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Meyer KJ, Mercer HE, Roos BR, Fingert JH, Anderson MG. Minimal phenotypes in transgenic mice with the human LOXL1/LOXL1-AS1 locus associated with exfoliation glaucoma. Vision Res 2024; 223:108464. [PMID: 39151208 DOI: 10.1016/j.visres.2024.108464] [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: 05/17/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024]
Abstract
Exfoliation syndrome is a leading cause of secondary glaucoma worldwide. Among the risk-factors for exfoliation syndrome and exfoliation glaucoma that have been investigated, a genetic association with 15q24.1 is among the most striking. The leading candidates for the causal gene at this locus are LOXL1 and/or LOXL1-AS1, but studies have not yet coalesced in establishing, or ruling out, either candidate. Here, we contribute to studies of the 15q24.1 locus by making a partially humanized mouse model in which 166 kb of human genomic DNA from the 15q24.1 locus was introduced into the mouse genome via BAC transgenesis (B6-Tg(RP11-71M11)Andm). Transgenic expression of human genes in the BAC was only detectable for LOXL1-AS1. One cohort of 34 mice (21 experimental hemizygotes and 13 non-carrier control littermates) was assessed by slit-lamp exams and SD-OCT imaging at early (1-2 months) and mid (4-5 months) time points; fundus exams were performed at 5 months of age. A second smaller cohort (3 hemizygotes) were aged extensively (>12 months) to screen for overt abnormalities. Across all genotypes and ages, 136 slit-lamp exams, 128 SD-OCT exams, and 42 fundus exams detected no overt indices of exfoliation syndrome. Quantitatively, small, but statistically significant, age-related declines in ganglion cell complex thickness and total retinal thickness were detected in the hemizygotes at 4 months of age. Overall, this study demonstrates complexity in gene regulation from the 15q24.1 locus and suggests that LOXL1-AS1 is unlikely to be a monogenic cause of exfoliation syndrome but may contribute to glaucomatous retinal damage.
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Affiliation(s)
- Kacie J Meyer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Hannah E Mercer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States
| | - Ben R Roos
- Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, United States; Institute for Vision Research, University of Iowa, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States; Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, IA, United States.
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Soundappan K, Cai J, Yu H, Dhamodaran K, Baidouri H, Vranka JA, Xu H, Raghunathan V, Liu Y. Influence of Dexamethasone-Induced Matrices on the TM Transcriptome. Exp Eye Res 2024:110069. [PMID: 39233306 DOI: 10.1016/j.exer.2024.110069] [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: 05/16/2024] [Revised: 08/06/2024] [Accepted: 09/02/2024] [Indexed: 09/06/2024]
Abstract
Pathologic bidirectional interactions between the extracellular matrix (ECM) and cells within the human trabecular meshwork (hTM) contribute to ocular hypertension. An in vitro model is needed to study these cell-matrix interactions and their effect on outflow homeostasis. This study aimed to determine whether pathogenic ECM derived from dexamethasone (DEX)-treated hTM cultures induces clinically relevant glaucoma-like changes in healthy hTM cells at the transcriptional level. Corneoscleral rims from non-glaucoma donors were used to isolate primary hTM cells after validation according to the consensus recommendations for TM culture. Normal hTM cells (n=5) were plated on a coverslip and treated with 100nM DEX or ethanol for four weeks. These cultures were then decellularized, plated with primary hTM cells, and allowed to grow for another 72 hours. RNA was extracted from these hTM cells for stranded total RNA-Seq. Sequencing libraries prepared using the Zymo-Seq RiboFree Total RNA library kit were pooled and sequenced using Illumina NovaSeq 6000. After quality control, sequence reads were aligned to the human genome build hg19. Differential expression (DE) analyses were performed using paired multi-factorial ANOVA. The expression of several DE genes associated with glaucoma (ANGPTL2, PDE7B, C22orf23, COL4A1, ADAM12, IFT122, SEMA6C) was validated using EvaGreen-based Droplet Digital PCR (ddPCR) assays. Gene ontology analyses of the DE genes were performed using the PANTHER and NDEx IQA databases, and functional analyses were performed with the DAVID Bioinformatics software. Using a cutoff of p-value <0.05 and fold change ≥2.0, our differential analysis identified 267 up- and 135 down-regulated genes in DEX-induced ECM-treated cells compared to the control. These differentially expressed genes were found to play a significant role in pathways such as cytokine and oxidative stress-induced inflammation, integrin signaling, matrix remodeling, and angiogenesis. These findings were further supported by previously performed proteomics studies using the same model. Using ddPCR, we validated the expression of seven genes associated with risk of primary open-angle glaucoma. These results not only provide support for the pathogenic ECM model of steroid-induced glaucoma, but also demonstrate that the pathologic changes induced by this model are indeed found at the transcriptional level. These findings further demonstrate that matrix changes significantly influence cell expression profiles which enable further understanding of the molecular mechanisms underlying glaucomatous changes in the TM. However, future studies with a larger and more diverse set of samples and longer timepoints are needed to confirm the utility of this model for mechanistic studies.
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Affiliation(s)
- Keerti Soundappan
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Jingwen Cai
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Hongfang Yu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Kamesh Dhamodaran
- College of Optometry, University of Houston, Houston, TX, United States
| | - Hasna Baidouri
- College of Optometry, University of Houston, Houston, TX, United States
| | - Janice A Vranka
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Hongyan Xu
- Department of Biostatistics, Data Science and Epidemiology, Augusta University, Augusta, GA, United States
| | | | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States; James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States.
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Mbatchou J, McPeek MS. JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression. Am J Hum Genet 2024; 111:1750-1769. [PMID: 39025064 PMCID: PMC11339629 DOI: 10.1016/j.ajhg.2024.06.010] [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: 12/15/2023] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
Joint association analysis of multiple traits with multiple genetic variants can provide insight into genetic architecture and pleiotropy, improve trait prediction, and increase power for detecting association. Furthermore, some traits are naturally high-dimensional, e.g., images, networks, or longitudinally measured traits. Assessing significance for multitrait genetic association can be challenging, especially when the sample has population sub-structure and/or related individuals. Failure to adequately adjust for sample structure can lead to power loss and inflated type 1 error, and commonly used methods for assessing significance can work poorly with a large number of traits or be computationally slow. We developed JASPER, a fast, powerful, robust method for assessing significance of multitrait association with a set of genetic variants, in samples that have population sub-structure, admixture, and/or relatedness. In simulations, JASPER has higher power, better type 1 error control, and faster computation than existing methods, with the power and speed advantage of JASPER increasing with the number of traits. JASPER is potentially applicable to a wide range of association testing applications, including for multiple disease traits, expression traits, image-derived traits, and microbiome abundances. It allows for covariates, ascertainment, and rare variants and is robust to phenotype model misspecification. We apply JASPER to analyze gene expression in the Framingham Heart Study, where, compared to alternative approaches, JASPER finds more significant associations, including several that indicate pleiotropic effects, most of which replicate previous results, while others have not previously been reported. Our results demonstrate the promise of JASPER for powerful multitrait analysis in structured samples.
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Affiliation(s)
- Joelle Mbatchou
- Regeneron Genetics Center, Tarrytown, NY 10591, USA; Department of Statistics, The University of Chicago, Chicago, IL 60637, USA
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
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Mackey DA, Bigirimana D, Staffieri SE. Integrating Genetics in Glaucoma Screening. J Glaucoma 2024; 33:S49-S53. [PMID: 39149951 PMCID: PMC11332373 DOI: 10.1097/ijg.0000000000002425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/02/2024] [Indexed: 08/17/2024]
Abstract
PRCIS As additional glaucoma genes are identified and classified, polygenic risk scores will be refined, facilitating early diagnosis and treatment. Ensuring genetic research is equitable to prevent glaucoma blindness worldwide is crucial. PURPOSE To review the progress in glaucoma genetics over the past 25 years, including the identification of genes with varying contributions to the disease and the development of polygenic risk scores. METHODS/RESULTS Over the last 2 and a half decades, glaucoma genetics has evolved from identifying genes with Mendelian inheritance patterns, such as myocilin and CYP1B1, to the discovery of hundreds of genes associated with the disease. Polygenic risk scores have been developed, primarily based on research in Northern European populations, and efforts to refine these scores are ongoing. However, there is a question regarding their applicability to other ethnic groups, especially those at higher risk of primary open angle glaucoma, like individuals of African ancestry. Glaucoma is highly heritable and family history can be used for cascade clinical screening programs, but these will not be feasible in all populations. Thus, cascade genetic testing using well-established genes such as myocilin may help improve glaucoma diagnosis. In addition, ongoing investigations seek to identify pathogenic genetic variants within genes like myocilin. CONCLUSIONS The expanding availability of genetic testing for various diseases and early access to genetic risk information necessitates further research to determine when and how to act on specific genetic results. Polygenic risk scores involving multiple genes with subtle effects will require continuous refinement to improve clinical utility. This is crucial for effectively interpreting an individual's risk of developing glaucoma and preventing blindness.
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Affiliation(s)
| | - Deus Bigirimana
- Glaucoma Investigation and Research Unit, Royal Victorian Eye and Ear Hospital
| | - Sandra Elfride Staffieri
- Centre for Eye Research Australia Ltd., Royal Victorian Eye and Ear Hospital
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
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Kolovos A, Hassall MM, Siggs OM, Souzeau E, Craig JE. Polygenic Risk Scores Driving Clinical Change in Glaucoma. Annu Rev Genomics Hum Genet 2024; 25:287-308. [PMID: 38599222 DOI: 10.1146/annurev-genom-121222-105817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Glaucoma is a clinically heterogeneous disease and the world's leading cause of irreversible blindness. Therapeutic intervention can prevent blindness but relies on early diagnosis, and current clinical risk factors are limited in their ability to predict who will develop sight-threatening glaucoma. The high heritability of glaucoma makes it an ideal substrate for genetic risk prediction, with the bulk of risk being polygenic in nature. Here, we summarize the foundations of glaucoma genetic risk, the development of polygenic risk prediction instruments, and emerging opportunities for genetic risk stratification. Although challenges remain, genetic risk stratification will significantly improve glaucoma screening and management.
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Affiliation(s)
- Antonia Kolovos
- Department of Ophthalmology, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia; , , ,
| | - Mark M Hassall
- Department of Ophthalmology, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia; , , ,
| | - Owen M Siggs
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia;
- Department of Ophthalmology, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia; , , ,
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia; , , ,
| | - Jamie E Craig
- Department of Ophthalmology, Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia; , , ,
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Founti P, Stuart K, Nolan WP, Khawaja AP, Foster PJ. Screening Strategies and Methodologies. J Glaucoma 2024; 33:S15-S20. [PMID: 39149948 DOI: 10.1097/ijg.0000000000002426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/02/2024] [Indexed: 08/17/2024]
Abstract
PRCIS While glaucoma is a leading cause of irreversible vision loss, it presents technical challenges in the design and implementation of screening. New technologies such as PRS and AI offer potential improvements in our ability to identify people at high risk of sight loss from glaucoma and may improve the viability of screening for this important disease. PURPOSE To review the current evidence and concepts around screening for glaucoma. METHODS/RESULTS A group of glaucoma-focused clinician scientists drew on knowledge and experience around glaucoma, its etiology, and the options for screening. Glaucoma is a chronic progressive optic neuropathy affecting around 76 million individuals worldwide and is the leading cause of irreversible blindness globally. Early stages of the disease are asymptomatic meaning a substantial proportion of cases remain undiagnosed. Early detection and timely intervention reduce the risk of glaucoma-related visual morbidity. However, imperfect tests and a relatively low prevalence currently limit the viability of population-based screening approaches. The diagnostic yield of opportunistic screening strategies, relying on the identification of disease during unrelated health care encounters, such as cataract clinics and diabetic retinopathy screening programs, focusing on older people and/or those with a family history, are hindered by a large number of false-positive and false-negative results. Polygenic risk scores (PRS) offer personalized risk assessment for adult-onset glaucoma. In addition, artificial intelligence (AI) algorithms have shown impressive performance, comparable to expert humans, in discriminating between potentially glaucomatous and non-glaucomatous eyes. These emerging technologies may offer a meaningful improvement in diagnostic yield in glaucoma screening. CONCLUSIONS While glaucoma is a leading cause of irreversible vision loss, it presents technical challenges in the design and implementation of screening. New technologies such as PRS and AI offer potential improvements in our ability to identify people at high risk of sight loss from glaucoma and may improve the viability of screening for this important disease.
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Affiliation(s)
| | - Kelsey Stuart
- Ocular Informatics Group, Population and Data Sciences Research Theme, University College London Institute of Ophthalmology
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology
| | - Winifred P Nolan
- Glaucoma Service, Moorfields Eye Hospital NHS Foundation Trust
- International Centre for Eye Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Anthony P Khawaja
- Glaucoma Service, Moorfields Eye Hospital NHS Foundation Trust
- Ocular Informatics Group, Population and Data Sciences Research Theme, University College London Institute of Ophthalmology
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology
| | - Paul J Foster
- Glaucoma Service, Moorfields Eye Hospital NHS Foundation Trust
- Ocular Informatics Group, Population and Data Sciences Research Theme, University College London Institute of Ophthalmology
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology
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7
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Akiyama M, Tamiya G, Fujiwara K, Shiga Y, Yokoyama Y, Hashimoto K, Sato M, Sato K, Narita A, Hashimoto S, Ueda E, Furuta Y, Hata J, Miyake M, Ikeda HO, Suda K, Numa S, Mori Y, Morino K, Murakami Y, Shimokawa S, Nakamura S, Yawata N, Fujisawa K, Yamana S, Mori K, Ikeda Y, Miyata K, Mori K, Ogino K, Koyanagi Y, Kamatani Y, Ninomiya T, Sonoda KH, Nakazawa T. Genetic Risk Stratification of Primary Open-Angle Glaucoma in Japanese Individuals. Ophthalmology 2024:S0161-6420(24)00362-2. [PMID: 39023470 DOI: 10.1016/j.ophtha.2024.05.026] [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: 12/24/2023] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 07/20/2024] Open
Abstract
PURPOSE To assess the impact of genetic risk estimation for primary open-angle glaucoma (POAG) in Japanese individuals. DESIGN Cross-sectional analysis. PARTICIPANTS Genetic risk scores (GRSs) were constructed based on a genome-wide association study (GWAS) of POAG in Japanese people. A total of 3625 Japanese individuals, including 1191 patients and 2434 controls (Japanese Tohoku), were used for the model selection. We also evaluated the discriminative accuracy of constructed GRSs in a dataset comprising 1034 patients and 1147 controls (the Japan Glaucoma Society Omics Group [JGS-OG] and the Genomic Research Committee of the Japanese Ophthalmological Society [GRC-JOS]) and 1900 participants from a population-based study (Hisayama Study). METHODS We evaluated 2 types of GRSs: polygenic risk scores using the pruning and thresholding procedure and a GRS using variants associated with POAG in the GWAS of the International Glaucoma Genetics Consortium (IGGC). We selected the model with the highest areas under the receiver operating characteristic curve (AUC). In the population-based study, we evaluated the correlations between GRS and ocular measurements. MAIN OUTCOME MEASURE Proportion of patients with POAG after stratification according to the GRS. RESULTS We found that a GRS using 98 variants, which showed genome-wide significance in the IGGC, showed the best discriminative accuracy (AUC, 0.65). In the Japanese Tohoku, the proportion of patients with POAG in the top 10% individuals was significantly higher than that in the lowest 10% (odds ratio [OR], 6.15; 95% confidence interval [CI], 4.35-8.71). In the JGS-OG and GRC-JOS, we confirmed similar impact of POAG GRS (AUC, 0.64; OR [top vs. bottom decile], 5.81; 95% CI, 3.79-9.01). In the population-based study, POAG prevalence was significantly higher in the top 20% individuals of the GRS compared with the bottom 20% (9.2% vs. 5.0%). However, the discriminative accuracy was low (AUC, 0.56). The POAG GRS was correlated positively with intraocular pressure (r = 0.08: P = 4.0 × 10-4) and vertical cup-to-disc ratio (r = 0.11; P = 4.0 × 10-6). CONCLUSIONS The GRS showed moderate discriminative accuracy for POAG in the Japanese population. However, risk stratification in the general population showed relatively weak discriminative performance. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Masato Akiyama
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kohta Fujiwara
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yukihiro Shiga
- Department of Neuroscience, Université de Montréal, Montréal, Canada; Neuroscience Division, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Canada; Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yu Yokoyama
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masataka Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Sawako Hashimoto
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Emi Ueda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Furuta
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jun Hata
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hanako O Ikeda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Suda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shogo Numa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Mori
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuya Morino
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sakurako Shimokawa
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shun Nakamura
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuyo Yawata
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kimihiko Fujisawa
- Department of Ophthalmology, Japan Community Healthcare Organization Kyushu Hospital, Fukuoka, Japan
| | - Satoshi Yamana
- Department of Ophthalmology, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Kenichiro Mori
- Department of Ophthalmology, Aso Iizuka Hospital, Iizuka, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | | | - Keisuke Mori
- Department of Ophthalmology, International University of Health and Welfare, Nasu-shiobara, Tochigi, Japan
| | - Ken Ogino
- Department of Ophthalmology, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | - Yoshito Koyanagi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan.
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8
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Tran JH, Kang J, Han E, Gupta U, Seresirikachorn K, Vy HMT, Zhao Y, Rocheleau G, Luo Y, Lee R, Do R, Friedman DS, Kang JH, Wiggs JL, Pasquale LR, Segrè AV, Zebardast N. Use of Diagnostic Codes for Primary Open-Angle Glaucoma Polygenic Risk Score Construction in Electronic Health Record-Linked Biobanks. Am J Ophthalmol 2024; 267:204-212. [PMID: 38906208 DOI: 10.1016/j.ajo.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/23/2024]
Abstract
PURPOSE Polygenic risk scores (PRSs) likely predict risk and prognosis of glaucoma. We compared the PRS performance for primary open-angle glaucoma (POAG), defined using International Classification of Diseases (ICD) codes vs manual medical record review. DESIGN Retrospective cohort study. METHODS We identified POAG cases in the Mount Sinai BioMe and Mass General Brigham (MGB) biobanks using ICD codes. We confirmed POAG based on optical coherence tomograms and visual fields. In a separate 5% sample, the absence of POAG was confirmed with intraocular pressure and cup-disc ratio criteria. We used genotype data and either self-reported glaucoma diagnoses or ICD-10 codes for glaucoma diagnoses from the UK Biobank and the lassosum method to compute a genome-wide POAG PRS. We compared the area under the curve (AUC) for POAG prediction based on ICD codes vs medical records. RESULTS We reviewed 804 of 996 BioMe and 367 of 1006 MGB ICD-identified cases. In BioMe and MGB, respectively, positive predictive value was 53% and 55%; negative predictive value was 96% and 97%; sensitivity was 97% and 97%; and specificity was 44% and 53%. Adjusted PRS AUCs for POAG using ICD codes vs manual record review in BioMe were not statistically different (P ≥.21) by ancestry: 0.77 vs 0.75 for African, 0.80 vs 0.80 for Hispanic, and 0.81 vs 0.81 for European. Results were similar in MGB (P ≥.18): 0.72 vs 0.80 for African, 0.83 vs 0.86 for Hispanic, and 0.74 vs 0.73 for European. CONCLUSIONS A POAG PRS performed similarly using either manual review or ICD codes in 2 electronic health record-linked biobanks; manual assessment of glaucoma status might not be necessary for some PRS studies. However, caution should be exercised when using ICD codes for glaucoma diagnosis given their low specificity (44%-53%) for manually confirmed cases of glaucoma.
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Affiliation(s)
- Jessica H Tran
- From the Department of Ophthalmology (J.H.T., E.H., R.L., L.R.P.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joyce Kang
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Elaine Han
- From the Department of Ophthalmology (J.H.T., E.H., R.L., L.R.P.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Urvi Gupta
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Kasem Seresirikachorn
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Ha My T Vy
- The Charles Bronfman Institute for Personalized Medicine (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yan Zhao
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yuyang Luo
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel Lee
- From the Department of Ophthalmology (J.H.T., E.H., R.L., L.R.P.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences (H.M.T.V., G.R., R.D.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David S Friedman
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Jae H Kang
- Channing Division of Network Medicine (J.H.K.), Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Janey L Wiggs
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Louis R Pasquale
- From the Department of Ophthalmology (J.H.T., E.H., R.L., L.R.P.), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ayellet V Segrè
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Nazlee Zebardast
- Department of Ophthalmology (J.K., U.G., K.S., Y.Z., Y.L., D.S.F., J.L.W., A.V.S., N.Z.), Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA.
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9
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Rämö JT, Gorman B, Weng LC, Jurgens SJ, Singhanetr P, Tieger MG, van Dijk EH, Halladay CW, Wang X, Brinks J, Choi SH, Luo Y, Pyarajan S, Nealon CL, Gorin MB, Wu WC, Sobrin L, Kaarniranta K, Yzer S, Palotie A, Peachey NS, Turunen JA, Boon CJ, Ellinor PT, Iyengar SK, Daly MJ, Rossin EJ. Rare genetic variation in VE-PTP is associated with central serous chorioretinopathy, venous dysfunction and glaucoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.08.24307013. [PMID: 38766240 PMCID: PMC11100937 DOI: 10.1101/2024.05.08.24307013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Central serous chorioretinopathy (CSC) is a fluid maculopathy whose etiology is not well understood. Abnormal choroidal veins in CSC patients have been shown to have similarities with varicose veins. To identify potential mechanisms, we analyzed genotype data from 1,477 CSC patients and 455,449 controls in FinnGen. We identified an association for a low-frequency (AF=0.5%) missense variant (rs113791087) in the gene encoding vascular endothelial protein tyrosine phosphatase (VE-PTP) (OR=2.85, P=4.5×10-9). This was confirmed in a meta-analysis of 2,452 CSC patients and 865,767 controls from 4 studies (OR=3.06, P=7.4×10-15). Rs113791087 was associated with a 56% higher prevalence of retinal abnormalities (35.3% vs 22.6%, P=8.0×10-4) in 708 UK Biobank participants and, surprisingly, with varicose veins (OR=1.31, P=2.3×10-11) and glaucoma (OR=0.82, P=6.9×10-9). Predicted loss-of-function variants in VEPTP, though rare in number, were associated with CSC in All of Us (OR=17.10, P=0.018). These findings highlight the significance of VE-PTP in diverse ocular and systemic vascular diseases.
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Affiliation(s)
- Joel T Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Massachusetts Eye and Ear, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Bryan Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Lu-Chen Weng
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Panisa Singhanetr
- Massachusetts Eye and Ear, Boston, MA, USA
- Mettapracharak Eye Institute, Mettapracharak (Wat Rai Khing) Hospital, Nakhon Pathom, Thailand
| | - Marisa G Tieger
- New England Eye Center, Tufts Medical Center, Boston, MA, USA
| | - Elon Hc van Dijk
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christopher W Halladay
- Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI, USA
| | - Xin Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joost Brinks
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Yuyang Luo
- Massachusetts Eye and Ear, Boston, MA, USA
| | - Saiju Pyarajan
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - Cari L Nealon
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
| | - Michael B Gorin
- Department of Ophthalmology, David Geffen School of Medicine, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wen-Chih Wu
- Section of Cardiology, Medical Service, VA Providence Healthcare System, Providence, RI, USA
| | - Lucia Sobrin
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Kai Kaarniranta
- Department of Ophthalmology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Suzanne Yzer
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neal S Peachey
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Joni A Turunen
- Folkhälsan Research Center, Biomedicum, Helsinki, Finland
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Camiel Jf Boon
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudha K Iyengar
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elizabeth J Rossin
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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10
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Lin F, Li Y, Wang J, Jardines S, King R, Chrenek MA, Wiggs JL, Boatright JH, Geisert EE. POU6F2, a risk factor for glaucoma, myopia and dyslexia, labels specific populations of retinal ganglion cells. Sci Rep 2024; 14:10096. [PMID: 38698014 PMCID: PMC11066091 DOI: 10.1038/s41598-024-60444-5] [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: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
Pou6f2 is a genetic connection between central corneal thickness (CCT) in the mouse and a risk factor for developing primary open-angle glaucoma. POU6F2 is also a risk factor for several conditions in humans, including glaucoma, myopia, and dyslexia. Recent findings demonstrate that POU6F2-positive retinal ganglion cells (RGCs) comprise a number of RGC subtypes in the mouse, some of which also co-stain for Cdh6 and Hoxd10. These POU6F2-positive RGCs appear to be novel of ON-OFF directionally selective ganglion cells (ooDSGCs) that do not co-stain with CART or SATB2 (typical ooDSGCs markers). These POU6F2-positive cells are sensitive to damage caused by elevated intraocular pressure. In the DBA/2J mouse glaucoma model, heavily-labeled POU6F2 RGCs decrease by 73% at 8 months of age compared to only 22% loss of total RGCs (labeled with RBPMS). Additionally, Pou6f2-/- mice suffer a significant loss of acuity and spatial contrast sensitivity along with an 11.4% loss of total RGCs. In the rhesus macaque retina, POU6F2 labels the large parasol ganglion cells that form the magnocellular (M) pathway. The association of POU6F2 with the M-pathway may reveal in part its role in human glaucoma, myopia, and dyslexia.
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Affiliation(s)
- Fangyu Lin
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Ying Li
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Jiaxing Wang
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Sandra Jardines
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Rebecca King
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Micah A Chrenek
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
| | - Janey L Wiggs
- Massachusetts Eye and Ear, Harvard Medical School Boston, Boston, MA, USA
| | - Jeffrey H Boatright
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA
- Atlanta Veterans Administration Center for Visual and Neurocognitive Rehabilitation, Decatur, GA, USA
| | - Eldon E Geisert
- Department of Ophthalmology, Emory University, 1365B Clifton Road NE, Atlanta, GA, 30322, USA.
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11
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Yun JS, Jung SH, Lee SN, Jung SM, Won HH, Kim D, Choi JA. Polygenic risk score-based phenome-wide association for glaucoma and its impact on disease susceptibility in two large biobanks. J Transl Med 2024; 22:355. [PMID: 38622600 PMCID: PMC11020996 DOI: 10.1186/s12967-024-05152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Glaucoma is a leading cause of worldwide irreversible blindness. Considerable uncertainty remains regarding the association between a variety of phenotypes and the genetic risk of glaucoma, as well as the impact they exert on the glaucoma development. METHODS We investigated the associations of genetic liability for primary open angle glaucoma (POAG) with a wide range of potential risk factors and to assess its impact on the risk of incident glaucoma. The phenome-wide association study (PheWAS) approach was applied to determine the association of POAG polygenic risk score (PRS) with a wide range of phenotypes in 377, 852 participants from the UK Biobank study and 43,623 participants from the Penn Medicine Biobank study, all of European ancestry. Participants were stratified into four risk tiers: low, intermediate, high, and very high-risk. Cox proportional hazard models assessed the relationship of POAG PRS and ocular factors with new glaucoma events. RESULTS In both discovery and replication set in the PheWAS, a higher genetic predisposition to POAG was specifically correlated with ocular disease phenotypes. The POAG PRS exhibited correlations with low corneal hysteresis, refractive error, and ocular hypertension, demonstrating a strong association with the onset of glaucoma. Individuals carrying a high genetic burden exhibited a 9.20-fold, 11.88-fold, and 28.85-fold increase in glaucoma incidence when associated with low corneal hysteresis, high myopia, and elevated intraocular pressure, respectively. CONCLUSION Genetic susceptibility to POAG primarily influences ocular conditions, with limited systemic associations. Notably, the baseline polygenic risk for POAG robustly associates with new glaucoma events, revealing a large combined effect of genetic and ocular risk factors on glaucoma incidents.
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Affiliation(s)
- Jae-Seung Yun
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Su-Nam Lee
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jin A Choi
- Department of Ophthalmology, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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12
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Harris A, Verticchio Vercellin A, Weinreb RN, Khawaja A, MacGregor S, Pasquale LR. Lessons From The Glaucoma Foundation Think Tank 2023: A Patient-Centric Approach to Glaucoma. J Glaucoma 2024; 33:e1-e14. [PMID: 38129952 DOI: 10.1097/ijg.0000000000002353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
PRCIS The main takeaways also included that BIG DATA repositories and AI are important combinatory tools to foster novel strategies to prevent and stabilize glaucoma and, in the future, recover vision loss from the disease. PURPOSE To summarize the main topics discussed during the 28th Annual Glaucoma Foundation Think Tank Meeting "A Patient-Centric Approach to Glaucoma" held in New York on June 9 and 10, 2023. METHODS The highlights of the sessions on BIG DATA, genetics, modifiable lifestyle risk factors, female sex hormones, and neuroprotection in the field of primary open angle glaucoma (POAG) were summarized. RESULTS The researchers discussed the importance of BIG DATA repositories available at national and international levels for POAG research, including the United Kingdom Biobank. Combining genotyped large cohorts worldwide, facilitated by artificial intelligence (AI) and machine-learning approaches, led to the milestone discovery of 312 genome-wide significant disease loci for POAG. While these loci could be combined into a polygenic risk score with clinical utility, Think Tank meeting participants also provided analytical epidemiological evidence that behavioral risk factors modify POAG polygenetic risk, citing specific examples related to caffeine and alcohol use. The impact of female sex hormones on POAG pathophysiology was discussed, as was neuroprotection and the potential use of AI to help mitigate specific challenges faced in clinical trials and speed approval of neuroprotective agents. CONCLUSIONS The experts agreed on the importance of genetics in defining individual POAG risk and highlighted the additional crucial role of lifestyle, gender, blood pressure, and vascular risk factors. The main takeaways also included that BIG DATA repositories and AI are important combinatory tools to foster novel strategies to prevent and stabilize glaucoma and, in the future, recover vision loss from the disease.
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Affiliation(s)
- Alon Harris
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY
| | | | - Robert N Weinreb
- Viterbi Family Department of Ophthalmology, Hamilton Glaucoma Center, Shiley Eye Institute, UC San Diego, La Jolla, CA
| | - Anthony Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY
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13
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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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14
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Lo Faro V, Bhattacharya A, Zhou W, Zhou D, Wang Y, Läll K, Kanai M, Lopera-Maya E, Straub P, Pawar P, Tao R, Zhong X, Namba S, Sanna S, Nolte IM, Okada Y, Ingold N, MacGregor S, Snieder H, Surakka I, Shortt J, Gignoux C, Rafaels N, Crooks K, Verma A, Verma SS, Guare L, Rader DJ, Willer C, Martin AR, Brantley MA, Gamazon ER, Jansonius NM, Joos K, Cox NJ, Hirbo J. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation. Cell Rep Med 2024; 5:101430. [PMID: 38382466 PMCID: PMC10897632 DOI: 10.1016/j.xcrm.2024.101430] [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: 01/05/2022] [Revised: 03/28/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness globally, shows disparity in prevalence and manifestations across ancestries. We perform meta-analysis across 15 biobanks (of the Global Biobank Meta-analysis Initiative) (n = 1,487,441: cases = 26,848) and merge with previous multi-ancestry studies, with the combined dataset representing the largest and most diverse POAG study to date (n = 1,478,037: cases = 46,325) and identify 17 novel significant loci, 5 of which were ancestry specific. Gene-enrichment and transcriptome-wide association analyses implicate vascular and cancer genes, a fifth of which are primary ciliary related. We perform an extensive statistical analysis of SIX6 and CDKN2B-AS1 loci in human GTEx data and across large electronic health records showing interaction between SIX6 gene and causal variants in the chr9p21.3 locus, with expression effect on CDKN2A/B. Our results suggest that some POAG risk variants may be ancestry specific, sex specific, or both, and support the contribution of genes involved in programmed cell death in POAG pathogenesis.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dan Zhou
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Esteban Lopera-Maya
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands
| | - Peter Straub
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Priyanka Pawar
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Serena Sanna
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands; Institute for Genetics and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Nathan Ingold
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ida Surakka
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anurag Verma
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shefali S Verma
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Guare
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Cristen Willer
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milam A Brantley
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nomdo M Jansonius
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands
| | - Karen Joos
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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15
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Loo Y, Chan ASY, Khor CC, Aung T, Wang Z. Rodent genetically modified models of glaucoma. Mol Aspects Med 2024; 95:101229. [PMID: 38039744 DOI: 10.1016/j.mam.2023.101229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
Glaucoma, one of the leading causes of irreversible blindness worldwide, is a complex and heterogenous disease. While environmental factors are important, it is well-recognized that the disease has a strong heritable component. With the advent of large-cohort genome wide association studies, a myriad of genetic risk loci has been linked to different forms of glaucoma. Animal models have been an indispensable tool in characterizing these loci, especially if they lie within coding regions in the genome. Not only do these models connect genotype to phenotype, advancing our understanding of glaucoma pathogenesis in the process, they also have valuable utility as a platform for the pre-clinical testing of potential therapies. In this review, we will outline genetic models used for studying the major forms of glaucoma, including primary open angle glaucoma, normal tension glaucoma, primary angle closure glaucoma, pigmentary glaucoma, pseudoexfoliation glaucoma, and early onset glaucoma, including congenital and developmental glaucoma, and how studying these models have helped shed light on human glaucoma.
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Affiliation(s)
- Yunhua Loo
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Anita Sook Yee Chan
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Chiea Chuen Khor
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Tin Aung
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Zhenxun Wang
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.
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16
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Kondkar AA, Sultan T, Azad TA, Khatlani T, Alshehri AA, Osman EA, Lobo GP, Almobarak FA, Al-Obeidan SA. Common Variants rs429358 and rs7412 in APOE Gene Are Not Associated with POAG in a Saudi Cohort. BIOLOGY 2024; 13:62. [PMID: 38275738 PMCID: PMC10813158 DOI: 10.3390/biology13010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Adult-onset glaucoma, an age-related neurodegenerative disease, is very prevalent among the elderly Arabs of Saudi origin. This study investigated the association between apolipoprotein E (APOE) gene variants (rs429358 and rs7412) and primary open-angle glaucoma (POAG) in Arabs of Saudi origin. A case-control genetic association study involving 179 POAG patients and 251 controls utilized Sanger sequencing to genotype APOE gene variants. The allele frequencies and genotype distributions for rs429358 and rs7412 did not show significant associations with POAG. The haplotype analysis revealed apoε3 (87.6% and 87.4%) as the most prevalent, followed by ε4 (2.8% and 3.6%) and ε2 (9.6% and 8.9%) in the controls and POAG patients, respectively. Although the ε2/ε3 genotype and ε2-carriers displayed a more than two-fold increased risk, statistical significance was not reached. Notably, these polymorphisms did not affect clinical markers, such as intraocular pressure and cup/disc ratio. The logistic regression analysis demonstrated no significant influence of age, sex, rs429358, or rs7412 polymorphisms on POAG. In conclusion, within the Saudi cohort, APOE variants (rs429358 and rs7412) do not appear to be associated with POAG and are not substantial risk factors for its development. However, additional population-based studies are required to validate these findings.
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Affiliation(s)
- Altaf A. Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
- Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia
- King Saud University Medical City, King Saud University, Riyadh 11411, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
| | - Taif A. Azad
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
| | - Tanvir Khatlani
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University of Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia;
| | - Abdulaziz A. Alshehri
- Department of Ophthalmology, Imam Abdulrahman Alfaisal Hospital, Riyadh 14723, Saudi Arabia;
| | - Essam A. Osman
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
| | - Glenn P. Lobo
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55347, USA;
| | - Faisal A. Almobarak
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
| | - Saleh A. Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia; (T.S.); (T.A.A.); (E.A.O.); (F.A.A.); (S.A.A.-O.)
- Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia
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17
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Milla E, Laguna J, Alforja MS, Pascual B, Gamundi MJ, Borràs E, Hernán I, Muniesa MJ, Pazos M, Duch S, Carballo M, Jodar M. Next-generation sequencing-based gene panel tests for the detection of rare variants and hypomorphic alleles associated with primary open-angle glaucoma. PLoS One 2024; 19:e0282133. [PMID: 38241218 PMCID: PMC10798505 DOI: 10.1371/journal.pone.0282133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is a complex disease with a strong hereditably component. Several genetic variants have recently been associated with POAG, partially due to technological improvements such as next-generation sequencing (NGS). The aim of this study was to genetically analyze patients with POAG to determine the contribution of rare variants and hypomorphic alleles associated with glaucoma as a future method of diagnosis and early treatment. Seventy-two genes potentially associated with adult glaucoma were studied in 61 patients with POAG. Additionally, we sequenced the coding sequence of CYP1B1 gene in 13 independent patients to deep analyze the potential association of hypomorphic CYP1B1 alleles in the pathogenesis of POAG. We detected nine rare variants in 16% of POAG patients studied by NGS. Those rare variants are located in CYP1B1, SIX6, CARD10, MFN1, OPTC, OPTN, and WDR36 glaucoma-related genes. Hypomorphic variants in CYP1B1 and SIX6 genes have been identified in 8% of the total POAG patient assessed. Our findings suggest that NGS could be a valuable tool to clarify the impact of genetic component on adult glaucoma. However, in order to demonstrate the contribution of these rare variants and hypomorphic alleles to glaucoma, segregation and functional studies would be necessary. The identification of new variants and hypomorphic alleles in glaucoma patients will help to configure the genetic identity of these patients, in order to make an early and precise molecular diagnosis.
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Affiliation(s)
- Elena Milla
- Glaucoma Unit, Department of Ophthalmology, ICOF, Hospital Clínic de Barcelona, Barcelona, Spain
- Innova Ocular-ICO, Barcelona, Spain
| | - Javier Laguna
- Department of Biochemistry and Molecular Genetics, CDB, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Mª. Socorro Alforja
- Glaucoma Unit, Department of Ophthalmology, ICOF, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Beatriz Pascual
- Molecular Genetics Unit, Hospital de Terrassa, Barcelona, Spain
| | | | - Emma Borràs
- Molecular Genetics Unit, Hospital de Terrassa, Barcelona, Spain
| | - Imma Hernán
- Molecular Genetics Unit, Hospital de Terrassa, Barcelona, Spain
| | - María Jesús Muniesa
- Glaucoma Unit, Department of Ophthalmology, ICOF, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Marta Pazos
- Glaucoma Unit, Department of Ophthalmology, ICOF, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Miguel Carballo
- Molecular Genetics Unit, Hospital de Terrassa, Barcelona, Spain
| | - Meritxell Jodar
- Department of Biochemistry and Molecular Genetics, CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Department of Biomedicine, Faculty of Medicine and Biomedical Sciences, University of Barcelona, Barcelona, Spain
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18
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Mbatchou J, McPeek MS. JASPER: fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571948. [PMID: 38187553 PMCID: PMC10769254 DOI: 10.1101/2023.12.18.571948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Joint association analysis of multiple traits with multiple genetic variants can provide insight into genetic architecture and pleiotropy, improve trait prediction and increase power for detecting association. Furthermore, some traits are naturally high-dimensional, e.g., images, networks or longitudinally measured traits. Assessing significance for multitrait genetic association can be challenging, especially when the sample has population sub-structure and/or related individuals. Failure to adequately adjust for sample structure can lead to power loss and inflated type 1 error, and commonly used methods for assessing significance can work poorly with a large number of traits or be computationally slow. We developed JASPER, a fast, powerful, robust method for assessing significance of multitrait association with a set of genetic variants, in samples that have population sub-structure, admixture and/or relatedness. In simulations, JASPER has higher power, better type 1 error control, and faster computation than existing methods, with the power and speed advantage of JASPER increasing with the number of traits. JASPER is potentially applicable to a wide range of association testing applications, including for multiple disease traits, expression traits, image-derived traits and microbiome abundances. It allows for covariates, ascertainment and rare variants and is robust to phenotype model misspecification. We apply JASPER to analyze gene expression in the Framingham Heart Study, where, compared to alternative approaches, JASPER finds more significant associations, including several that indicate pleiotropic effects, some of which replicate previous results, while others have not previously been reported. Our results demonstrate the promise of JASPER for powerful multitrait analysis in structured samples.
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Affiliation(s)
- Joelle Mbatchou
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
- Department of Statistics, The University of Chicago, Chicago, IL 60637, USA
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, IL 60637, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
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19
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Stuart KV, Khawaja AP. Genomics enabling personalised glaucoma care. Br J Ophthalmol 2023; 108:5-9. [PMID: 37989536 DOI: 10.1136/bjo-2023-324618] [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: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 11/23/2023]
Abstract
Glaucoma is a leading cause of visual impairment and a significant public health concern, but despite ongoing advances in our understanding of the disease, several important clinical challenges remain. With the number of affected people projected to increase substantially over coming decades, novel approaches to screening, risk stratification, therapy and glaucoma research are essential to deal with this expanding burden in an efficient and cost-effective manner. Genomics may hold the key to unlocking further biological insights and enabling precision medicine, in which glaucoma care is tailored to the individual patient, based on their unique profile for disease. Here, we provide an overview of how genomics may enable cost-effective targeted population screening and personalised predictions of risk, response to treatment and effective lifestyle advice. Given rapid advances in genetic testing technology and a move towards population-level genotyping, these early results have several important implications that promise to revolutionise the way in which glaucoma is detected and managed in years to come.
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Affiliation(s)
- Kelsey V Stuart
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
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20
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Pandino I, Giammaria S, Zingale GA, Roberti G, Michelessi M, Coletta M, Manni G, Agnifili L, Vercellin AV, Harris A, Oddone F, Sbardella D. Ubiquitin proteasome system and glaucoma: A survey of genetics and molecular biology studies supporting a link with pathogenic and therapeutic relevance. Mol Aspects Med 2023; 94:101226. [PMID: 37950974 DOI: 10.1016/j.mam.2023.101226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 11/13/2023]
Abstract
Glaucoma represents a group of progressive neurodegenerative diseases characterized by the loss of retinal ganglion cells (RGCs) and their axons with subsequent visual field impairment. The disease develops through largely uncharacterized molecular mechanisms, that are likely to occur in different localized cell types, either in the anterior (e.g., trabecular meshwork cells) or posterior (e.g., Muller glia, retinal ganglion cells) segments of the eye. Genomic and preclinical studies suggest that glaucoma pathogenesis may develop through altered ubiquitin (Ub) signaling. Ubiquitin conjugation, referred to as ubiquitylation, is a major post-synthetic modification catalyzed by E1-E2-E3 enzymes, that profoundly regulates the turnover, trafficking and biological activity of the targeted protein. The development of new technologies, including proteomics workflows, allows the biology of ubiquitin signaling to be described in health and disease. This post-translational modification is emerging as a key role player in neurodegeneration, gaining relevance for novel therapeutic options, such as in the case of Proteolysis Targeting Chimeras technology. Although scientific evidence supports a link between Ub and glaucoma, their relationship is still not well-understood. Therefore, this review provides a detailed research-oriented discussion on current evidence of Ub signaling in glaucoma. A review of genomic and genetic data is provided followed by an in-depth discussion of experimental data on ASB10, parkin and optineurin, which are proteins that play a key role in Ub signaling and have been associated with glaucoma.
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Affiliation(s)
| | | | | | | | | | | | - Gianluca Manni
- IRCCS Fondazione Bietti, Rome, Italy; DSCMT University of Tor Vergata, Rome, Italy
| | - Luca Agnifili
- Ophthalmology Clinic, Department of Medicine and Aging Science, University "G. D'Annunzio" of Chieti-Pescara, Italy
| | | | - Alon Harris
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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21
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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