: Molecular and Metabolic Turbulences and Potential Interventions. Annu Rev Vis Sci 2021; 7:633-664. [PMID: 34061570 PMCID: PMC11375453 DOI: 10.1146/annurev-vision-100419-114940] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multifaceted and divergent manifestations across tissues and cell types have curtailed advances in deciphering the cellular events that accompany advanced age and contribute to morbidities and mortalities. Increase in human lifespan during the past century has heightened awareness of the need to prevent age-associated frailty of neuronal and sensory systems to allow a healthy and productive life. In this review, we discuss molecular and physiological attributes of aging of the retina, with a goal of understanding age-related impairment of visual function. We highlight the epigenome-metabolism nexus and proteostasis as key contributors to retinal aging and discuss lifestyle changes as potential modulators of retinal function. Finally, we deliberate promising intervention strategies for promoting healthy aging of the retina for improved vision.
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Affiliation(s)
- Laura Campello
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Nivedita Singh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Anupam K Mondal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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Sak A, Bannik K, Groneberg M, Stuschke M. Chaetocin induced chromatin condensation: effect on DNA repair signaling and survival. Int J Radiat Biol 2021; 97:494-506. [PMID: 33428851 DOI: 10.1080/09553002.2021.1872813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE The aim of the present study was to evaluate the effect of the histone lysine-methyltransferase (HKMT) inhibitor chaetocin on chromatin structure and its effect on ionizing radiation (IR) induced DNA damage response. METHODS Concentration and time-dependent effects of chaetocin on chromatin clustering and its reversibility were analyzed by immunofluorescent assays in the non-small cell lung carcinoma (NSCLC) cell lines H460 and H1299Q4 and in human skin fibroblasts. In addition, IR induced damage response (γH2AX, 53BP1, and pATM foci formation) was studied by immunofluorescent assays. The effect on survival was determined by performing single-cell clonogenic assays. RESULTS Chaetocin significantly increased the radiation sensitivity of H460 (F test on nonlinear regression, p < .0011) and of H1299 (p = .0201). In addition, treatment with 15 nM chaetocin also decreased the total radiation doses that control 50% of the plaque monolayers (TCD50) from 17.2 ± 0.3 Gy to 7.3 ± 0.4 Gy (p < .0001) in H1299 cells and from 11.6 ± 0.1 Gy to 6.5 ± 0.3 Gy (p < .0001). Phenotypically, chaetocin led to a time and concentration-dependent clustering of the chromatin in H1299 as well as in fibroblasts, but not in H460 cells. This phenotype of chaetocin induced chromatin clustering (CICC) was reversible and depended on the expression of the HKMTs SUV39H1 and G9a. Treatment with siRNA for SUV39h1 and G9a significantly reduced the CICC phenotype. Immunofluorescent assay results showed that the CICC phenotype was enriched for the heterochromatic marker proteins H3K9me3 and HP1α. γH2AX foci formation was not affected, neither in cells with normal nor with CICC phenotype. In contrast, repair signaling with 53BP1 and pATM foci formation was significantly reduced in the CICC phenotype. CONCLUSIONS Treatment with chaetocin increased the radiation sensitivity of cells in vitro and DNA damage response, especially of 53BP1 and ATM-dependent repair by affecting chromatin structure. The obtained results support the potential use of natural HKMT inhibitors such as chaetocin or other bioactive compounds in improving radiosensitivity of cancer cells.
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Affiliation(s)
- A Sak
- Department of Radiotherapy, Universitätsklinikum Essen, Essen, Germany
| | - K Bannik
- Department of Radiotherapy, Universitätsklinikum Essen, Essen, Germany
| | - M Groneberg
- Department of Radiotherapy, Universitätsklinikum Essen, Essen, Germany
| | - M Stuschke
- Department of Radiotherapy, Universitätsklinikum Essen, Essen, Germany
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Zhou Y, Shao C. Histone methylation can either promote or reduce cellular radiosensitivity by regulating DNA repair pathways. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108362. [PMID: 34083050 DOI: 10.1016/j.mrrev.2020.108362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Radiotherapy is one of the primary modalities for cancer treatment, and its efficiency usually relies on cellular radiosensitivity. DNA damage repair is a core content of cellular radiosensitivity, and the primary mechanism of which includes non-homologous end-joining (NHEJ) and homologous recombination (HR). By affecting DNA damage repair, histone methylation regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs) participates in the regulation of cellular radiosensitivity via three mechanisms: (a) recruiting DNA repair-related proteins, (b) regulating the expressions of DNA repair genes, and (c) mediating the dynamic change of chromatin. Interestingly, both aberrantly high and low levels of histone methylation could impede DNA repair processes. Here we reviewed the mechanisms of the dual effects of histone methylation on cell response to radiation. Since some inhibitors of HMTs and HDMs are reported to increase cellular radiosensitivity, understanding their molecular mechanisms may be helpful in developing new drugs for the therapy of radioresistant tumors.
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Affiliation(s)
- Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, No. 2094 Xie-Tu Road, Shanghai, 200032, China.
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11
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Geomagnetic Shielding Enhances Radiation Resistance by Promoting DNA Repair Process in Human Bronchial Epithelial Cells. Int J Mol Sci 2020; 21:ijms21239304. [PMID: 33291307 PMCID: PMC7730591 DOI: 10.3390/ijms21239304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 01/28/2023] Open
Abstract
With the advent of long-duration space explorations, ionizing radiation (IR) may pose a constant threat to astronauts without the protection of Earth’s magnetic field, or hypomagnetic field (HMF). However, the potential biological effects of a HMF on the cellular response to IR have not been well characterized so far. In this study, immortalized human bronchial epithelial cells were exposed to X-rays under either a geomagnetic field (GMF, ~50 uT) or HMF (<50 nT) culture condition. A significant increase of the cell survival rate in HMF after radiation was observed by colony formation analysis. The kinetics of DNA double-strand breaks (DSBs), determined by γH2AX foci formation and disappearance, presented a faster decrease of foci-positive cells and a significantly lower mean number of γH2AX foci per nucleus in HMF-cultured cells than in GMF-cultured cells after radiation. In addition, a γH2AX/53BP1 colocalization assay showed an upregulated DSB recovery rate in HMF cultured cells. These findings provided the first evidence that HMF exposure may enhance the cellular DSB repair efficiency upon radiation, and consequently modulate the genotoxic effects of IR.
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12
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Differences in the Response to DNA Double-Strand Breaks between Rod Photoreceptors of Rodents, Pigs, and Humans. Cells 2020; 9:cells9040947. [PMID: 32290532 PMCID: PMC7226979 DOI: 10.3390/cells9040947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 01/18/2023] Open
Abstract
Genome editing (GE) represents a powerful approach to fight inherited blinding diseases in which the underlying mutations cause the degeneration of the light sensing photoreceptor cells of the retina. Successful GE requires the efficient repair of DNA double-stranded breaks (DSBs) generated during the treatment. Rod photoreceptors of adult mice have a highly specialized chromatin organization, do not efficiently express a variety of DSB response genes and repair DSBs very inefficiently. The DSB repair efficiency in rods of other species including humans is unknown. Here, we used ionizing radiation to analyze the DSB response in rods of various nocturnal and diurnal species, including genetically modified mice, pigs, and humans. We show that the inefficient repair of DSBs in adult mouse rods does not result from their specialized chromatin organization. Instead, the DSB repair efficiency in rods correlates with the level of Kruppel-associated protein-1 (KAP1) expression and its ataxia-telangiectasia mutated (ATM)-dependent phosphorylation. Strikingly, we detected robust KAP1 expression and phosphorylation only in human rods but not in rods of other diurnal species including pigs. Hence, our study provides important information about the uniqueness of the DSB response in human rods which needs to be considered when choosing model systems for the development of GE strategies.
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13
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Collin GB, Gogna N, Chang B, Damkham N, Pinkney J, Hyde LF, Stone L, Naggert JK, Nishina PM, Krebs MP. Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss. Cells 2020; 9:cells9040931. [PMID: 32290105 PMCID: PMC7227028 DOI: 10.3390/cells9040931] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. The progression of PR cell loss with postnatal age was documented in mutant alleles of genes grouped by biological function. As anticipated, a wide range in the onset and rate of cell loss was observed among the reported models. The analysis underscored relationships between RD genes and ciliary function, transcription-coupled DNA damage repair, and cellular chloride homeostasis. Comparing the mouse gene list to human RD genes identified in the RetNet database revealed that mouse models are available for 40% of the known human diseases, suggesting opportunities for future research. This work may provide insight into the molecular players and pathways through which PR degenerative disease occurs and may be useful for planning translational studies.
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Affiliation(s)
- Gayle B. Collin
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Navdeep Gogna
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Bo Chang
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Nattaya Damkham
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jai Pinkney
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lillian F. Hyde
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lisa Stone
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Jürgen K. Naggert
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Patsy M. Nishina
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
| | - Mark P. Krebs
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
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14
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Pasquini G, Cora V, Swiersy A, Achberger K, Antkowiak L, Müller B, Wimmer T, Fraschka SAK, Casadei N, Ueffing M, Liebau S, Stieger K, Busskamp V. Using Transcriptomic Analysis to Assess Double-Strand Break Repair Activity: Towards Precise in vivo Genome Editing. Int J Mol Sci 2020; 21:E1380. [PMID: 32085662 PMCID: PMC7073035 DOI: 10.3390/ijms21041380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Mutations in more than 200 retina-specific genes have been associated with inherited retinal diseases. Genome editing represents a promising emerging field in the treatment of monogenic disorders, as it aims to correct disease-causing mutations within the genome. Genome editing relies on highly specific endonucleases and the capacity of the cells to repair double-strand breaks (DSBs). As DSB pathways are cell-cycle dependent, their activity in postmitotic retinal neurons, with a focus on photoreceptors, needs to be assessed in order to develop therapeutic in vivo genome editing. Three DSB-repair pathways are found in mammalian cells: Non-homologous end joining (NHEJ); microhomology-mediated end joining (MMEJ); and homology-directed repair (HDR). While NHEJ can be used to knock out mutant alleles in dominant disorders, HDR and MMEJ are better suited for precise genome editing, or for replacing entire mutation hotspots in genomic regions. Here, we analyzed transcriptomic in vivo and in vitro data and revealed that HDR is indeed downregulated in postmitotic neurons, whereas MMEJ and NHEJ are active. Using single-cell RNA sequencing analysis, we characterized the dynamics of DSB repair pathways in the transition from dividing cells to postmitotic retinal cells. Time-course bulk RNA-seq data confirmed DSB repair gene expression in both in vivo and in vitro samples. Transcriptomic DSB repair pathway profiles are very similar in adult human, macaque, and mouse retinas, but not in ground squirrel retinas. Moreover, human-induced pluripotent stem-cell-derived neurons and retinal organoids can serve as well suited in vitro testbeds for developing genomic engineering approaches in photoreceptors. Our study provides additional support for designing precise in vivo genome-editing approaches via MMEJ, which is active in mature photoreceptors.
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Affiliation(s)
- Giovanni Pasquini
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Virginia Cora
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Anka Swiersy
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Kevin Achberger
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Lena Antkowiak
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sabine Anne-Kristin Fraschka
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Marius Ueffing
- Department of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Volker Busskamp
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
- Universitäts-Augenklinik Bonn, University of Bonn, Dept. of Ophthalmology, 53127 Bonn, Germany
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15
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Feodorova Y, Falk M, Mirny LA, Solovei I. Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Trends Cell Biol 2020; 30:276-289. [PMID: 31980345 DOI: 10.1016/j.tcb.2019.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023]
Abstract
The cell nucleus is a remarkably well-organized organelle with membraneless but distinct compartments of various functions. The largest of them, euchromatin and heterochromatin, are spatially segregated in such a way that the transcriptionally active genome occupies the nuclear interior, whereas silent genomic loci are preferentially associated with the nuclear envelope. This rule is broken by rod photoreceptor cells of nocturnal mammals, in which the two major compartments have inverted positions. The inversion and dense compaction of heterochromatin converts these nuclei into microlenses that focus light and facilitate nocturnal vision. As is often the case in biology, when a mutation helps to understand normal processes and structures, inverted nuclei have served as a tool to unravel general principles of nuclear organization, including mechanisms of heterochromatin tethering to the nuclear envelope, autonomous behavior of small genomic segments, and euchromatin-heterochromatin segregation.
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Affiliation(s)
- Yana Feodorova
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
| | - Martin Falk
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, University of Chicago, 929 E 57th St, Chicago, IL 60637, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Irina Solovei
- Biozentrum, Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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16
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Subramanian K, Weigert M, Borsch O, Petzold H, Garcia-Ulloa A, Myers EW, Ader M, Solovei I, Kreysing M. Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice. eLife 2019; 8:49542. [PMID: 31825309 PMCID: PMC6974353 DOI: 10.7554/elife.49542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/11/2019] [Indexed: 01/06/2023] Open
Abstract
Rod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and the underlying mechanisms remains unclear. It is widely assumed that improvements in nocturnal vision would depend on maximization of photon capture at the expense of image detail. Here, we show that retinal optical quality improves 2-fold during terminal development, and that this enhancement is caused by nuclear inversion. We further demonstrate that improved retinal contrast transmission, rather than photon-budget or resolution, enhances scotopic contrast sensitivity by 18–27%, and improves motion detection capabilities up to 10-fold in dim environments. Our findings therefore add functional significance to a prominent exception of nuclear organization and establish retinal contrast transmission as a decisive determinant of mammalian visual perception.
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Affiliation(s)
- Kaushikaram Subramanian
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Oliver Borsch
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heike Petzold
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany.,Department of Computer Science, Technische Universität Dresden, Dresden, Germany
| | - Marius Ader
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Irina Solovei
- Biozentrum, Ludwig Maximilians Universität, München, Germany
| | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Cluster of Excellence, Physics of Life, Technische Universität Dresden, Dresden, Germany
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17
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Dyka FM, Molday LL, Chiodo VA, Molday RS, Hauswirth WW. Dual ABCA4-AAV Vector Treatment Reduces Pathogenic Retinal A2E Accumulation in a Mouse Model of Autosomal Recessive Stargardt Disease. Hum Gene Ther 2019; 30:1361-1370. [PMID: 31418294 DOI: 10.1089/hum.2019.132] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Autosomal recessive Stargardt disease is the most common inherited macular degeneration in humans. It is caused by mutations in the retina-specific ATP binding cassette transporter A4 (ABCA4) that is essential for the clearance of all-trans-retinal from photoreceptor cells. Loss of this function results in the accumulation of toxic bisretinoids in the outer segment disk membranes and their subsequent transfer into adjacent retinal pigment epithelium (RPE) cells. This ultimately leads to the Stargardt disease phenotype of increased retinal autofluorescence and progressive RPE and photoreceptor cell loss. Adeno-associated virus (AAV) vectors have been widely used in gene therapeutic applications, but their limited cDNA packaging capacity of ∼4.5 kb has impeded their use for transgenes exceeding this limit. AAV dual vectors were developed to overcome this size restriction. In this study, we have evaluated the in vitro expression of ABCA4 using three options: overlap, transplicing, and hybrid ABCA4 dual vector systems. The hybrid system was the most efficient of these dual vector alternatives and used to express the full-length ABCA4 in Abca4-/- mice. The full-length ABCA4 protein correctly localized to photoreceptor outer segments. Moreover, treatment of Abca4-/- mice with this ABCA4 hybrid dual vector system resulted in a reduced accumulation of the lipofuscin/N-retinylidene-N-retinylethanolamine (A2E) autofluorescence in vivo, and retinal A2E quantification supported these findings. These results show that the hybrid AAV dual vector option is both safe and therapeutic in mice, and the delivered ABCA4 transgene is functional and has a significant effect on reducing A2E accumulation in the Abca4-/- mouse model of Stargardt disease.
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Affiliation(s)
- Frank M Dyka
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vince A Chiodo
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W Hauswirth
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida
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18
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Verra DM, Sajdak BS, Merriman DK, Hicks D. Diurnal rodents as pertinent animal models of human retinal physiology and pathology. Prog Retin Eye Res 2019; 74:100776. [PMID: 31499165 DOI: 10.1016/j.preteyeres.2019.100776] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022]
Abstract
This presentation will survey the retinal architecture, advantages, and limitations of several lesser-known rodent species that provide a useful diurnal complement to rats and mice. These diurnal rodents also possess unusually cone-rich photoreceptor mosaics that facilitate the study of cone cells and pathways. Species to be presented include principally the Sudanian Unstriped Grass Rat and Nile Rat (Arvicanthis spp.), the Fat Sand Rat (Psammomys obesus), the degu (Octodon degus) and the 13-lined ground squirrel (Ictidomys tridecemlineatus). The retina and optic nerve in several of these species demonstrate unusual resilience in the face of neuronal injury, itself an interesting phenomenon with potential translational value.
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Affiliation(s)
- Daniela M Verra
- Department of Neurobiology of Rhythms, Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS UPR 3212, Strasbourg, France
| | | | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - David Hicks
- Department of Neurobiology of Rhythms, Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS UPR 3212, Strasbourg, France.
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19
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Marnef A, Finoux AL, Arnould C, Guillou E, Daburon V, Rocher V, Mangeat T, Mangeot PE, Ricci EP, Legube G. A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair. Genes Dev 2019; 33:1175-1190. [PMID: 31395742 PMCID: PMC6719620 DOI: 10.1101/gad.324012.119] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/26/2019] [Indexed: 02/01/2023]
Abstract
The ribosomal DNA (rDNA) represents a particularly unstable locus undergoing frequent breakage. DNA double-strand breaks (DSBs) within rDNA induce both rDNA transcriptional repression and nucleolar segregation, but the link between the two events remains unclear. Here we found that DSBs induced on rDNA trigger transcriptional repression in a cohesin- and HUSH (human silencing hub) complex-dependent manner throughout the cell cycle. In S/G2 cells, transcriptional repression is further followed by extended resection within the interior of the nucleolus, DSB mobilization at the nucleolar periphery within nucleolar caps, and repair by homologous recombination. We showed that nuclear envelope invaginations frequently connect the nucleolus and that rDNA DSB mobilization, but not transcriptional repression, involves the nuclear envelope-associated LINC complex and the actin pathway. Altogether, our data indicate that rDNA break localization at the nucleolar periphery is not a direct consequence of transcriptional repression but rather is an active process that shares features with the mobilization of persistent DSB in active genes and heterochromatin.
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Affiliation(s)
- Aline Marnef
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Anne-Laure Finoux
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Coline Arnould
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Emmanuelle Guillou
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Virginie Daburon
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Vincent Rocher
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Thomas Mangeat
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Philippe E Mangeot
- International Center for Infectiology Research (CIRI), Ecole Normale Supérieure de Lyon (ENS), U1111, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR5308, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1, Université Lyon, Lyon F-6900, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC), Ecole Normale Supérieure de Lyon (ENS), U1210, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR5239, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1, Université de Lyon, Lyon F-69007, France
| | - Gaëlle Legube
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
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20
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Galitska G, Biolatti M, Griffante G, Gugliesi F, Pasquero S, Dell'Oste V, Landolfo S. Catch me if you can: the arms race between human cytomegalovirus and the innate immune system. Future Virol 2019. [DOI: 10.2217/fvl-2018-0189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human cytomegalovirus (HCMV), a common opportunistic pathogen of significant clinical importance, targets immunocompromised individuals of the human population worldwide. The absence of a licensed vaccine and the low efficacy of currently available drugs remain a barrier to combating the global infection. The HCMV's ability to modulate and escape innate immune responses remains a critical step in the ongoing search for potential drug targets. Here, we describe the complex interplay between HCMV and the host immune system, focusing on different evasion strategies that the virus has employed to subvert innate immune responses. We especially highlight the mechanisms and role of host antiviral restriction factors and provide insights into viral modulation of pro-inflammatory NF-κB and interferon signaling pathways.
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Affiliation(s)
- Ganna Galitska
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Gloria Griffante
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Francesca Gugliesi
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Selina Pasquero
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Valentina Dell'Oste
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
| | - Santo Landolfo
- Department of Public Health & Pediatric Sciences, University of Turin, Turin, Italy
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21
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Bhatia V, Valdés-Sánchez L, Rodriguez-Martinez D, Bhattacharya SS. Formation of 53BP1 foci and ATM activation under oxidative stress is facilitated by RNA:DNA hybrids and loss of ATM-53BP1 expression promotes photoreceptor cell survival in mice. F1000Res 2018; 7:1233. [PMID: 30345028 PMCID: PMC6171737 DOI: 10.12688/f1000research.15579.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/18/2023] Open
Abstract
Background: Photoreceptors, light-sensing neurons in retina, are central to vision. Photoreceptor cell death (PCD) is observed in most inherited and acquired retinal dystrophies. But the underlying molecular mechanism of PCD is unclear. Photoreceptors are sturdy neurons that survive high oxidative and phototoxic stress, which are known threats to genome stability. Unexpectedly, DNA damage response in mice photoreceptors is compromised; mainly due to loss of crucial DNA repair proteins, ATM and 53BP1. We tried to understand the molecular function of ATM and 53BP1 in response to oxidative stress and how suppression of DNA repair response in mice retina affect photoreceptor cell survival. Methods: We use the state of art cell biology methods and structure-function analysis of mice retina. RNA:DNA hybrids (S9.6 antibody and Hybrid-binding domain of RNaseH1) and DNA repair foci (gH2AX and 53BP1) are quantified by confocal microscopy, in retinal sections and cultured cell lines. Oxidative stress, DNA double strand break, RNaseH1 expression and small-molecule kinase-inhibitors were used to understand the role of ATM and RNA:DNA hybrids in DNA repair. Lastly, retinal structure and function of ATM deficient mice, in Retinal degeneration 1 (Pde6brd1) background, is studied using Immunohistochemistry and Electroretinography. Results: Our work has three novel findings: firstly, both human and mice photoreceptor cells specifically accumulate RNA:DNA hybrids, a structure formed by re-hybridization of nascent RNA with template DNA during transcription. Secondly, RNA:DNA-hybrids promote ataxia-telangiectasia mutated (ATM) activation during oxidative stress and 53BP1-foci formation during downstream DNA repair process. Thirdly, loss of ATM -in murine photoreceptors- protract DNA repair but also promote their survival. Conclusions: We propose that due to high oxidative stress and accumulation of RNA:DNA-hybrids in photoreceptors, expression of ATM is tightly regulated to prevent PCD. Inefficient regulation of ATM expression could be central to PCD and inhibition of ATM-activation could suppress PCD in retinal dystrophy patients.
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Affiliation(s)
- Vaibhav Bhatia
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Lourdes Valdés-Sánchez
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Daniel Rodriguez-Martinez
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Shom Shankar Bhattacharya
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
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22
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Hofmann S, Dehn S, Businger R, Bolduan S, Schneider M, Debyser Z, Brack-Werner R, Schindler M. Dual role of the chromatin-binding factor PHF13 in the pre- and post-integration phases of HIV-1 replication. Open Biol 2018; 7:rsob.170115. [PMID: 29021215 PMCID: PMC5666080 DOI: 10.1098/rsob.170115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/08/2017] [Indexed: 12/23/2022] Open
Abstract
Viruses interact with multiple host cell factors. Some of these are required to promote viral propagation, others have roles in inhibiting infection. Here, we delineate the function of the cellular factor PHF13 (or SPOC1), a putative HIV-1 restriction factor. Early in the HIV-1 replication cycle PHF13 increased the number of integrated proviral copies and the number of infected cells. However, after HIV-1 integration, high levels of PHF13 suppressed viral gene expression. The antiviral activity of PHF13 is counteracted by the viral accessory protein Vpr, which mediates PHF13 degradation. Altogether, the transcriptional master regulator and chromatin binding protein PHF13 does not have purely repressive effects on HIV-1 replication, but also promotes viral integration. By the functional characterization of the dual role of PHF13 during the HIV-1 replication cycle, we reveal a surprising and intricate mechanism through which HIV-1 might regulate the switch from integration to viral gene expression. Furthermore, we identify PHF13 as a cellular target specifically degraded by HIV-1 Vpr.
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Affiliation(s)
- Stephan Hofmann
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Sandra Dehn
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Ramona Businger
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Bolduan
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Martha Schneider
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Ruth Brack-Werner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - Michael Schindler
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany .,Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
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23
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Müller B, Ellinwood NM, Lorenz B, Stieger K. Detection of DNA Double Strand Breaks by γH2AX Does Not Result in 53bp1 Recruitment in Mouse Retinal Tissues. Front Neurosci 2018; 12:286. [PMID: 29765300 PMCID: PMC5938408 DOI: 10.3389/fnins.2018.00286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022] Open
Abstract
Gene editing is an attractive potential treatment of inherited retinopathies. However, it often relies on endogenous DNA repair. Retinal DNA repair is incompletely characterized in humans and animal models. We investigated recruitment of the double stranded break (DSB) repair complex of γH2AX and 53bp1 in both developing and mature mouse neuroretinas. We evaluated the immunofluorescent retinal expression of these proteins during development (P07-P30) in normal and retinal degeneration models, as well as in potassium bromate induced DSB repair in normal adult (3 months) retinal explants. The two murine retinopathy models used had different mutations in Pde6b: the severe rd1 and the milder rd10 models. Compared to normal adult retina, we found increased numbers of γH2AX positive foci in all retinal neurons of the developing retina in both model and control retinas, as well as in wild type untreated retinal explant cultures. In contrast, the 53bp1 staining of the retina differed both in amount and character between cell types at all ages and in all model systems. There was strong pan nuclear staining in ganglion, amacrine, and horizontal cells, and cone photoreceptors, which was attenuated. Rod photoreceptors did not stain unequivocally. In all samples, 53bp1 stained foci only rarely occurred. Co-localization of 53bp1 and γH2AX staining was a very rare event (< 1% of γH2AX foci in the ONL and < 3% in the INL), suggesting the potential for alternate DSB sensing and repair proteins in the murine retina. At a minimum, murine retinal DSB repair does not appear to follow canonical pathways, and our findings suggests further investigation is warranted.
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Affiliation(s)
- Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - N M Ellinwood
- Department of Animal Science and Veterinary Clinical Science, Iowa State University, Ames, IA, United States
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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24
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König A, Zöller N, Kippenberger S, Bernd A, Kaufmann R, Layer PG, Heselich A. Non-thermal near-infrared exposure photobiomodulates cellular responses to ionizing radiation in human full thickness skin models. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:115-123. [DOI: 10.1016/j.jphotobiol.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/18/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
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25
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Tschulakow AV, Dittmann K, Huber SM, Klumpp D, Stegen B, Schraermeyer U, Rodemann HP, Julien-Schraermeyer S. The radioprotector ortho-phospho-L-tyrosine (pTyr) attenuates the side effects of fractionated irradiation in retinoblastoma mouse models but also decreases the local tumour control. Radiother Oncol 2017; 124:462-467. [PMID: 28711224 DOI: 10.1016/j.radonc.2017.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Radiotherapy (RT) is used to treat retinoblastoma (Rb), the most frequent ocular tumour in children. Besides eradicating the tumour, RT can cause severe side effects including secondary malignancies. This study aimed to define whether the radioprotector ortho-phospho-L-tyrosine (pTyr) prevents RT-induced side effects and affects local tumour control in a xenograft and a genetic orthotopic Rb mouse model. METHODS B6;129-Rb1tm3Tyj/J (Rb+/-) and Y79-Rb cell-xenografted nude mice were fractionated external beam irradiated (15 fractions of 5Gy 6MV photons during 3weeks) with or without pTyr pre-treatment (100mg/kg BW, 16h prior to each irradiation). One, three, six and nine months after RT, tumour control and RT toxicity were evaluated using in vivo imaging and histology. We also analysed pTyr dependant post irradiation cell survival and p53 activity in vitro. RESULTS In vitro pTyr pre-treatment showed no radioprotection on Y79 cells, but led to p53 stabilisation in unirradiated Y79 cells and to a facilitation of radiation-induced p21 up-regulation, confirming a modulation of p53 activity by pTyr. In both mouse models, secondary tumours were undetectable. In Rb+/- mice, pTyr significantly lowered RT-induced greying of the fur, retinal thickness reduction and photoreceptor loss. However, in the xenografted Rb model, pTyr considerably decreased RT-mediated tumour control, which was observed in 16 out of 22 control eyes but in none of the 24 pTyr treated eyes. CONCLUSIONS In Rb+/- mice pTyr significantly prevents RT-induced greying of the fur as well as retinal degeneration. However, since non-irradiated control mice were not used in our study, a formal possibility exists that the effect shown in the retina of Rb+/- mice may be due to ageing of the animals and/or actions of pTyr alone. Unfortunately, as tested in a xenograft model, pTyr treatment reduced the control of Rb tumours.
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Affiliation(s)
- Alexander V Tschulakow
- Division of Experimental Vitreoretinal Surgery, Centre for Ophthalmology, University of Tuebingen, Germany
| | - Klaus Dittmann
- Division of Radiobiology & Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University of Tuebingen, Germany
| | - Dominik Klumpp
- Department of Radiation Oncology, University of Tuebingen, Germany
| | - Benjamin Stegen
- Department of Radiation Oncology, University of Tuebingen, Germany
| | - Ulrich Schraermeyer
- Division of Experimental Vitreoretinal Surgery, Centre for Ophthalmology, University of Tuebingen, Germany
| | - H Peter Rodemann
- Division of Radiobiology & Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Germany
| | - Sylvie Julien-Schraermeyer
- Division of Experimental Vitreoretinal Surgery, Centre for Ophthalmology, University of Tuebingen, Germany.
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26
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Abstract
Ataxia Telangiectasia Mutated (ATM) has been known for decades as the main kinase mediating the DNA Double-Strand Break Response (DDR). Extensive studies have revealed its dual role in locally promoting detection and repair of DSBs as well as in activating global DNA damage checkpoints. However, recent studies pinpoint additional unanticipated functions for ATM in modifying both the local chromatin landscape and the global chromosome organization, more particularly at persistent breaks. Given the emergence of a novel and unexpected class of DSBs prevalently arising in transcriptionally active genes and intrinsically difficult to repair, a specific role of ATM at refractory DSBs could be an important and so far overlooked feature of Ataxia Telangiectasia (A-T) a severe disorder associated with ATM mutations.
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
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27
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In vivo genome editing as a potential treatment strategy for inherited retinal dystrophies. Prog Retin Eye Res 2016; 56:1-18. [PMID: 27623223 DOI: 10.1016/j.preteyeres.2016.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022]
Abstract
In vivo genome editing represents an emerging field in the treatment of monogenic disorders, as it may constitute a solution to the current hurdles in classic gene addition therapy, which are the low levels and limited duration of transgene expression. Following the introduction of a double strand break (DSB) at the mutational site by highly specific endonucleases, such as TALENs (transcription activator like effector nucleases) or RNA based nucleases (clustered regulatory interspaced short palindromic repeats - CRISPR-Cas), the cell's own DNA repair machinery restores integrity to the DNA strand and corrects the mutant sequence, thus allowing the cell to produce protein levels as needed. The DNA repair happens either through the error prone non-homologous end-joining (NHEJ) pathway or with high fidelity through homology directed repair (HDR) in the presence of a DNA donor template. A third pathway called microhomology mediated endjoining (MMEJ) has been recently discovered. In this review, the authors focus on the different DNA repair mechanisms, the current state of the art tools for genome editing and the particularities of the retina and photoreceptors with regard to in vivo therapeutic approaches. Finally, current attempts in the field of retinal in vivo genome editing are discussed and future directions of research identified.
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28
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Chung HR, Xu C, Fuchs A, Mund A, Lange M, Staege H, Schubert T, Bian C, Dunkel I, Eberharter A, Regnard C, Klinker H, Meierhofer D, Cozzuto L, Winterpacht A, Di Croce L, Min J, Will H, Kinkley S. PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. eLife 2016; 5. [PMID: 27223324 PMCID: PMC4915813 DOI: 10.7554/elife.10607] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 05/19/2016] [Indexed: 02/04/2023] Open
Abstract
PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes. DOI:http://dx.doi.org/10.7554/eLife.10607.001 In human and other eukaryotic cells, DNA is packaged around proteins called histones to form a structure known as chromatin. Chemical tags added to the histones alter how the DNA is packaged and the activity of the genes encoded by that DNA. For example, many active genes are packaged around histone H3 proteins that have “Lysine 4 tri-methyl” tags attached to them. Another protein that is associated with chromatin is called PHF13 and it has several roles, including repairing damaged DNA. However, it was not known whether PHF13 binds to chromatin via the chemical tags, or in another way. Ho-Ryun, Xu, Fuchs et al. used several biochemical techniques in mouse and human cells to explore how PHF13 specifically interacts with chromatin. These experiments showed that PHF13 binds specifically to DNA and to two types of methyl tags (lysine 4-tri-methyl or lysine 4-di-methyl). These chemical tags are predominantly found at active promoters as well as at a small subset of less active promoters known as bivalent promoters. PHF13 interacted with other proteins on the chromatin that are known to either drive or repress gene activity and it’s depletion affected the activity of many genes. Whether PHF13 increased or decreased gene activity depended on whether it was bound to active or bivalent promoters. The active promoters targeted by PHF13 had higher numbers of the tri-methyl tags whereas the di-methyl tags were more common on the bivalent promoters. These findings provide preliminary evidence that a protein binding to different methyl tags in the same place on histone H3 can have opposite effects on gene activity. Ho-Ryun, Xu, Fuchs et al. now intend to find out more about the other proteins that interact with PHF13 on chromatin. DOI:http://dx.doi.org/10.7554/eLife.10607.002
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Affiliation(s)
- Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chao Xu
- Structural Genomics Consortium, Toronto, Canada
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mund
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Hannah Staege
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Tobias Schubert
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anton Eberharter
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | - Catherine Regnard
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | - Henrike Klinker
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | | | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andreas Winterpacht
- Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Luciano Di Croce
- Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys, Barcelona, Spain
| | - Jinrong Min
- Structural Genomics Consortium, Toronto, Canada
| | - Hans Will
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sarah Kinkley
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
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29
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Mayer M, Kaiser N, Layer PG, Frohns F. Cell Cycle Regulation and Apoptotic Responses of the Embryonic Chick Retina by Ionizing Radiation. PLoS One 2016; 11:e0155093. [PMID: 27163610 PMCID: PMC4862647 DOI: 10.1371/journal.pone.0155093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/25/2016] [Indexed: 11/25/2022] Open
Abstract
Ionizing radiation (IR) exerts deleterious effects on the developing brain, since proliferative neuronal progenitor cells are highly sensitive to IR-induced DNA damage. Assuming a radiation response that is comparable to mammals, the chick embryo would represent a lower vertebrate model system that allows analysis of the mechanisms underlying this sensitivity, thereby contributing to the reduction, refinement and replacement of animal experiments. Thus, this study aimed to elucidate the radiation response of the embryonic chick retina in three selected embryonic stages. Our studies reveal a lack in the radiation-induced activation of a G1/S checkpoint, but rapid abrogation of G2/M progression after IR in retinal progenitors throughout development. Unlike cell cycle control, radiation-induced apoptosis (RIA) showed strong variations between its extent, dose dependency and temporal occurrence. Whereas the general sensitivity towards RIA declined with ongoing differentiation, its dose dependency constantly increased with age. For all embryonic stages RIA occurred during comparable periods after irradiation, but in older animals its maximum shifted towards earlier post-irradiation time points. In summary, our results are in good agreement with data from the developing rodent retina, strengthening the suitability of the chick embryo for the analysis of the radiation response in the developing central nervous system.
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Affiliation(s)
- Margot Mayer
- Developmental Biology and Neurogenetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Nicole Kaiser
- Developmental Biology and Neurogenetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Paul G Layer
- Developmental Biology and Neurogenetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Florian Frohns
- Developmental Biology and Neurogenetics, Darmstadt University of Technology, Darmstadt, Germany
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30
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Seasonal and post-trauma remodeling in cone-dominant ground squirrel retina. Exp Eye Res 2016; 150:90-105. [PMID: 26808487 DOI: 10.1016/j.exer.2016.01.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/14/2015] [Accepted: 01/14/2016] [Indexed: 02/02/2023]
Abstract
With a photoreceptor mosaic containing ∼85% cones, the ground squirrel is one of the richest known mammalian sources of these important retinal cells. It also has a visual ecology much like the human's. While the ground squirrel retina is understandably prominent in the cone biochemistry, physiology, and circuitry literature, far less is known about the remodeling potential of its retinal pigment epithelium, neurons, macroglia, or microglia. This review aims to summarize the data from ground squirrel retina to this point in time, and to relate them to data from other brain areas where appropriate. We begin with a survey of the ground squirrel visual system, making comparisons with traditional rodent models and with human. Because this animal's status as a hibernator often goes unnoticed in the vision literature, we then present a brief primer on hibernation biology. Next we review what is known about ground squirrel retinal remodeling concurrent with deep torpor and with rapid recovery upon re-warming. Notable here is rapidly-reversible, temperature-dependent structural plasticity of cone ribbon synapses, as well as pre- and post-synaptic plasticity throughout diverse brain regions. It is not yet clear if retinal cell types other than cones engage in torpor-associated synaptic remodeling. We end with the small but intriguing literature on the ground squirrel retina's remodeling responses to insult by retinal detachment. Notable for widespread loss of (cone) photoreceptors, there is surprisingly little remodeling of the RPE or Müller cells. Microglial activation appears minimal, and remodeling of surviving second- and third-order neurons seems absent, but both require further study. In contrast, traumatic brain injury in the ground squirrel elicits typical macroglial and microglial responses. Overall, the data to date strongly suggest a heretofore unrecognized, natural checkpoint between retinal deafferentiation and RPE and Müller cell remodeling events. As we continue to discover them, the unique ways by which ground squirrel retina responds to hibernation or injury may be adaptable to therapeutic use.
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31
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Direct measurement of the 3-dimensional DNA lesion distribution induced by energetic charged particles in a mouse model tissue. Proc Natl Acad Sci U S A 2015; 112:12396-401. [PMID: 26392532 DOI: 10.1073/pnas.1508702112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Charged particles are increasingly used in cancer radiotherapy and contribute significantly to the natural radiation risk. The difference in the biological effects of high-energy charged particles compared with X-rays or γ-rays is determined largely by the spatial distribution of their energy deposition events. Part of the energy is deposited in a densely ionizing manner in the inner part of the track, with the remainder spread out more sparsely over the outer track region. Our knowledge about the dose distribution is derived solely from modeling approaches and physical measurements in inorganic material. Here we exploited the exceptional sensitivity of γH2AX foci technology and quantified the spatial distribution of DNA lesions induced by charged particles in a mouse model tissue. We observed that charged particles damage tissue nonhomogenously, with single cells receiving high doses and many other cells exposed to isolated damage resulting from high-energy secondary electrons. Using calibration experiments, we transformed the 3D lesion distribution into a dose distribution and compared it with predictions from modeling approaches. We obtained a radial dose distribution with sub-micrometer resolution that decreased with increasing distance to the particle path following a 1/r2 dependency. The analysis further revealed the existence of a background dose at larger distances from the particle path arising from overlapping dose deposition events from independent particles. Our study provides, to our knowledge, the first quantification of the spatial dose distribution of charged particles in biologically relevant material, and will serve as a benchmark for biophysical models that predict the biological effects of these particles.
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32
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Petersen-Jones S, Meek K. DNA damage: offing KAP to stay focused in the dark. Curr Biol 2014; 24:R392-4. [PMID: 24845667 DOI: 10.1016/j.cub.2014.03.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To optimize night vision, nocturnal mammals exploit the light refractive properties of heterochromatin, adopting a unique nuclear structure that positions heterochromatin at the center of the nucleus focusing light on photoreceptors. This strategy comes at the expense of genome protection because DNA breaks cannot be repaired in dense heterochromatin.
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Affiliation(s)
- Simon Petersen-Jones
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, MI 48823, USA; College of Veterinary Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Katheryn Meek
- Department of Microbiology and Molecular Genetics, and Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI 48823, USA; College of Veterinary Medicine, Michigan State University, East Lansing, MI 48823, USA.
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