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Daniszewski M, Senabouth A, Liang HH, Han X, Lidgerwood GE, Hernández D, Sivakumaran P, Clarke JE, Lim SY, Lees JG, Rooney L, Gulluyan L, Souzeau E, Graham SL, Chan CL, Nguyen U, Farbehi N, Gnanasambandapillai V, McCloy RA, Clarke L, Kearns LS, Mackey DA, Craig JE, MacGregor S, Powell JE, Pébay A, Hewitt AW. Retinal ganglion cell-specific genetic regulation in primary open-angle glaucoma. CELL GENOMICS 2022; 2:100142. [PMID: 36778138 PMCID: PMC9903700 DOI: 10.1016/j.xgen.2022.100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 03/08/2021] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
To assess the transcriptomic profile of disease-specific cell populations, fibroblasts from patients with primary open-angle glaucoma (POAG) were reprogrammed into induced pluripotent stem cells (iPSCs) before being differentiated into retinal organoids and compared with those from healthy individuals. We performed single-cell RNA sequencing of a total of 247,520 cells and identified cluster-specific molecular signatures. Comparing the gene expression profile between cases and controls, we identified novel genetic associations for this blinding disease. Expression quantitative trait mapping identified a total of 4,443 significant loci across all cell types, 312 of which are specific to the retinal ganglion cell subpopulations, which ultimately degenerate in POAG. Transcriptome-wide association analysis identified genes at loci previously associated with POAG, and analysis, conditional on disease status, implicated 97 statistically significant retinal ganglion cell-specific expression quantitative trait loci. This work highlights the power of large-scale iPSC studies to uncover context-specific profiles for a genetically complex disease.
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Affiliation(s)
- Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anne Senabouth
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Helena H. Liang
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Jordan E. Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Shiang Y. Lim
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia
| | - Jarmon G. Lees
- O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia,Department of Medicine, St Vincent’s Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart L. Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Chia-Ling Chan
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Uyen Nguyen
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Nona Farbehi
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Rachael A. McCloy
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lisa S. Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - David A. Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Crawley, WA 6009, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Joseph E. Powell
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW 2052, Australia,Corresponding author
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,Corresponding author
| | - Alex W. Hewitt
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia,Corresponding author
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Huang G, Liang D, Luo L, Lan C, Luo C, Xu H, Lai J. Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma. J Clin Lab Anal 2022; 36:e24215. [PMID: 35028972 PMCID: PMC8842314 DOI: 10.1002/jcla.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Background Primary open‐angle glaucoma (POAG) is the commonest form of glaucoma which is estimated to cause bilaterally blind within 11.1 million people by 2020. Therefore, the primary objectives of this study were to investigate the clinical significance of single‐nucleotide polymorphisms (SNPs) in the lncRNAs MALAT1 and ANRIL in a Chinese Han POAG cohort. Methods Three hundred and forty‐six glaucoma patients and 263 healthy controls were recruited, and totally 14 SNPs in MALAT1 and ANRIL were genotyped between the two populations. Results The MALAT1 SNPs rs619586 (A>G), rs3200401 (C>T), and rs664589 (C>G) were associated with POAG risk, and the ANRIL SNPs rs2383207 (A>G), rs564398 (A>G), rs2157719 (A>G), rs7865618 (G>A), and rs4977574 (A>G) were associated with POAG (p < 0.05). The MALAT1 haplotypes ACG and ATC, comprised rs619586, rs3200401, and rs664589, increased POAG risk, and the ANRIL haplotype AAGAA, made up of rs2383207, rs7865618, rs4977574, rs564398, and rs2157719, show a significantly increased risk of POAG. In addition, rs619586 (A>G) of MALAT1 and rs564398/rs2157719 of ANRIL were associated with a smaller vertical cup‐to‐disc ratio, while rs619586 of MALAT1 and rs2383207/rs4977574 of ANRIL were associated with higher intraocular pressure in the POAG population. Conclusion Single‐nucleotide polymorphisms and haplotypes in ANRIL and MALAT1 were associated with POAG onset in our study population, which provide more possibilities to POAG diagnosis and treatment.
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Affiliation(s)
- Guoqiang Huang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Dong Liang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Lidan Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chenghong Lan
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chengfeng Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Hongwang Xu
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Jiangfeng Lai
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
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Wu J, Liu LL, Cao M, Hu A, Hu D, Luo Y, Wang H, Zhong JN. DNA methylation plays important roles in retinal development and diseases. Exp Eye Res 2021; 211:108733. [PMID: 34418429 DOI: 10.1016/j.exer.2021.108733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang Province, China
| | - Lin-Lin Liu
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Miao Cao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Ang Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Die Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China; Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Yan Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China
| | - Hui Wang
- Department of Ophthalmology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
| | - Jia-Ning Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi Province, China.
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Che D, Fang Z, Mai H, Xu Y, Fu L, Zhou H, Zhang L, Pi L, Gu X. The lncRNA ANRIL Gene rs2151280 GG Genotype is Associated with Increased Susceptibility to Recurrent Miscarriage in a Southern Chinese Population. J Inflamm Res 2021; 14:2865-2872. [PMID: 34234511 PMCID: PMC8256094 DOI: 10.2147/jir.s304801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/31/2021] [Indexed: 12/19/2022] Open
Abstract
Background Genetic factors may play an important role in susceptibility to recurrent miscarriage. Some cardiovascular disease-related candidate genes have been shown to be associated with recurrent miscarriage. Long noncoding RNA ANRIL has been confirmed to be associated with susceptibility to various diseases, such as cardiovascular disease. However, it remains unclear whether the ANRIL gene polymorphism is related to recurrent miscarriage susceptibility. Methods Three ANRIL gene polymorphisms (rs2151280, rs1063192 and rs564398) were genotyped in 819 controls and 610 recurrent miscarriage patients through TaqMan real-time polymerase chain reaction. The odds ratios and 95% confidence intervals (CIs) were used to assess the strength of each association. Results Our results showed that the ANRIL rs2151280 GG genotype was associated with increased susceptibility to recurrent miscarriage (GG vs AA: adjusted OR=1.527, 95% CI=1.051–2.218, p=0.0262; GG vs AG/AA adjusted OR=1.460, 95% CI=1.021–2.089, p=0.0381). By combining the analysis of the risk genotypes in the three SNPs, we found that individuals with 2–3 risk genotypes had a significantly increased risk of recurrent miscarriage compared with those with a 0–1 risk genotype (adjusted OR=1.728, 95% CI=1.112–2.683, p=0.0149). This risk was more significant in subgroups of women less than 35–40 years of age and women with 2–3 miscarriages. Conclusion These results suggested that a specific SNP in the ANRIL gene may be associated with increased susceptibility to recurrent miscarriage in a southern Chinese population.
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Affiliation(s)
- Di Che
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhenzhen Fang
- Program of Molecular Medicine, Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hanran Mai
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Yufen Xu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - LanYan Fu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Huazhong Zhou
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Linyuan Zhang
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lei Pi
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaoqiong Gu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China
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Molecular Genetics of Glaucoma: Subtype and Ethnicity Considerations. Genes (Basel) 2020; 12:genes12010055. [PMID: 33396423 PMCID: PMC7823611 DOI: 10.3390/genes12010055] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022] Open
Abstract
Glaucoma, the world’s leading cause of irreversible blindness, is a complex disease, with differential presentation as well as ethnic and geographic disparities. The multifactorial nature of glaucoma complicates the study of genetics and genetic involvement in the disease process. This review synthesizes the current literature on glaucoma and genetics, as stratified by glaucoma subtype and ethnicity. Primary open-angle glaucoma (POAG) is the most common cause of glaucoma worldwide, with the only treatable risk factor (RF) being the reduction of intraocular pressure (IOP). Genes associated with elevated IOP or POAG risk include: ABCA1, AFAP1, ARHGEF12, ATXN2, CAV1, CDKN2B-AS1, FOXC1, GAS7, GMDS, SIX1/SIX6, TMCO1, and TXNRD2. However, there are variations in RF and genetic factors based on ethnic and geographic differences; it is clear that unified molecular pathways accounting for POAG pathogenesis remain uncertain, although inflammation and senescence likely play an important role. There are similar ethnic and geographic complexities in primary angle closure glaucoma (PACG), but several genes have been associated with this disorder, including MMP9, HGF, HSP70, MFRP, and eNOS. In exfoliation glaucoma (XFG), genes implicated include LOXL1, CACNA1A, POMP, TMEM136, AGPAT1, RBMS3, and SEMA6A. Despite tremendous progress, major gaps remain in resolving the genetic architecture for the various glaucoma subtypes across ancestries. Large scale carefully designed studies are required to advance understanding of genetic loci as RF in glaucoma pathophysiology and to improve diagnosis and treatment options.
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