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Ahmad I. CRISPR/Cas9—A Promising Therapeutic Tool to Cure Blindness: Current Scenario and Future Prospects. Int J Mol Sci 2022; 23:ijms231911482. [PMID: 36232782 PMCID: PMC9569777 DOI: 10.3390/ijms231911482] [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: 07/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR-based targeted genome editing is bringing revolutionary changes in the research arena of biological sciences. CRISPR/Cas9 has been explored as an efficient therapeutic tool for the treatment of genetic diseases. It has been widely used in ophthalmology research by using mouse models to correct pathogenic mutations in the eye stem cells. In recent studies, CRISPR/Cas9 has been used to correct a large number of mutations related to inherited retinal disorders. In vivo therapeutic advantages for retinal diseases have been successfully achieved in some rodents. Current advances in the CRISPR-based gene-editing domain, such as modified Cas variants and delivery approaches have optimized its application to treat blindness. In this review, recent progress and challenges of the CRISPR-Cas system have been discussed to cure blindness and its prospects.
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Affiliation(s)
- Irshad Ahmad
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; ; Tel.: +966-13-8608393
- Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
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2
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Li Z, Tang Y, Cai J, Wu S, Song F. MPP7 as a Novel Biomarker of Esophageal Cancer: MPP7 Knockdown Inhibits Esophageal Cancer Cell Migration and Invasion. Life (Basel) 2022; 12:life12091381. [PMID: 36143417 PMCID: PMC9501138 DOI: 10.3390/life12091381] [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] [Received: 08/02/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
MAGUK p55 scaffold protein 7 (MPP7) is a member of the stardust family of membrane-associated guanosine kinase protein P55 and plays a role in the establishment of epithelial cell polarity. However, its potential implication in human esophageal cancer is unclear. In this study, we investigated the expression profile of MPP7 and its functional impact on esophagus cancer. Expression analyses of immunohistochemical microarrays with survival and prognostic information of 103 patients with esophageal cancer demonstrated that MPP7 was overexpressed in 52 patients, who showed poor survival rates. The transcriptional expression of MPP7 in esophageal cancer in TCGA database increased successively from normal epithelial, to esophageal adenocarcinoma, to esophageal squamous cell carcinoma. Transcriptome sequencing after MPP7 knockdown in esophageal carcinoma cells showed that wound-healing-associated proteins were down-regulated, and the TGF-β pathway was one of the important signaling pathways. A loss-of-function study showed that the knockdown of MPP7 inhibited cell migration and invasion. These results could be verified in a model of tumor cells injected into the tail vein and subcutaneous tumor of nude mice. Herein, our results indicated that MPP7 could have an oncogenic role in human esophagus cancer, thus demonstrating its potential as a novel biomarker for the diagnosis and/or treatment of esophagus cancer.
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Affiliation(s)
- Zhaodong Li
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1#Yixue Yuan Road, Yuzhong District, Chongqing 400016, China
| | - Yongyao Tang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1#Yixue Yuan Road, Yuzhong District, Chongqing 400016, China
| | - Jing Cai
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1#Yixue Yuan Road, Yuzhong District, Chongqing 400016, China
| | - Shunlong Wu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Fangzhou Song
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 1#Yixue Yuan Road, Yuzhong District, Chongqing 400016, China
- Correspondence: ; Tel.: +86-23-68485958
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3
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Tolman NG, Balasubramanian R, Macalinao DG, Kearney AL, MacNicoll KH, Montgomery CL, de Vries WN, Jackson IJ, Cross SH, Kizhatil K, Nair KS, John SWM. Genetic background modifies vulnerability to glaucoma-related phenotypes in Lmx1b mutant mice. Dis Model Mech 2021; 14:dmm.046953. [PMID: 33462143 PMCID: PMC7903917 DOI: 10.1242/dmm.046953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Variants in the LIM homeobox transcription factor 1-beta (LMX1B) gene predispose individuals to elevated intraocular pressure (IOP), a key risk factor for glaucoma. However, the effect of LMX1B mutations varies widely between individuals. To better understand the mechanisms underlying LMX1B-related phenotypes and individual differences, we backcrossed the Lmx1bV265D (also known as Lmx1bIcst ) allele onto the C57BL/6J (B6), 129/Sj (129), C3A/BLiA-Pde6b+ /J (C3H) and DBA/2J-Gpnmb+ (D2-G) mouse strain backgrounds. Strain background had a significant effect on the onset and severity of ocular phenotypes in Lmx1bV265D/+ mutant mice. Mice of the B6 background were the most susceptible to developing abnormal IOP distribution, severe anterior segment developmental anomalies (including malformed eccentric pupils, iridocorneal strands and corneal abnormalities) and glaucomatous nerve damage. By contrast, Lmx1bV265D mice of the 129 background were the most resistant to developing anterior segment abnormalities, had less severe IOP elevation than B6 mutants at young ages and showed no detectable nerve damage. To identify genetic modifiers of susceptibility to Lmx1bV265D -induced glaucoma-associated phenotypes, we performed a mapping cross between mice of the B6 (susceptible) and 129 (resistant) backgrounds. We identified a modifier locus on Chromosome 18, with the 129 allele(s) substantially lessening severity of ocular phenotypes, as confirmed by congenic analysis. By demonstrating a clear effect of genetic background in modulating Lmx1b-induced phenotypes, providing a panel of strains with different phenotypic severities and identifying a modifier locus, this study lays a foundation for better understanding the roles of LMX1B in glaucoma with the goal of developing new treatments.
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Affiliation(s)
- Nicholas G. Tolman
- Howard Hughes Medical Institute, Department of Ophthalmology, Columbia University Medical Center, and Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA,Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02115, USA,The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Revathi Balasubramanian
- Howard Hughes Medical Institute, Department of Ophthalmology, Columbia University Medical Center, and Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA
| | | | | | | | - Christa L. Montgomery
- Howard Hughes Medical Institute, Department of Ophthalmology, Columbia University Medical Center, and Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA
| | | | - Ian J. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sally H. Cross
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - K. Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Simon W. M. John
- Howard Hughes Medical Institute, Department of Ophthalmology, Columbia University Medical Center, and Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA,The Jackson Laboratory, Bar Harbor, ME 04609, USA,Author for correspondence ()
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4
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Trivli A, Zervou MI, Goulielmos GN, Spandidos DA, Detorakis ET. Primary open angle glaucoma genetics: The common variants and their clinical associations (Review). Mol Med Rep 2020; 22:1103-1110. [PMID: 32626970 PMCID: PMC7339808 DOI: 10.3892/mmr.2020.11215] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Glaucoma is a group of progressive optic neuropathies that have in common characteristic optic nerve head changes, loss of retinal ganglion cells and visual field defects. Among the large family of glaucomas, primary open‑angle glaucoma (POAG) is the most common type, a complex and heterogeneous disorder with environmental and genetic factors contributing to its pathogenesis. Approximately 5% of POAG is currently attributed to single‑gene or Mendelian forms of glaucoma. Genetic linkage analysis and genome‑wide association studies have identified various genomic loci, paving the path to understanding the pathogenesis of this enigmatic, blinding disease. In this review we summarize the most common variants reported thus far and their possible clinical correlations.
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Affiliation(s)
- Alexandra Trivli
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
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5
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Waseem NH, Low S, Shah AZ, Avisetti D, Ostergaard P, Simpson M, Niemiec KA, Martin-Martin B, Aldehlawi H, Usman S, Lee PS, Khawaja AP, Ruddle JB, Shah A, Sackey E, Day A, Jiang Y, Swinfield G, Viswanathan A, Alfano G, Chakarova C, Cordell HJ, Garway-Heath DF, Khaw PT, Bhattacharya SS, Waseem A, Foster PJ. Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma. PLoS Genet 2020; 16:e1008721. [PMID: 32339198 PMCID: PMC7233598 DOI: 10.1371/journal.pgen.1008721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 05/18/2020] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
Current estimates suggest 50% of glaucoma blindness worldwide is caused by primary angle-closure glaucoma (PACG) but the causative gene is not known. We used genetic linkage and whole genome sequencing to identify Spermatogenesis Associated Protein 13, SPATA13 (NM_001166271; NP_001159743, SPATA13 isoform I), also known as ASEF2 (Adenomatous polyposis coli-stimulated guanine nucleotide exchange factor 2), as the causal gene for PACG in a large seven-generation white British family showing variable expression and incomplete penetrance. The 9 bp deletion, c.1432_1440del; p.478_480del was present in all affected individuals with angle-closure disease. We show ubiquitous expression of this transcript in cell lines derived from human tissues and in iris, retina, retinal pigment and ciliary epithelia, cornea and lens. We also identified eight additional mutations in SPATA13 in a cohort of 189 unrelated PACS/PAC/PACG samples. This gene encodes a 1277 residue protein which localises to the nucleus with partial co-localisation with nuclear speckles. In cells undergoing mitosis SPATA13 isoform I becomes part of the kinetochore complex co-localising with two kinetochore markers, polo like kinase 1 (PLK-1) and centrosome-associated protein E (CENP-E). The 9 bp deletion reported in this study increases the RAC1-dependent guanine nucleotide exchange factors (GEF) activity. The increase in GEF activity was also observed in three other variants identified in this study. Taken together, our data suggest that SPATA13 is involved in the regulation of mitosis and the mutations dysregulate GEF activity affecting homeostasis in tissues where it is highly expressed, influencing PACG pathogenesis.
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Affiliation(s)
- Naushin H. Waseem
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
| | - Sancy Low
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
- Department of Ophthalmology, St. Thomas’ Hospital, Westminster Bridge Road, London, United Kingdom
| | - Amna Z. Shah
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Deepa Avisetti
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Pia Ostergaard
- Medical Genetics Unit, St. George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Michael Simpson
- Genetics and Molecular Medicine, King’s College London, Great Maze Pond, London, United Kingdom
| | - Katarzyna A. Niemiec
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Belen Martin-Martin
- Blizard Advanced Light Microscopy, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Hebah Aldehlawi
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Pak Sang Lee
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Jonathan B. Ruddle
- Department of Ophthalmology, University of Melbourne, Victoria, Australia
| | - Ameet Shah
- Department of Ophthalmology, Royal Free Hospital NHS Foundation Trust, Pond Street, London, United Kingdom
| | - Ege Sackey
- Medical Genetics Unit, St. George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Alexander Day
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
| | - Yuzhen Jiang
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
| | - Geoff Swinfield
- Society of Genealogists, Goswell Road, London, United Kingdom
| | - Ananth Viswanathan
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Giovanna Alfano
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | | | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - David F. Garway-Heath
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Peng T. Khaw
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Shomi S. Bhattacharya
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, United Kingdom
| | - Paul J. Foster
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, City Road, London, United Kingdom
- UCL Institute of Ophthalmology, Bath Street, London, United Kingdom
- * E-mail:
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6
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Kulyté A, Lundbäck V, Lindgren CM, Luan J, Lotta LA, Langenberg C, Arner P, Strawbridge RJ, Dahlman I. Genome-wide association study of adipocyte lipolysis in the GENetics of adipocyte lipolysis (GENiAL) cohort. Mol Metab 2020; 34:85-96. [PMID: 32180562 PMCID: PMC7021539 DOI: 10.1016/j.molmet.2020.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Lipolysis, hydrolysis of triglycerides to fatty acids in adipocytes, is tightly regulated, poorly understood, and, if perturbed, can lead to metabolic diseases including obesity and type 2 diabetes. The goal of this study was to identify the genetic regulators of lipolysis and elucidate their molecular mechanisms. METHODS Adipocytes from abdominal subcutaneous adipose tissue biopsies were isolated and were incubated without (spontaneous lipolysis) or with a catecholamine (stimulated lipolysis) to analyze lipolysis. DNA was extracted and genome-wide genotyping and imputation conducted. After quality control, 939 samples with genetic and lipolysis data were available. Genome-wide association studies of spontaneous and stimulated lipolysis were conducted. Subsequent in vitro gene expression analyses were used to identify candidate genes and explore their regulation of adipose tissue biology. RESULTS One locus on chromosome 19 demonstrated genome-wide significance with spontaneous lipolysis. 60 loci showed suggestive associations with spontaneous or stimulated lipolysis, of which many influenced both traits. In the chromosome 19 locus, only HIF3A was expressed in the adipocytes and displayed genotype-dependent gene expression. HIF3A knockdown in vitro increased lipolysis and the expression of key lipolysis-regulating genes. CONCLUSIONS In conclusion, we identified a genetic regulator of spontaneous lipolysis and provided evidence of HIF3A as a novel key regulator of lipolysis in subcutaneous adipocytes as the mechanism through which the locus influences adipose tissue biology.
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Affiliation(s)
- Agné Kulyté
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Veroniqa Lundbäck
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Cecilia M Lindgren
- Big Data Institute at the Li Ka Shing Center for Health Information and Discovery, University of Oxford, Oxford, UK; Wellcome Center for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Center, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Luca A Lotta
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Peter Arner
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK; Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden; Health Data Research UK, UK
| | - Ingrid Dahlman
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden.
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7
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Kim YW, Kim YJ, Cheong HS, Shiga Y, Hashimoto K, Song YJ, Kim SH, Choi HJ, Nishiguchi KM, Kawai Y, Nagasaki M, Nakazawa T, Park KH, Kim DM, Jeoung JW. Exploring the Novel Susceptibility Gene Variants for Primary Open-Angle Glaucoma in East Asian Cohorts: The GLAU-GENDISK Study. Sci Rep 2020; 10:221. [PMID: 31937794 PMCID: PMC6959350 DOI: 10.1038/s41598-019-57066-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Primary open-angle glaucoma (POAG) can develop even within normal ranges of intraocular pressure, and this type of glaucoma (so-called ‘normal-tension glaucoma [NTG]’) is highly prevalent in East Asia including Korea and Japan. We conducted exome chip analysis to identify low-frequency and rare variants associated with POAG from the primary cohort (309 POAG patients and 5,400 control, all Koreans). For replication, Korean (310 POAG patients and 5,612 controls) and Japanese (565 POAG patients and 1,104 controls) cohorts were further investigated by targeted genotyping. SNP rs116121322 in LRRC27 showed nominally significant association with POAG in the discovery cohort (OR = 29.85, P = 2E–06). This SNP was validated in the Korean replication cohort but only in the NTG subgroups (OR = 9.86, P = 0.007). Japanese replication cohort did not show significant association with POAG (P .00.44). However, the meta-analysis in the entire cohort revealed significant association of rs116121322 with POAG (ORcombined = 10.28, Pcombined = 1.4E–07). The LRRC27 protein expression was confirmed from human trabecular meshwork cells. For gene-based testing, METTL20 showed a significant association in POAG (Pcombined = 0.002) and in the subgroup of NTG (Pcombined = 0.02), whereas ZNF677 were significantly associated with only in the subgroup of high-tension glaucoma (Pcombined = 1.5E–06). Our findings may provide further genetic backgrounds into the pathogenesis of POAG, especially for the patients who have lower baseline intraocular pressures.
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Affiliation(s)
- Yong Woo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Yu Jeong Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Yukihiro Shiga
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yong Ju Song
- Department of Ophthalmology, Chosun University College of Medicine, Gwangju, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Hospital, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Koji M Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Ki Ho Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Dong Myung Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea. .,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea.
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8
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Chen M, Yu X, Xu J, Ma J, Chen X, Chen B, Gu Y, Wang K. Association of Gene Polymorphisms With Primary Open Angle Glaucoma: A Systematic Review and Meta-Analysis. ACTA ACUST UNITED AC 2019; 60:1105-1121. [PMID: 30901387 DOI: 10.1167/iovs.18-25922] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Min Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Xiaoning Yu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Jia Xu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Jian Ma
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Xinyi Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Binbin Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yuxiang Gu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Kaijun Wang
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
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9
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Kondkar AA, Sultan T, Almobarak FA, Kalantan H, Abu-Amero KK, Al-Obeidan SA. Plexin domain containing 2 (PLXDC2) gene polymorphism rs7081455 may not influence POAG risk in a Saudi cohort. BMC Res Notes 2018; 11:733. [PMID: 30326957 PMCID: PMC6192173 DOI: 10.1186/s13104-018-3848-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 11/18/2022] Open
Abstract
Objective Plexin domain containing 2 (PLXDC2), a cell surface transmembrane protein receptor for pigment epithelium derived factor, is expressed in many tissues including the eye. Polymorphism rs7081455 flanking PLXDC2 has been associated with primary open angle glaucoma (POAG) and its clinical phenotypes and may have a role in POAG. Rs7081455 was genotyped in POAG cases (n = 188) and non-glaucomatous controls (n = 164) of Saudi origin using Taq-Man® to determine any association of this variant with POAG and its endophenotypes. Results The risk variant, ‘G’ allele, frequency was 0.56 and 0.52 in controls and POAG cases, respectively (p = 0.197) with was no significant deviation from Hardy–Weinberg equilibrium. Genotype analysis between cases and controls revealed no significant distribution under additive (p = 0.482), dominant (p = 0.590) and recessive models (p = 0.228). In addition, glaucoma specific phenotypic traits such as intraocular pressure (IOP) and cup/disc ratio; and number of anti-glaucoma medications, used to assess severity of the disease, were also statistically non-significant. Furthermore, regression analysis showed no significant effect of age, sex and genotype on disease outcome. Rs7081455 was not associated with POAG or its clinical phenotypes such as IOP and cup/disc ratio and hence may not be a significant risk factor for POAG patients of Saudi origin. Electronic supplementary material The online version of this article (10.1186/s13104-018-3848-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Altaf A Kondkar
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.
| | - Tahira Sultan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Faisal A Almobarak
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Hatem Kalantan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Saleh A Al-Obeidan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
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10
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Wang HW, Sun P, Chen Y, Jiang LP, Wu HP, Zhang W, Gao F. Research progress on human genes involved in the pathogenesis of glaucoma (Review). Mol Med Rep 2018; 18:656-674. [PMID: 29845210 PMCID: PMC6059695 DOI: 10.3892/mmr.2018.9071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
Glaucoma is the leading cause of irreversible blindness globally. It is known that the incidence of glaucoma is closely associated with inheritance. A large number of studies have suggested that genetic factors are involved in the occurrence and development of glaucoma, and even affect the drug sensitivity and prognosis of glaucoma. In the present review, 22 loci of glaucoma are presented, including the relevant genes (myocilin, interleukin 20 receptor subunit B, optineurin, ankyrin repeat- and SOCS box-containing protein 10, WD repeat-containing protein 36, EGF-containing fibulin-like extracellular matrix protein 1, neurotrophin 4, TANK-binding kinase 1, cytochrome P450 subfamily I polypeptide 1, latent transforming growth factor β binding protein 2 and TEK tyrosine kinase endothelial) and 74 other genes (including toll-like receptor 4, sine oculis homeobox Drosophila homolog of 1, doublecortin-like kinase 1, RE repeats-encoding gene, retinitis pigmentosa GTPase regulator-interacting protein, lysyl oxidase-like protein 1, heat-shock 70-kDa protein 1A, baculoviral IAP repeat-containing protein 6, 5,10-methylenetetrahydrofolate reductase and nitric oxide synthase 3 and nanophthalmos 1) that are more closely associated with glaucoma. The pathogenesis of these glaucoma-associated genes, glaucomatous genetics and genetic approaches, as well as glaucomatous risk factors, including increasing age, glaucoma family history, high myopia, diabetes, ocular trauma, smoking, intraocular pressure increase and/or fluctuation were also discussed.
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Affiliation(s)
- Hong-Wei Wang
- Department of Ophthalmology, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Peng Sun
- Department of Ophthalmology, Longgang District People's Hospital, Shenzhen, Guangdong 518172, P.R. China
| | - Yao Chen
- Department of Ophthalmology, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Li-Ping Jiang
- Department of Ophthalmology, The First Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang 161041, P.R. China
| | - Hui-Ping Wu
- Department of The Scientific Research, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
| | - Wen Zhang
- Medical School, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Feng Gao
- Department of Hospital Administration, Jingjiang People's Hospital, Jingjiang, Jiangsu 214500, P.R. China
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11
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Singh M, Tyagi SC. Genes and genetics in eye diseases: a genomic medicine approach for investigating hereditary and inflammatory ocular disorders. Int J Ophthalmol 2018; 11:117-134. [PMID: 29376001 DOI: 10.18240/ijo.2018.01.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Past 25y have witnessed an exponential increase in knowledge and understanding of ocular diseases and their respective genetic underpinnings. As a result, scientists have mapped many genes and their variants that can influence vision and health of our eyes. Based on these findings, it is becoming clear that an early diagnosis employing genetic testing can help evaluate patients' conditions for instituting treatment plan(s) and follow-up care to avoid vision complications later. For example, knowing family history becomes crucial for inherited eye diseases as it can benefit members in family who may have similar eye diseases or predispositions. Therefore, gathering information from an elaborate examination along with complete assessment of past medical illness by ophthalmologists followed by consultation with geneticists can help create a roadmap for making diagnosis and treatment precise and beneficial. In this review, we present an update on ocular genomic medicine that we believe has tremendous potential towards unraveling genetic implications in ocular diseases and patients' susceptibilities. We also discuss translational aspects of genetic ophthalmology and genome engineering that may help advance molecular diagnostics and therapeutics.
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Affiliation(s)
- Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Suresh C Tyagi
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
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12
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Niche harmony search algorithm for detecting complex disease associated high-order SNP combinations. Sci Rep 2017; 7:11529. [PMID: 28912584 PMCID: PMC5599559 DOI: 10.1038/s41598-017-11064-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 08/17/2017] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association study is especially challenging in detecting high-order disease-causing models due to model diversity, possible low or even no marginal effect of the model, and extraordinary search and computations. In this paper, we propose a niche harmony search algorithm where joint entropy is utilized as a heuristic factor to guide the search for low or no marginal effect model, and two computationally lightweight scores are selected to evaluate and adapt to diverse of disease models. In order to obtain all possible suspected pathogenic models, niche technique merges with HS, which serves as a taboo region to avoid HS trapping into local search. From the resultant set of candidate SNP-combinations, we use G-test statistic for testing true positives. Experiments were performed on twenty typical simulation datasets in which 12 models are with marginal effect and eight ones are with no marginal effect. Our results indicate that the proposed algorithm has very high detection power for searching suspected disease models in the first stage and it is superior to some typical existing approaches in both detection power and CPU runtime for all these datasets. Application to age-related macular degeneration (AMD) demonstrates our method is promising in detecting high-order disease-causing models.
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13
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Genetic variants associated with primary open angle glaucoma in Indian population. Genomics 2017; 109:27-35. [PMID: 27851990 DOI: 10.1016/j.ygeno.2016.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 01/26/2023]
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14
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Mookherjee S, Banerjee D, Chakraborty S, Mukhopadhyay I, Sen A, Ray K. Evaluation of the IL1 Gene Cluster Single Nucleotide Polymorphisms in Primary Open-Angle Glaucoma Pathogenesis. Genet Test Mol Biomarkers 2016; 20:633-636. [PMID: 27533638 DOI: 10.1089/gtmb.2015.0344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AIMS Dysregulation of the immune system has previously been implicated in glaucoma pathogenesis. In this study, we investigated the potential association of SNPs in the IL1 gene cluster, consisting of nine genes, with primary open-angle glaucoma (POAG) cases. These cases presented with low to normal intraocular pressures (<20 mmHg), and are referred to as non-high tension glaucoma (non-HTG) cases. MATERIALS AND METHODS In this biphasic study, the discovery phase was conducted with 198 non-HTG cases and 112 controls from eastern India. A total of 68 single nucleotide polymorphisms (SNPs) spanning the IL1 nine-gene cluster region were genotyped using the MALDI-TOF based Sequenom platform. SNPs, which were found to be significantly associated with non-HTG cases in the first phase of the study, were further genotyped by Sanger sequencing in a replication cohort consisting of 194 non-HTG cases and 242 controls. RESULTS In the discovery phase, two nonsynonymous SNPs (rs3811046 and rs3811047), located in the IL1F7 gene and in an intergenic region, respectively were found to be weakly associated with non-HTG cases. However, the association was not sustained in the replication cohort. CONCLUSION Our study did not reveal any reproducible association of SNPs in the IL1 gene cluster with POAG.
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Affiliation(s)
- Suddhasil Mookherjee
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | - Deblina Banerjee
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | - Subhadip Chakraborty
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
| | | | | | - Kunal Ray
- 1 Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology , Kolkata, India
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