1
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Rämö JT, Gorman BR, Weng LC, Jurgens SJ, Singhanetr P, Tieger MG, van Dijk EH, Halladay CW, Wang X, Hauser BM, Kim SH, Brinks J, Choi SH, Luo Y, Pyarajan S, Nealon CL, Gorin MB, Wu WC, Anthony SA, Roncone DP, 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 PTPRB is associated with central serous chorioretinopathy, varicose veins and glaucoma. Nat Commun 2025; 16:4127. [PMID: 40319023 PMCID: PMC12049426 DOI: 10.1038/s41467-025-58686-6] [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: 05/13/2024] [Accepted: 03/28/2025] [Indexed: 05/07/2025] Open
Abstract
Central serous chorioretinopathy is an eye disease characterized by fluid buildup under the central retina whose etiology is not well understood. Abnormal choroidal veins in central serous chorioretinopathy patients have been shown to have similarities with varicose veins. To identify potential mechanisms, we analyzed genotype data from 1,477 patients and 455,449 controls in FinnGen. We identified an association for a low-frequency (allele frequency = 0.5%) missense variant (rs113791087) in PTPRB, the gene encoding vascular endothelial protein tyrosine phosphatase (odds ratio=2.85, P = 4.5 × 10-9). This was confirmed in a meta-analysis of 2,452 patients and 865,767 controls from 4 studies (odds ratio=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 increased risk of varicose veins (odds ratio=1.31, P = 2.3 × 10-11) and reduced risk of glaucoma (odds ratio=0.82, P = 6.9 × 10-9). Predicted loss-of-function variants in PTPRB, though rare in number, were associated with central serous chorioretinopathy in All of Us (odds ratio=17.09, P = 0.018). These findings highlight the significance of vascular endothelial protein tyrosine phosphatase in diverse ocular and systemic veno-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 R 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 Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, 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
| | - Blake M Hauser
- Massachusetts Eye and Ear, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Soo Hyun Kim
- Massachusetts Eye and Ear, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, 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
| | - Scott A Anthony
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
| | - David P Roncone
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, OH, 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, Leiden University Medical Center, Leiden, The Netherlands
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, 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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2
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Rivas MA, Chang C. Efficient storage and regression computation for population-scale genome sequencing studies. Bioinformatics 2025; 41:btaf067. [PMID: 39932865 PMCID: PMC11893150 DOI: 10.1093/bioinformatics/btaf067] [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: 07/24/2024] [Revised: 01/07/2025] [Accepted: 02/06/2025] [Indexed: 02/13/2025] Open
Abstract
MOTIVATION The growing availability of large-scale population biobanks has the potential to significantly advance our understanding of human health and disease. However, the massive computational and storage demands of whole genome sequencing (WGS) data pose serious challenges, particularly for underfunded institutions or researchers in developing countries. This disparity in resources can limit equitable access to cutting-edge genetic research. RESULTS We present novel algorithms and regression methods that dramatically reduce both computation time and storage requirements for WGS studies, with particular attention to rare variant representation. By integrating these approaches into PLINK 2.0, we demonstrate substantial gains in efficiency without compromising analytical accuracy. In an exome-wide association analysis of 19.4 million variants for the body mass index phenotype in 125 077 individuals (AllofUs project data), we reduced runtime from 695.35 min (11.5 h) on a single machine to 1.57 min with 30 GB of memory and 50 threads (or 8.67 min with 4 threads). Additionally, the framework supports multi-phenotype analyses, further enhancing its flexibility. AVAILABILITY AND IMPLEMENTATION Our optimized methods are fully integrated into PLINK 2.0 and can be accessed at: https://www.cog-genomics.org/plink/2.0/.
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Affiliation(s)
- Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, United States
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3
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Rivas MA, Chang C. Efficient storage and regression computation for population-scale genome sequencing studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.04.11.589062. [PMID: 38659813 PMCID: PMC11042230 DOI: 10.1101/2024.04.11.589062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In the era of big data in human genetics, large-scale biobanks aggregating genetic data from diverse populations have emerged as important for advancing our understanding of human health and disease. However, the computational and storage demands of whole genome sequencing (WGS) studies pose significant challenges, especially for researchers from underfunded institutions or developing countries, creating a disparity in research capabilities. We introduce new approaches that significantly enhance computational efficiency and reduce data storage requirements for WGS studies. By developing algorithms for compressed storage of genetic data, focusing particularly on optimizing the representation of rare variants, and designing regression methods tailored for the scale and complexity of WGS data, we significantly lower computational and storage costs. We integrate our approach into PLINK 2.0. The implementation demonstrates considerable reductions in storage space and computational time without compromising analytical accuracy, as evidenced by the application to the AllofUs project data. We optimized the runtime of an exome-wide association analysis involving 19.4 million variants and the body mass index phenotype of 125,077 individuals, reducing it from 695.35 minutes (approximately 11.5 hours) on a single machine to just 1.57 minutes using 30 GB of memory and 50 threads (or 8.67 minutes with 4 threads). Additionally, we extended this approach to support multi-phenotype analyses. We anticipate that our approach will enable researchers across the globe to unlock the potential of population biobanks, accelerating the pace of discoveries that can improve our understanding of human health and disease.
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Affiliation(s)
- Manuel A. Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA 94305
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Moujane F, Zhang C, Knight R, Lee JY, Deng SX, Zheng JJ. Corneal Stromal Stem Cell-Derived Extracellular Vesicles Attenuate ANGPTL7 Expression in the Human Trabecular Meshwork. Transl Vis Sci Technol 2025; 14:21. [PMID: 39847376 PMCID: PMC11759583 DOI: 10.1167/tvst.14.1.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 12/16/2024] [Indexed: 01/30/2025] Open
Abstract
Purpose Regulating intraocular pressure (IOP), mainly via the trabecular meshwork (TM), is critical in developing glaucoma. Whereas current treatments aim to lower IOP, directly targeting the dysfunctional TM tissue for therapeutic intervention has proven challenging. In our study, we utilized Dexamethasone (Dex)-treated TM cells as a model to investigate how extracellular vesicles (EVs) from immortalized corneal stromal stem cells (imCSSCs) could influence ANGPTL7 and MYOC genes expression within TM cells. Methods Human TM cell lines were isolated and cultured from donor corneoscleral rims. EVs were purified from imCSSC conditioned media (CM) using size exclusion chromatography and characterized by nanoparticle tracking analysis, transmission electron microscopy (TEM), and ExoView technology. TM cells were treated with either Dex alone or with EVs for 5 days. Quantitative polymerase chain reaction (PCR) was carried out to quantify the mRNA level of MYOC and ANGPTL7. Results A notable increase in the expression levels of MYOC and ANGPTL7 genes was observed compared with untreated TM cells (control). Furthermore, upon comparing Dex-treated TM cells with those receiving both Dex and EV treatments, a statistically significant reduction in ANGPTL7 expression (P < 0.05) was detected. Conclusions The present study demonstrates that imCSSCs-derived EVs can effectively decrease the expression of ANGPLT7, a gene associated with fibrosis and implicated in the abnormal elevation of IOP in patients with glaucoma. Translational Relevance Our study shows that imCSSC-derived EVs can specifically target ANGPTL7 expression, making them a promising preclinical therapy for glaucoma.
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Affiliation(s)
- Faycal Moujane
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Ophthalmology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Chi Zhang
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Robert Knight
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - John Y. Lee
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sophie X. Deng
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Jie J. Zheng
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
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5
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Tanigawa Y, Kellis M. Hypometric genetics: Improved power in genetic discovery by incorporating quality control flags. Am J Hum Genet 2024; 111:2478-2493. [PMID: 39442521 PMCID: PMC11568753 DOI: 10.1016/j.ajhg.2024.09.008] [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: 05/02/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/25/2024] Open
Abstract
Balancing the tradeoff between quantity and quality of phenotypic data is critical in omics studies. Measurements below the limit of quantification (BLQ) are often tagged in quality control fields, but these flags are currently underutilized in human genetics studies. Extreme phenotype sampling is advantageous for mapping rare variant effects. We hypothesize that genetic drivers, along with environmental and technical factors, contribute to the presence of BLQ flags. Here, we introduce "hypometric genetics" (hMG) analysis and uncover a genetic basis for BLQ flags, indicating an additional source of genetic signal for genetic discovery, especially from phenotypic extremes. Applying our hMG approach to n = 227,469 UK Biobank individuals with metabolomic profiles, we reveal more than 5% heritability for BLQ flags and report biologically relevant associations, for example, at APOC3, APOA5, and PDE3B loci. For common variants, polygenic scores trained only for BLQ flags predict the corresponding quantitative traits with 91% accuracy, validating the genetic basis. For rare coding variant associations, we find an asymmetric 65.4% higher enrichment of metabolite-lowering associations for BLQ flags, highlighting the impact of putative loss-of-function variants with large effects on phenotypic extremes. Joint analysis of binarized BLQ flags and the corresponding quantitative metabolite measurements improves power in Bayesian rare variant aggregation tests, resulting in an average of 181% more prioritized genes. Our approach is broadly applicable to omics profiling. Overall, our results underscore the benefit of integrating quality control flags and quantitative measurements and highlight the advantage of joint analysis of population-based samples and phenotypic extremes in human genetics studies.
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Affiliation(s)
- Yosuke Tanigawa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke AE, Ganel L, Hawes A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Di Gioia A, Rajagopal VM, Lopez A, Varela JR, Alegre-Díaz J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton JD, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalogue of protein-coding variation in 983,578 individuals. Nature 2024; 631:583-592. [PMID: 38768635 PMCID: PMC11254753 DOI: 10.1038/s41586-024-07556-0] [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: 06/19/2023] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of which have not been previously reported. From precise quantitative estimates of selection against heterozygous loss of function (LOF), we identify 3,988 LOF-intolerant genes, including 86 that were previously assessed as tolerant and 1,153 that lack established disease annotation. We also define regions of missense depletion at high resolution. Notably, 1,482 genes have regions that are depleted of missense variants despite being tolerant of pLOF variants. Finally, we estimate that 3% of individuals have a clinically actionable genetic variant, and that 11,773 variants reported in ClinVar with unknown significance are likely to be deleterious cryptic splice sites. To facilitate variant interpretation and genetics-informed precision medicine, we make this resource of coding variation from the RGC-ME dataset publicly accessible through a variant allele frequency browser.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Liron Ganel
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Jesús Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Jaime Berumen
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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7
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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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8
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Brown SFK, Nguyen H, Mzyk P, De Ieso ML, Unser AM, Brown I, Ramesh P, Afzaal H, Ahmed F, Torrejon KY, Nhan A, Markrush D, Daly T, Knecht E, McConaughy W, Halmos S, Liu ZL, Rennard R, Peterson A, Stamer WD. ANGPTL7 and Its Role in IOP and Glaucoma. Invest Ophthalmol Vis Sci 2024; 65:22. [PMID: 38497513 PMCID: PMC10950037 DOI: 10.1167/iovs.65.3.22] [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: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
Purpose Loss-of-function variants in the ANGPTL7 gene are associated with protection from glaucoma and reduced intraocular pressure (IOP). We investigated the role of ANGPTL7 in IOP homeostasis and its potential as a target for glaucoma therapeutics. Methods IOP, outflow facility, and outflow tissue morphology of Angptl7 knockout (KO) mice were assessed with and without dexamethasone (Dex). ANGPTL7 was quantified in conditioned media from human trabecular meshwork cells in response to Dex, in effluent from perfused human donor eyes, and in aqueous humor from human patients treated with steroids. Antibodies to ANGPTL7 were generated and tested in three-dimensional (3D) culture of outflow cells and perfused human donor eyes. Rabbits were injected intravitreally with a neutralizing antibody targeting ANGPTL7, and IOP was measured. Results IOP was significantly elevated, but outflow facility and outflow tissue morphology were not different between Angptl7 KO mice and littermates. When challenged with Dex, IOP increased in wild-type but not Angptl7 KO mice. In human samples, increased ANGPTL7 was seen in the aqueous humor of patients treated with steroids, regardless of glaucoma status. Using 3D culture, recombinant ANGPTL7 decreased, and ANGPTL7-blocking antibodies increased hydraulic conductivity. Significantly, outflow facility increased in human eyes treated ex vivo with ANGPTL7-blocking antibodies, and IOP decreased for 21 days in rabbits after a single injection of blocking antibodies. Conclusions Using multiple models, we have demonstrated that excess ANGPTL7 increases outflow resistance and IOP and that neutralizing ANGPTL7 has beneficial effects in both naïve and steroid-induced hypertensive eyes, thus motivating the development of ANGPTL7-targeting therapeutics for the treatment of glaucoma.
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Affiliation(s)
| | - Hien Nguyen
- Broadwing Bio, Waltham, Massachusetts, United States
| | - Philip Mzyk
- Duke University, Durham, North Carolina, United States
| | | | | | - Ian Brown
- Broadwing Bio, Waltham, Massachusetts, United States
| | | | - Hira Afzaal
- Humonix Biosciences, Albany, New York, United States
| | - Feryan Ahmed
- Humonix Biosciences, Albany, New York, United States
| | | | - Alan Nhan
- Alloy Therapeutics, Waltham, Massachusetts, United States
| | | | - Tom Daly
- Alloy Therapeutics, Waltham, Massachusetts, United States
| | - Ellie Knecht
- Alloy Therapeutics, Waltham, Massachusetts, United States
| | | | - Sara Halmos
- Alloy Therapeutics, Waltham, Massachusetts, United States
| | | | - Rachel Rennard
- Alloy Therapeutics, Waltham, Massachusetts, United States
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9
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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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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10
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Xiao X, Chen CB, Wu Z, Ye Y, Deng F, Cao Y, Liu P, Zhang M. Novel mutation in EFEMP1 identified from two Chinese POAG families differentially activated endoplasmic reticulum stress markers and induced glaucoma in mouse. J Cell Biochem 2024; 125:45-58. [PMID: 38083999 DOI: 10.1002/jcb.30466] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 01/16/2024]
Abstract
Primary open-angle glaucoma (POAG) is the most common type of glaucoma. Using whole-exome sequencing, we identified two independent families diagnosed as POAG from the China with a novel EFEMP1 variant (Exon3, c.175A>C p.Met59Leu); Three previously reported variants c.1160G>A p.R387Q, c.1189T>C p.Y397H, and c.1429C>T p.R477C in EFEPM1 from 55 sporadic POAG individuals were also identified. The variant c.175A>C p.Met59Leu co-segregated with the disease phenotype within the families. Immunoprecipitation and western blot assays showed that all three EFEMP1 mutants (p.Met59Leu, pArg140Trp, pArg345Trp) increased intracellular protein aggregations, and pMet59Leu and pArg140Arg also enhanced their extracellular proteins secretion, compared to WT in HEK293T. The differential regulations to endoplasmic reticulum (ER) stress markers ATF4, GPR78/94, and CHOP, and differential phosphorylation activations to CREB at Ser133, AKT at Ser473, p44/42 at Thr202/Tyr204, and STAT3 at Tyr705, were also detected among the mutants and WT. Finally, we revealed a significant increment of intraocular pressure and obvious reduction of RGC cells at the sixth week following intravitreal injection of adenovirus 5 (Ad5) expressing in pMet59Leu compared to WT and GFP controls. Together, variant c.175A>C p.Met59Leu in EFEMP1 is pathogenic and different mutants in EFEMP1 triggered distinct signaling pathways, explaining the reason of mutation-dependent disease phenotypes of EFEMP1.
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Affiliation(s)
- Xiaoqiang Xiao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Chong-Bo Chen
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Zhenggen Wu
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Yuhang Ye
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Fang Deng
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Yingjie Cao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Pingting Liu
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
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11
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Sharif NA. Gene therapies and gene product-based drug candidates for normalizing and preserving tissue functions in animal models of ocular hypertension and glaucoma. Mol Aspects Med 2023; 94:101218. [PMID: 37976898 DOI: 10.1016/j.mam.2023.101218] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/01/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
More than 76 million people worldwide are afflicted with the neurodegenerative eye diseases described and grouped together as glaucoma. A common feature amongst the many forms of glaucoma is chronically elevated intraocular pressure (IOP) within the anterior chamber of the eye that physically damages the retina, optic nerve and parts of the brain connected with visual perception. The mediators of the contusing raised IOP responsible for such damage and loss of vision include locally released inflammatory agents, tissue remodeling enzymes and infiltrating immune cells which damage the retinal ganglion cell (RGC) axons and eventually kill a significant number of the RGCs. Additional culprits include genetic defects of the patient that involve aberrations in receptors, enzymes and/or endogenous ligands and possible over- or under-production of the latter. Other genetic abnormalities may include issues with signal transduction machinery within key cells of critical tissues in the front (e.g. trabecular meshwork [TM] and Schlemm's canal [SC]) and back of the eye (e.g. retinal ganglion cells and their axons). Genome-wide associated studies (GWAS) coupled with next generation sequencing have provided powerful linkage of certain gene defects and polymorphic variants to the onset and progression of diseases of the tissues involved in fluid dynamics in the TM and SC, and many retinal elements (lamina cribosa, optic nerve head) at the back of the eye which cause ocular hypertension (OHT) and glaucomatous optic neuropathy (GON), respectively. Despite the availability of some drugs, fluid drainage microshunts and full surgical techniques to lower and control intraocular pressure, the major modifiable biomarker of open-angle and other forms of glaucoma, their side-effect profiles, less than optimum effectiveness and short duration of action present opportunities to clinically manage the glaucomas with next generation of treatments with high therapeutic indices, including gene therapies. Thus, identification, characterization and deployment of genetic data coupled with traditional drug discovery and novel gene replacement, gene editing and genetic engineering technologies may provide some solutions to the aforementioned problems. These aspects will be discussed in this article.
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Affiliation(s)
- Najam A Sharif
- Eye-APC Duke-NUS Medical School, Singapore, 169856, Singapore; Institute of Ophthalmology, University College London, London, W2 1PG, UK; Imperial College of Science and Technology, St. Mary's Campus, London, WC1E 6BT, UK; Department of Pharmacy Sciences, Creighton University, Omaha, NE, 68178, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, 77004, USA; Department of Pharmacology and Neuroscience, University of North Texas Health Sciences Center, Fort Worth, TX, 76107, USA; Singapore Eye Research Institute, Singapore, 169856, Singapore; Global Research & Development, Nanoscope Therapeutics Inc., Dallas, TX 75207, USA.
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12
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Thorin E, Labbé P, Lambert M, Mury P, Dagher O, Miquel G, Thorin-Trescases N. Angiopoietin-Like Proteins: Cardiovascular Biology and Therapeutic Targeting for the Prevention of Cardiovascular Diseases. Can J Cardiol 2023; 39:1736-1756. [PMID: 37295611 DOI: 10.1016/j.cjca.2023.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Despite the best pharmacologic tools available, cardiovascular diseases (CVDs) remain a major cause of morbidity and mortality in developed countries. After 2 decades of research, new therapeutic targets, such as angiopoietin-like proteins (ANGPTLs), are emerging. ANGPTLs belong to a family of 8 members, from ANGPTL1 to ANGPTL8; they have structural homology with angiopoietins and are secreted in the circulation. ANGPTLs display a multitude of physiological and pathologic functions; they contribute to inflammation, angiogenesis, cell death, senescence, hematopoiesis, and play a role in repair, maintenance, and tissue homeostasis. ANGPTLs-particularly the triad ANGPTL3, 4, and 8-have an established role in lipid metabolism through the regulation of triacylglycerol trafficking according to the nutritional status. Some ANGPTLs also contribute to glucose metabolism. Therefore, dysregulation in ANGPTL expression associated with abnormal circulating levels are linked to a plethora of CVD and metabolic disorders including atherosclerosis, heart diseases, diabetes, but also obesity and cancers. Because ANGPTLs bind to different receptors according to the cell type, antagonists are therapeutically inadequate. Recently, direct inhibitors of ANGPTLs, mainly ANGPTL3, have been developed, and specific monoclonal antibodies and antisense oligonucleotides are currently being tested in clinical trials. The aim of the current review is to provide an up-to-date preclinical and clinical overview on the function of the 8 members of the ANGPTL family in the cardiovascular system, their contribution to CVD, and the therapeutic potential of manipulating some of them.
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Affiliation(s)
- Eric Thorin
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada; Faculty of Medicine, Department of Pharmacology, Université de Montréal, Montréal, Québec, Canada; Faculty of Medicine, Department of Surgery, Université de Montréal, Montréal, Québec, Canada.
| | - Pauline Labbé
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Mélanie Lambert
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada; Faculty of Medicine, Department of Pharmacology, Université de Montréal, Montréal, Québec, Canada
| | - Pauline Mury
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada; Faculty of Medicine, Department of Pharmacology, Université de Montréal, Montréal, Québec, Canada
| | - Olina Dagher
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada; Faculty of Medicine, Department of Surgery, Université de Montréal, Montréal, Québec, Canada; Department of Cardiac Sciences, Libin Cardiovascular Institute, Calgary, Alberta, Canada
| | - Géraldine Miquel
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
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13
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Tanigawa Y, Kellis M. Power of inclusion: Enhancing polygenic prediction with admixed individuals. Am J Hum Genet 2023; 110:1888-1902. [PMID: 37890495 PMCID: PMC10645553 DOI: 10.1016/j.ajhg.2023.09.013] [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: 01/23/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Admixed individuals offer unique opportunities for addressing limited transferability in polygenic scores (PGSs), given the substantial trans-ancestry genetic correlation in many complex traits. However, they are rarely considered in PGS training, given the challenges in representing ancestry-matched linkage-disequilibrium reference panels for admixed individuals. Here we present inclusive PGS (iPGS), which captures ancestry-shared genetic effects by finding the exact solution for penalized regression on individual-level data and is thus naturally applicable to admixed individuals. We validate our approach in a simulation study across 33 configurations with varying heritability, polygenicity, and ancestry composition in the training set. When iPGS is applied to n = 237,055 ancestry-diverse individuals in the UK Biobank, it shows the greatest improvements in Africans by 48.9% on average across 60 quantitative traits and up to 50-fold improvements for some traits (neutrophil count, R2 = 0.058) over the baseline model trained on the same number of European individuals. When we allowed iPGS to use n = 284,661 individuals, we observed an average improvement of 60.8% for African, 11.6% for South Asian, 7.3% for non-British White, 4.8% for White British, and 17.8% for the other individuals. We further developed iPGS+refit to jointly model the ancestry-shared and -dependent genetic effects when heterogeneous genetic associations were present. For neutrophil count, for example, iPGS+refit showed the highest predictive performance in the African group (R2 = 0.115), which exceeds the best predictive performance for the White British group (R2 = 0.090 in the iPGS model), even though only 1.49% of individuals used in the iPGS training are of African ancestry. Our results indicate the power of including diverse individuals for developing more equitable PGS models.
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Affiliation(s)
- Yosuke Tanigawa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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Moon CE, Kim CH, Jung JH, Cho YJ, Choi KY, Han K, Seo KY, Lee HK, Ji YW. Integrated Analysis of Transcriptome and Proteome of the Human Cornea and Aqueous Humor Reveal Novel Biomarkers for Corneal Endothelial Cell Dysfunction. Int J Mol Sci 2023; 24:15354. [PMID: 37895034 PMCID: PMC10607268 DOI: 10.3390/ijms242015354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Earlier studies have reported that elevated protein levels in the aqueous humor (AH) are associated with corneal endothelial cell dysfunction (CECD), but the details of the underlying mechanism as well as specific biomarkers for CECD remain elusive. In the present study, we aimed to identify protein markers in AH directly associated with changes to corneal endothelial cells (CECs), as AH can be easily obtained for analysis. We carried out an in-depth proteomic analysis of patient-derived AH as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. We first determined differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) from CECs and AH in CECD, respectively. By combining transcriptomic and proteomic analyses, 13 shared upregulated markers and 22 shared downregulated markers were observed between DEGs and DEPs. Among these 35 candidates from biomarker profiling, three upregulated markers were finally verified via data-independent acquisition (DIA) proteomic analysis using additional individual AH samples, namely metallopeptidase inhibitor 1 (TIMP1), Fc fragment of IgG binding protein (FCGBP), and angiopoietin-related protein 7 (ANGPTL7). Furthermore, we confirmed these AH biomarkers for CECD using individual immunoassay validation. Conclusively, our findings may provide valuable insights into the disease process and identify biofluid markers for the assessment of CEC function during BK development.
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Affiliation(s)
- Chae-Eun Moon
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
| | - Chang Hwan Kim
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
- Department of Ophthalmology, Yongin Severance Hospital, Yongin 16995, Republic of Korea
| | - Jae Hun Jung
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Young Joo Cho
- The Yonsei Eye Clinic, Seoul 06289, Republic of Korea
- Department of Ophthalmology, HanGil Eye Hospital, Incheon 21388, Republic of Korea
| | - Kee Yong Choi
- Department of Ophthalmology, HanGil Eye Hospital, Incheon 21388, Republic of Korea
| | - Kyusun Han
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
| | - Kyoung Yul Seo
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
| | - Hyung Keun Lee
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
- Department of Ophthalmology, Gangnam Severance Hospital, Seoul 06273, Republic of Korea
- College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Yong Woo Ji
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (C.-E.M.)
- Department of Ophthalmology, Yongin Severance Hospital, Yongin 16995, Republic of Korea
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15
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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16
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Aboobakar IF, Collantes ERA, Hauser MA, Stamer WD, Wiggs JL. Rare protective variants and glaucoma-relevant cell stressors modulate Angiopoietin-like 7 expression. Hum Mol Genet 2023; 32:2523-2531. [PMID: 37220876 PMCID: PMC10360392 DOI: 10.1093/hmg/ddad083] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Rare missense and nonsense variants in the Angiopoietin-like 7 (ANGPTL7) gene confer protection from primary open-angle glaucoma (POAG), though the functional mechanism remains uncharacterized. Interestingly, a larger variant effect size strongly correlates with in silico predictions of increased protein instability (r = -0.98), suggesting that protective variants lower ANGPTL7 protein levels. Here, we show that missense and nonsense variants cause aggregation of mutant ANGPTL7 protein in the endoplasmic reticulum (ER) and decreased levels of secreted protein in human trabecular meshwork (TM) cells; a lower secreted:intracellular protein ratio strongly correlates with variant effects on intraocular pressure (r = 0.81). Importantly, accumulation of mutant protein in the ER does not increase expression of ER stress proteins in TM cells (P > 0.05 for all variants tested). Cyclic mechanical stress, a glaucoma-relevant physiologic stressor, also significantly lowers ANGPTL7 expression in primary cultures of human Schlemm's canal (SC) cells (-2.4-fold-change, P = 0.01). Collectively, these data suggest that the protective effects of ANGPTL7 variants in POAG stem from lower levels of secreted protein, which may modulate responses to physiologic and pathologic ocular cell stressors. Downregulation of ANGPTL7 expression may therefore serve as a viable preventative and therapeutic strategy for this common, blinding disease.
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Affiliation(s)
- Inas F Aboobakar
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Edward Ryan A Collantes
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biomedical Engineering, Duke University School of Medicine, Durham, NC 27710, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
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17
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Gao XR, Chiariglione M, Choquet H, Arch AJ. 10 Years of GWAS in intraocular pressure. Front Genet 2023; 14:1130106. [PMID: 37124618 PMCID: PMC10130654 DOI: 10.3389/fgene.2023.1130106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
Intraocular pressure (IOP) is the only modifiable risk factor for glaucoma, the leading cause of irreversible blindness worldwide. In this review, we summarize the findings of genome-wide association studies (GWASs) of IOP published in the past 10 years and prior to December 2022. Over 190 genetic loci and candidate genes associated with IOP have been uncovered through GWASs, although most of these studies were conducted in subjects of European and Asian ancestries. We also discuss how these common variants have been used to derive polygenic risk scores for predicting IOP and glaucoma, and to infer causal relationship with other traits and conditions through Mendelian randomization. Additionally, we summarize the findings from a recent large-scale exome-wide association study (ExWAS) that identified rare variants associated with IOP in 40 novel genes, six of which are drug targets for clinical treatment or are being evaluated in clinical trials. Finally, we discuss the need for future genetic studies of IOP to include individuals from understudied populations, including Latinos and Africans, in order to fully characterize the genetic architecture of IOP.
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Affiliation(s)
- Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, United States
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
- Division of Human Genetics, The Ohio State University, Columbus, OH, United States
| | - Marion Chiariglione
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, United States
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, United States
| | - Alexander J. Arch
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, United States
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18
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Yamamoto A, Huang Y, Krajina BA, McBirney M, Doak AE, Qu S, Wang CL, Haffner MC, Cheung KJ. Metastasis from the tumor interior and necrotic core formation are regulated by breast cancer-derived angiopoietin-like 7. Proc Natl Acad Sci U S A 2023; 120:e2214888120. [PMID: 36853945 PMCID: PMC10013750 DOI: 10.1073/pnas.2214888120] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 03/01/2023] Open
Abstract
Necrosis in the tumor interior is a common feature of aggressive cancers that is associated with poor clinical prognosis and the development of metastasis. How the necrotic core promotes metastasis remains unclear. Here, we report that emergence of necrosis inside the tumor is correlated temporally with increased tumor dissemination in a rat breast cancer model and in human breast cancer patients. By performing spatially focused transcriptional profiling, we identified angiopoietin-like 7 (Angptl7) as a tumor-specific factor localized to the perinecrotic zone. Functional studies showed that Angptl7 loss normalizes central necrosis, perinecrotic dilated vessels, metastasis, and reduces circulating tumor cell counts to nearly zero. Mechanistically, Angptl7 promotes vascular permeability and supports vascular remodeling in the perinecrotic zone. Taken together, these findings show that breast tumors actively produce factors controlling central necrosis formation and metastatic dissemination from the tumor core.
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Affiliation(s)
- Ami Yamamoto
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Yin Huang
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Brad A. Krajina
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Margaux McBirney
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrea E. Doak
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
| | - Sixuan Qu
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Carolyn L. Wang
- Department of Radiology, University of Washington School of Medicine, Seattle, WA98195
| | - Michael C. Haffner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98109
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Kevin J. Cheung
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
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19
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Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
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Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
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20
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Lee B, Kim JY, Ryu YC, Lee K, Choi YM. Research Note: Expression levels of collagen-related genes in PSE conditions and white striping features of broiler pectoralis major muscle. Poult Sci 2023; 102:102471. [PMID: 36709586 PMCID: PMC9922951 DOI: 10.1016/j.psj.2022.102471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to compare the meat quality characteristics and collagen-related gene expression levels in the broiler pectoralis major (PM) muscle among the meat quality groups, including normal, pale, soft, and exudative (PSE), and white striping (WS) groups. The group was classified by their WS degree (moderate or severe striping) and quality traits including pH and lightness values at 24 h postmortem (normal group: pH24 h ≥5.7, 48≤L*≤53, without WS features; PSE group: pH24 h <5.7, L* >53, without WS features; WS group: pH24 h ≥5.7, 48≤L*≤53, with moderate or severe striping). The WS group revealed no differences in all measured meat quality traits compared to the normal group (P > 0.05). PM muscles exhibiting PSE conditions without WS indicated lower pH15 min and pH24 h values (P < 0.05). Whereas, lower lightness and cooking loss values were observed in the normal and WS groups compared to the PSE group (P < 0.05). No significant difference was observed in the level of type I collagen among the groups (P > 0.05), whereas a higher type III collagen level was observed in the WS group than in the other groups (P < 0.05). Additionally, the WS group showed a higher type IV collagen level compared to the normal group (P < 0.05) and a level not different from that of the PSE group (P > 0.05). In contrast, the expression levels of matrix metalloproteinase (MMP) 2, involved in type IV collagen degradation, and angiopoietin-like protein 7, associated with collagen accumulation, were higher in the WS group compared to the normal group (P < 0.05). However, no difference was detected in the MMP1 level among the all groups (P > 0.05). These results suggest that the occurrence of WS features in broiler PM muscle, unlike PSE and normal conditions, can be influenced by the expression levels of collagen-related genes associated with abnormalities in extracellular matrix components.
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Affiliation(s)
- Boin Lee
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju-Si 37224, South Korea,Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Jae Yeong Kim
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju-Si 37224, South Korea
| | - Youn Chul Ryu
- Division of Biotechnology, SARI, Jeju National University, Jeju-Si 63243, South Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Young Min Choi
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju-Si 37224, South Korea.
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21
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Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, et alKurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, Obeidat ME, Okafo G, Ollila HM, Palomäki A, Palotie T, Partanen J, Paul DS, Pelkonen M, Pendergrass RK, Petrovski S, Pitkäranta A, Platt A, Pulford D, Punkka E, Pussinen P, Raghavan N, Rahimov F, Rajpal D, Renaud NA, Riley-Gillis B, Rodosthenous R, Saarentaus E, Salminen A, Salminen E, Salomaa V, Schleutker J, Serpi R, Shen HY, Siegel R, Silander K, Siltanen S, Soini S, Soininen H, Sul JH, Tachmazidou I, Tasanen K, Tienari P, Toppila-Salmi S, Tukiainen T, Tuomi T, Turunen JA, Ulirsch JC, Vaura F, Virolainen P, Waring J, Waterworth D, Yang R, Nelis M, Reigo A, Metspalu A, Milani L, Esko T, Fox C, Havulinna AS, Perola M, Ripatti S, Jalanko A, Laitinen T, Mäkelä TP, Plenge R, McCarthy M, Runz H, Daly MJ, Palotie A. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 2023; 613:508-518. [PMID: 36653562 PMCID: PMC9849126 DOI: 10.1038/s41586-022-05473-8] [Show More Authors] [Citation(s) in RCA: 1888] [Impact Index Per Article: 944.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
Abstract
Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored1,2. FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10-11) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.
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Affiliation(s)
- Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Kati M Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mary P Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health, University of Tampere, Tampere, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Mattsson
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Päivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Pietro Della Briotta Parolo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Arto A Lehisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Masahiro Kanai
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumar Veerapen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Zhou
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sami Koskelainen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Paajanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vincent Llorens
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Kadri Reis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Benjamin Sun
- Translational Biology, Research and Development, Biogen, Cambridge, MA, USA
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher N Foley
- Optima Partners, Edinburgh, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | | | - Olli Carpen
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Oluwaseun A Dada
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Zhihao Ding
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | | | - Kari Eklund
- Division of Rheumatology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Orton Orthopedic Hospital, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Hilary Finucane
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | - Antti Hakanen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Åsa K Hedman
- Pfizer, New York, NY, USA
- Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Mikko Hiltunen
- Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Iiris Hovatta
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Laura Huilaja
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | | | | | | | - Heikki Joensuu
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Valtteri Julkunen
- Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Marc Jung
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Juhani Junttila
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Reetta Kälviäinen
- Epilepsy Center, Kuopio University Hospital, Kuopio, Finland
- Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Terhi Kilpi
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Veli-Matti Kosma
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Teijo Kuopio
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
| | - Venla Kurra
- Department of Clinical Genetics, Tampere University Hospital, Tampere, Finland
- Department of Clinical Genetics, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jari Laukkanen
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
- Department of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, Helsinki, Finland
| | - Anders Malarstig
- Pfizer, Cambridge, MA, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - Arto Mannermaa
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | | | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Tuomo Meretoja
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Marianna Niemi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- TAUCHI Research Center & Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Turku University Hospital and University of Turku, Turku, Finland
| | | | - Ma En Obeidat
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - George Okafo
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antti Palomäki
- Turku University Hospital and University of Turku, Turku, Finland
| | - Tuula Palotie
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Helsinki, Finland
- Finnish Hematological Biobank, Helsinki, Finland
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margit Pelkonen
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anne Pitkäranta
- Department of Otorhinolaryngology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Eero Punkka
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | | | | | - Deepak Rajpal
- Translational Sciences, Sanofi R&D, Framingham, MA, USA
| | - Nicole A Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rodosthenis Rodosthenous
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Eveliina Salminen
- Helsinki University Hospital, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Johanna Schleutker
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Raisa Serpi
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sanna Siltanen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Sirpa Soini
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Ioanna Tachmazidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kaisa Tasanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sanna Toppila-Salmi
- Department of Allergy, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, Helsinki University Hospital, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Jacob C Ulirsch
- 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
| | - Felix Vaura
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- University of Turku, Turku, Finland
| | - Petri Virolainen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Mari Nelis
- Genomics Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tarja Laitinen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tomi P Mäkelä
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | | | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 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
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
- 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.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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22
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Praveen K, Patel GC, Gurski L, Ayer AH, Persaud T, Still MD, Miloscio L, Van Zyl T, Di Gioia SA, Brumpton B, Krebs K, Åsvold BO, Chen E, Chavali VRM, Fury W, Gudiseva HV, Hyde S, Jorgenson E, Lefebvre S, Li D, Li A, Mclninch J, Patel B, Rabinowitz JS, Salowe R, Schurmann C, Seidelin AS, Stahl E, Sun D, Teslovich TM, Tybjærg-Hansen A, Willer C, Waldron S, Walley S, Yang H, Zaveri S, Hu Y, Hveem K, Melander O, Milani L, Stender S, O'Brien JM, Jones MB, Abecasis GR, Cantor MN, Weyne J, Karalis K, Economides A, Della Gatta G, Ferreira MA, Yancopoulos GD, Baras A, Romano C, Coppola G. ANGPTL7, a therapeutic target for increased intraocular pressure and glaucoma. Commun Biol 2022; 5:1051. [PMID: 36192519 PMCID: PMC9529959 DOI: 10.1038/s42003-022-03932-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/01/2022] [Indexed: 12/03/2022] Open
Abstract
Glaucoma is a leading cause of blindness. Current glaucoma medications work by lowering intraocular pressure (IOP), a risk factor for glaucoma, but most treatments do not directly target the pathological changes leading to increased IOP, which can manifest as medication resistance as disease progresses. To identify physiological modulators of IOP, we performed genome- and exome-wide association analysis in >129,000 individuals with IOP measurements and extended these findings to an analysis of glaucoma risk. We report the identification and functional characterization of rare coding variants (including loss-of-function variants) in ANGPTL7 associated with reduction in IOP and glaucoma protection. We validated the human genetics findings in mice by establishing that Angptl7 knockout mice have lower (~2 mmHg) basal IOP compared to wild-type, with a trend towards lower IOP also in heterozygotes. Conversely, increasing murine Angptl7 levels via injection into mouse eyes increases the IOP. We also show that acute Angptl7 silencing in adult mice lowers the IOP (~2-4 mmHg), reproducing the observations in knockout mice. Collectively, our data suggest that ANGPTL7 is important for IOP homeostasis and is amenable to therapeutic modulation to help maintain a healthy IOP that can prevent onset or slow the progression of glaucoma.
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Affiliation(s)
| | | | - Lauren Gurski
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Ariane H Ayer
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | | | | | | | - Tavé Van Zyl
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7030, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7600, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital Trondheim University Hospital, 7030, Trondheim, Norway
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7030, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7600, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030, Trondheim, Norway
| | - Esteban Chen
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Venkata R M Chavali
- Department of Ophthalmology, Pearlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Harini V Gudiseva
- Department of Ophthalmology, Pearlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Hyde
- Alnylam Pharmaceuticals, Inc, Cambridge, MA, 02142, USA
| | | | | | - Dadong Li
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Alexander Li
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | | | | | | | - Rebecca Salowe
- Department of Ophthalmology, Pearlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudia Schurmann
- Bayer AG, Pharmaceuticals, Research and Development, 13342, Berlin, Germany
| | - Anne-Sofie Seidelin
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eli Stahl
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | | | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cristen Willer
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Scott Waldron
- Alnylam Pharmaceuticals, Inc, Cambridge, MA, 02142, USA
| | - Sabrina Walley
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Hua Yang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Sarthak Zaveri
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Ying Hu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7030, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, 7600, Levanger, Norway
| | - Olle Melander
- Lund University, Department of Clinical Sciences Malmö, Malmö, Sweden
- Skåne University Hospital, Department of Emergency and Internal Medicine, Malmö, Sweden
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stefan Stender
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joan M O'Brien
- Department of Ophthalmology, Pearlman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Jonathan Weyne
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Katia Karalis
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
| | - Aris Economides
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, 10591, USA.
| | - Carmelo Romano
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
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23
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Karczewski KJ, Solomonson M, Chao KR, Goodrich JK, Tiao G, Lu W, Riley-Gillis BM, Tsai EA, Kim HI, Zheng X, Rahimov F, Esmaeeli S, Grundstad AJ, Reppell M, Waring J, Jacob H, Sexton D, Bronson PG, Chen X, Hu X, Goldstein JI, King D, Vittal C, Poterba T, Palmer DS, Churchhouse C, Howrigan DP, Zhou W, Watts NA, Nguyen K, Nguyen H, Mason C, Farnham C, Tolonen C, Gauthier LD, Gupta N, MacArthur DG, Rehm HL, Seed C, Philippakis AA, Daly MJ, Davis JW, Runz H, Miller MR, Neale BM. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. CELL GENOMICS 2022; 2:100168. [PMID: 36778668 PMCID: PMC9903662 DOI: 10.1016/j.xgen.2022.100168] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenhan Lu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Hye In Kim
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xiuwen Zheng
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Fedik Rahimov
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Mark Reppell
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Jeff Waring
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Howard Jacob
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | | | - Xing Chen
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xinli Hu
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S. Palmer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel P. Howrigan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas A. Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Huy Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cara Mason
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Farnham
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura D. Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - J. Wade Davis
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Melissa R. Miller
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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24
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Short and long-term effect of dexamethasone on the transcriptome profile of primary human trabecular meshwork cells in vitro. Sci Rep 2022; 12:8299. [PMID: 35585182 PMCID: PMC9117214 DOI: 10.1038/s41598-022-12443-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
In the quest of identifying newer molecular targets for the management of glucocorticoid-induced ocular hypertension (GC-OHT) and glaucoma (GCG), several microarray studies have attempted to investigate the genome-wide transcriptome profiling of primary human trabecular meshwork (TM) cells in response to dexamethasone (DEX). However, no studies are reported so far to demonstrate the temporal changes in the expression of genes in the cultured human TM cells in response to DEX treatment. Therefore, in the present study, the time-dependent changes in the genome-wide expression of genes in primary human TM cells after short (16 hours: 16 h) and long exposure (7 days: 7 d) of DEX was investigated using RNA sequencing. There were 199 (118 up-regulated; 81 down-regulated) and 525 (119 up-regulated; 406 down-regulated) DEGs in 16 h and 7 d treatment groups respectively. The unique genes identified in 16 h and 7 d treatment groups were 152 and 478 respectively. This study found a distinct gene signature and pathways between two treatment regimes. Longer exposure of DEX treatment showed a dys-regulation of Wnt and Rap1 signaling and so highlighted potential therapeutic targets for pharmacological management of GC-OHT/glaucoma.
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25
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Wang Z, Wiggs JL, Aung T, Khawaja AP, Khor CC. The genetic basis for adult onset glaucoma: Recent advances and future directions. Prog Retin Eye Res 2022; 90:101066. [PMID: 35589495 DOI: 10.1016/j.preteyeres.2022.101066] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/26/2022]
Abstract
Glaucoma, a diverse group of eye disorders that results in the degeneration of retinal ganglion cells, is the world's leading cause of irreversible blindness. Apart from age and ancestry, the major risk factor for glaucoma is increased intraocular pressure (IOP). In primary open-angle glaucoma (POAG), the anterior chamber angle is open but there is resistance to aqueous outflow. In primary angle-closure glaucoma (PACG), crowding of the anterior chamber angle due to anatomical alterations impede aqueous drainage through the angle. In exfoliation syndrome and exfoliation glaucoma, deposition of white flaky material throughout the anterior chamber directly interfere with aqueous outflow. Observational studies have established that there is a strong hereditable component for glaucoma onset and progression. Indeed, a succession of genome wide association studies (GWAS) that were centered upon single nucleotide polymorphisms (SNP) have yielded more than a hundred genetic markers associated with glaucoma risk. However, a shortcoming of GWAS studies is the difficulty in identifying the actual effector genes responsible for disease pathogenesis. Building on the foundation laid by GWAS studies, research groups have recently begun to perform whole exome-sequencing to evaluate the contribution of protein-changing, coding sequence genetic variants to glaucoma risk. The adoption of this technology in both large population-based studies as well as family studies are revealing the presence of novel, protein-changing genetic variants that could enrich our understanding of the pathogenesis of glaucoma. This review will cover recent advances in the genetics of primary open-angle glaucoma, primary angle-closure glaucoma and exfoliation glaucoma, which collectively make up the vast majority of all glaucoma cases in the world today. We will discuss how recent advances in research methodology have uncovered new risk genes, and how follow up biological investigations could be undertaken in order to define how the risk encoded by a genetic sequence variant comes into play in patients. We will also hypothesise how data arising from characterising these genetic variants could be utilized to predict glaucoma risk and the manner in which new therapeutic strategies might be informed.
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Affiliation(s)
- 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.
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Tin Aung
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - 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
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26
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Tan S, Wang P, Hu J, Wang X, Li H. NEDD9 Mediates the FAK/Src Signaling Pathway to Promote the Adhesion of Human Trabecular Meshwork Cells after Dexamethasone Treatment. Curr Eye Res 2022; 47:1156-1164. [PMID: 35577404 DOI: 10.1080/02713683.2022.2071945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PURPOSE The differential gene expression of neural precursor cell expressed developmentally downregulated 9 (NEDD9) in human trabecular meshwork (HTM) cells after dexamethasone (Dex) treatment was confirmed through gene expression profiling. However, the regulatory mechanism of NEDD9 expression in HTM cells remains unknown. In this study, we investigated NEDD9 expression in HTM cells and gained a better understanding of glucocorticoid-induced glaucoma (GIG) pathophysiology. METHODS The Gene Expression Omnibus database and GEO2R tool were used to identify differentially expressed genes in the GSE37474 and GSE124114 datasets, and NEDD9 gene expression was found to be upregulated. Human corneoscleral segments and HTM cells were treated with 100 nM Dex or an equal volume of ethanol (0.01%) for 7 days. NEDD9 expression in TM tissues was evaluated by immunohistochemistry, and NEED9 expression in HTM cells was confirmed by RT-qPCR and western blotting. HTM cell adhesive behaviors were assessed with a cell adhesion detection kit. NEDD9 expression was knocked down with short hairpin RNA in HTM cells, and FAK/Src signaling pathway activation was found to be regulated by NEDD9. RESULTS After 7 days of HTM cell Dex treatment, NEDD9 expression was upregulated to be approximately twice that of control. FAK, Src, phospho-FAK, and phospho-Src expression in Dex-treated HTM cells was markedly increased. Downregulation of NEDD9 expression reduced HTM cell adhesion to the surface of culture wells and simultaneously led to a reduction in FAK, Src, phospho-FAK and phospho-Src expression. CONCLUSIONS NEDD9 expression is upregulated in HTM cells after Dex treatment and promotes HTM cell adhesion. These findings underscore the contribution of NEDD9 overexpression to altered HTM cell adhesion during glucocorticoid therapy and may play a key role in GIG pathological progression. Considering the similarity between GIG and primary open-angle glaucoma (POAG), our findings suggest that targeting NEDD9 may be a new therapeutic strategy for POAG patients.
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Affiliation(s)
- Sisi Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, P. R. China
| | - Peng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, P. R. China
| | - Jianping Hu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, P. R. China
| | - Xiaochen Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, P. R. China
| | - Hong Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, P. R. China
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27
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Irlmeier R, Hughey JJ, Bastarache L, Denny JC, Chen Q. Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. Bioinformatics 2022; 38:2297-2306. [PMID: 35157022 PMCID: PMC10060718 DOI: 10.1093/bioinformatics/btac086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/14/2021] [Accepted: 02/09/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Logistic regression models are used in genomic studies to analyze the genetic data linked to electronic health records (EHRs), and do not take full usage of the time-to-event information available in EHRs. Previous work has shown that Cox regression, which can account for left truncation and right censoring in EHRs, increased the power to detect genotype-phenotype associations compared to logistic regression. We extend this to evaluate the relative performance of Cox regression and various logistic regression models in the presence of positive errors in event time (delayed event time), relating to recorded event time accuracy. RESULTS One Cox model and three logistic regression models were considered under different scenarios of delayed event time. Extensive simulations and a genomic study application were used to evaluate the impact of delayed event time. While logistic regression does not model the time-to-event directly, various logistic regression models used in the literature were more sensitive to delayed event time than Cox regression. Results highlighted the importance to identify and exclude the patients diagnosed before entry time. Cox regression had similar or modest improvement in statistical power over various logistic regression models at controlled type I error. This was supported by the empirical data, where the Cox models steadily had the highest sensitivity to detect known genotype-phenotype associations under all scenarios of delayed event time. AVAILABILITY AND IMPLEMENTATION Access to individual-level EHR and genotype data is restricted by the IRB. Simulation code and R script for data process are at: https://github.com/QingxiaCindyChen/CoxRobustEHR.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rebecca Irlmeier
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.,Department of Biomedical Sciences, Vanderbilt University, Nashville, TN 37203, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Joshua C Denny
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qingxia Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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28
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Aboobakar IF, Wiggs JL. The genetics of glaucoma: Disease associations, personalised risk assessment and therapeutic opportunities-A review. Clin Exp Ophthalmol 2022; 50:143-162. [PMID: 35037362 DOI: 10.1111/ceo.14035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/23/2022]
Abstract
Glaucoma refers to a heterogenous group of disorders characterised by progressive loss of retinal ganglion cells and associated visual field loss. Both early-onset and adult-onset forms of the disease have a strong genetic component. Here, we summarise the known genetic associations for various forms of glaucoma and the possible functional roles for these genes in disease pathogenesis. We also discuss efforts to translate genetic knowledge into clinical practice, including gene-based tests for disease diagnosis and risk-stratification as well as gene-based therapies.
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Affiliation(s)
- Inas F Aboobakar
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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29
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Tanigawa Y, Qian J, Venkataraman G, Justesen JM, Li R, Tibshirani R, Hastie T, Rivas MA. Significant sparse polygenic risk scores across 813 traits in UK Biobank. PLoS Genet 2022; 18:e1010105. [PMID: 35324888 PMCID: PMC8946745 DOI: 10.1371/journal.pgen.1010105] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 01/05/2023] Open
Abstract
We present a systematic assessment of polygenic risk score (PRS) prediction across more than 1,500 traits using genetic and phenotype data in the UK Biobank. We report 813 sparse PRS models with significant (p < 2.5 x 10-5) incremental predictive performance when compared against the covariate-only model that considers age, sex, types of genotyping arrays, and the principal component loadings of genotypes. We report a significant correlation between the number of genetic variants selected in the sparse PRS model and the incremental predictive performance (Spearman's ⍴ = 0.61, p = 2.2 x 10-59 for quantitative traits, ⍴ = 0.21, p = 9.6 x 10-4 for binary traits). The sparse PRS model trained on European individuals showed limited transferability when evaluated on non-European individuals in the UK Biobank. We provide the PRS model weights on the Global Biobank Engine (https://biobankengine.stanford.edu/prs).
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Affiliation(s)
- Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Junyang Qian
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Guhan Venkataraman
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Johanne Marie Justesen
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Ruilin Li
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California, United States of America
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Trevor Hastie
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Manuel A. Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
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30
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Sun M, Liu W, Zhou M. ANGPTL7 is transcriptionally regulated by SP1 and modulates glucocorticoid-induced cross-linked actin networks in trabecular meshwork cells via the RhoA/ROCK pathway. Cell Death Dis 2022; 8:50. [PMID: 35136015 PMCID: PMC8826420 DOI: 10.1038/s41420-022-00847-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/18/2022]
Abstract
Glaucoma is one of the leading causes of worldwide irreversible blindness. Lowering elevated intraocular pressure (IOP) is currently the only effective approach for controlling the progress of glaucoma. Angiopoietin-like 7 (ANGPTL7) takes a key part in elevated outflow resistance of aqueous humor in dysfunctional trabecular meshwork (TM), along with the formation of cross-linked actin networks (CLANs), leading to high IOP. In this study, we explored the role of the ANGPTL7 signaling pathway in CLAN formation. We detected the expression of ANGPTL7 in cultured primary TM cells treated with dexamethasone (DEX) and ethanol as a control using qRT-PCR and western blotting. Actin filaments were revealed by phalloidin staining. ANGPTL7 short hairpin RNA (shRNA) was applied to TM cells to examine the effect of ANGPTL7 on DEX-induced CLAN formation. Western blotting was used to assess the effect of ANGPTL7 on the RhoA/Rho-associated kinase (Rho-kinase/ROCK) signaling pathway. Bioinformatics, dual-luciferase reporter assays, and chromatin immunoprecipitation were employed to identify the transcription factors of ANGPTL7. Transcription factor specificity protein 1 (SP1) overexpression and silencing were performed to determine their roles in the modulation of ANGPTL7 expression. We found DEX-induced ANGPTL7 expression and stress fiber rearrangement in TM cells. ANGPTL7 knockdown effectively inhibited the formation of CLANs. Moreover, it was involved in the regulation of the RhoA/ROCK signaling pathway, further affecting DEX-induced CLAN formation. SP1 was identified as a transcription factor of ANGPTL7 which regulated ANGPTL7 level to mediate CLAN formation through the RhoA/ROCK signaling pathway. This study contributes to revealing the molecular mechanisms of ANGPTL7 in CLAN formation, which is involved in TM dysfunction and glaucoma pathogenesis.
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Affiliation(s)
- Mengsha Sun
- Department of Ophthalmology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenjia Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minwen Zhou
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,National Clinical Research Center for Eye Diseases, Shanghai, China. .,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.
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31
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Collantes ERA, Delfin MS, Fan B, Torregosa JMR, Siguan-Bell C, de Guzman Florcruz NV, Martinez JMD, Masna-Hidalgo BJ, Guzman VPT, Anotado-Flores JF, Levina FD, Hernandez SRC, Collantes AA, Sibulo MC, Rong S, Wiggs JL. EFEMP1 rare variants cause familial juvenile-onset open-angle glaucoma. Hum Mutat 2022; 43:240-252. [PMID: 34923728 PMCID: PMC8972201 DOI: 10.1002/humu.24320] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 02/03/2023]
Abstract
Juvenile open-angle glaucoma (JOAG) is a severe type of glaucoma with onset before age 40 and dominant inheritance. Using exome sequencing we identified 3 independent families from the Philippines with novel EFEMP1 variants (c.238A>T, p.Asn80Tyr; c.1480T>C, p.Ter494Glnext*29; and c.1429C>T, p.Arg477Cys) co-segregating with disease. Affected variant carriers (N = 34) exhibited severe disease with average age of onset of 16 years and with 76% developing blindness. To investigate functional effects, we transfected COS7 cells with vectors expressing the three novel EFEMP1 variants and showed that all three variants found in JOAG patients caused significant intracellular protein aggregation and retention compared to wild type and also compared to EFEMP1 variants associated with other ocular phenotypes including an early-onset form of macular degeneration, Malattia Leventinese/Doyne's Honeycomb retinal dystrophy. These results suggest that rare EFEMP1 coding variants can cause JOAG through a mechanism involving protein aggregation and retention, and that the extent of intracellular retention correlates with disease phenotype. This is the first report of EFEMP1 variants causing JOAG, expanding the EFEMP1 disease spectrum. Our results suggest that EFEMP1 mutations appear to be a relatively common cause of JOAG in Filipino families, an ethnically diverse population.
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Affiliation(s)
- Edward Ryan A. Collantes
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, USA
- Department of Ophthalmology, Manila Doctors Hospital, Manila, Philippines
| | - Manuel S. Delfin
- Department of Ophthalmology, Manila Doctors Hospital, Manila, Philippines
| | - Baojian Fan
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, USA
| | - Justine May R. Torregosa
- Department of Ophthalmology, Cebu Institute of Medicine, Cebu Velez General Hospital, Cebu City, Philippines
| | - Christine Siguan-Bell
- Department of Ophthalmology, Cebu Institute of Medicine, Cebu Velez General Hospital, Cebu City, Philippines
| | - Nilo Vincent de Guzman Florcruz
- Department of Ophthalmology and Visual Sciences, University of the Philippines-Philippine General Hospital, Manila, Philippines
- Glaucoma Service, Department of Ophthalmology, East Avenue Medical Center, Quezon City, Philippines
| | - Jose Maria D. Martinez
- Glaucoma Service, Department of Ophthalmology, East Avenue Medical Center, Quezon City, Philippines
| | | | | | | | - Faye D. Levina
- Department of Ophthalmology, Jose R. Reyes Memorial Medical Center, Manila, Philippines
| | | | | | | | - Shisong Rong
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, USA
| | - Janey L. Wiggs
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, USA
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32
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Liuska PJ, Lemmelä S, Havulinna AS, Kaarniranta K, Uusitalo H, Laivuori H, Kiiskinen T, Daly MJ, Palotie A, Turunen JA. Association of the MYOC p.(Gln368Ter) Variant With Glaucoma in a Finnish Population. JAMA Ophthalmol 2021; 139:762-768. [PMID: 34081096 DOI: 10.1001/jamaophthalmol.2021.1610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance The c.1102C>T, p.(Gln368Ter) variant in the myocilin (MYOC) gene is a known risk allele for glaucoma. It is the most common MYOC risk variant for glaucoma among individuals of European ancestry, and its prevalence is highest in Finland. Furthermore, exfoliation syndrome has high prevalence in Scandinavia, making the Finnish population ideal to study the association of the variant with different types of glaucoma. Objectives To examine the association and penetrance of MYOC p.(Gln368Ter) (rs74315329) variant with different types of glaucoma in a Finnish population. Design, Setting, and Participants This genetic association study included individuals of Finnish ancestry in the FinnGen project. The participants were collected from Finnish biobanks, and the disease end points were defined using nationwide registries. The MYOC c.1102C>T variant was either directly genotyped or imputed with microarrays. Recruitment of samples to FinnGen was initiated in 2017, and data analysis was performed between December 2019 and May 2020. Main Outcomes and Measures The main outcomes were odds ratios (ORs) and penetrance with different types of glaucoma and in different age groups. Results A total of 218 792 individuals were included in this study (mean [SD] age 52.4 [17.5] years; 123 579 women [56.5%]), including 8591 (3.9%) with glaucoma, 3412 (1.6%) with primary open-angle glaucoma, 1515 (0.7%) with exfoliation glaucoma, 892 (0.4%) with normal-tension glaucoma, and 4766 (2.2%) with suspected glaucoma. The minor allele frequency of MYOC p.(Gln368Ter) was 0.28%. Individuals with the heterozygous variant had higher odds of primary open-angle glaucoma (OR, 3.36; 95% CI, 2.55-4.37), overall glaucoma (OR, 2.58; 95% CI, 2.12-3.13), suspected glaucoma (OR, 2.53; 95% CI, 1.93-3.26), exfoliation glaucoma (OR, 2.61; 95% CI, 1.60-4.02), and undergoing glaucoma-related operations (OR, 5.45; 95% CI, 2.95-9.28). The penetrance of heterozygous MYOC p.(Gln368Ter) was 5.2% in individuals with primary open-angle glaucoma, 9.6% in individuals with glaucoma, 5.4% in individuals with suspected glaucoma, and 1.9% in individuals with exfoliation glaucoma. There was no significant association with normal-tension glaucoma (OR, 1.69; 95% CI, 0.72-3.35). Conclusions and Relevance This genetic association study found that the MYOC p.(Gln368Ter) variant was associated with exfoliation glaucoma. The association with normal-tension glaucoma could not be replicated. These findings suggest that MYOC p.(Gln368Ter) was associated with open-angle glaucoma and exfoliation glaucoma in a Finnish population.
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Affiliation(s)
- Perttu J Liuska
- Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Hannu Uusitalo
- TAYS Eye Center, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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33
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Kompella UB, Hartman RR, Patil MA. Extraocular, periocular, and intraocular routes for sustained drug delivery for glaucoma. Prog Retin Eye Res 2021; 82:100901. [PMID: 32891866 PMCID: PMC8317199 DOI: 10.1016/j.preteyeres.2020.100901] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 08/22/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
Although once daily anti-glaucoma drug therapy is a current clinical reality, most therapies require multiple dosing and there is an unmet need to develop convenient, safe, and effective sustained release drug delivery systems for long-term treatment to improve patient adherence and outcomes. One of the first sustained release drug delivery systems was approved for the reduction of intraocular pressure in glaucoma patients. It is a polymeric reservoir-type insert delivery system, Ocusert™, placed under the eyelid and on the ocular surface for zero-order drug release over one week. The insert, marketed in two strengths, released pilocarpine on the eye surface. While many clinicians appreciated this drug product, it was eventually discontinued. No similar sustained release non-invasive drug delivery system has made it to the market to date for treating glaucoma. Drug delivery systems under development include punctal plugs, ring-type systems, contact lenses, implants, microspheres, nanospheres, gels, and other depot systems placed in the extraocular, periocular, or intraocular regions including intracameral, supraciliary, and intravitreal spaces. This article discusses the advantages and disadvantages of the various routes of administration and delivery systems for sustained glaucoma therapy. It also provides the reader with some examples and discussion of drug delivery systems that could potentially be applied for glaucoma treatment. Interestingly, one intracamerally injected implant, Durysta™, was approved recently for sustained intraocular pressure reduction. However, long-term acceptance of such devices has yet to be established. The ultimate success of the delivery system will depend on efficacy relative to eye drop dosing, safety, reimbursement options, and patient acceptance. Cautious development efforts are warranted considering prior failed approaches for sustained glaucoma drug delivery. Neuroprotective approaches for glaucoma therapy including cell, gene, protein, and drug-combination therapies, mostly administered intravitreally, are also rapidly progressing towards assessment in humans.
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Affiliation(s)
- Uday B Kompella
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Colorado Center for Nanomedicine and Nanosafety, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Rachel R Hartman
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Madhoosudan A Patil
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Waksmunski AR, Song YE, Kinzy TG, Laux RA, Sewell J, Fuzzell D, Fuzzell S, Miller S, Wiggs JL, Pasquale LR, Skarie JM, Haines JL, Cooke Bailey JN. The GGLEAM Study: Understanding Glaucoma in the Ohio Amish. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:1551. [PMID: 33561996 PMCID: PMC7915874 DOI: 10.3390/ijerph18041551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022]
Abstract
Glaucoma leads to millions of cases of visual impairment and blindness around the world. Its susceptibility is shaped by both environmental and genetic risk factors. Although over 120 risk loci have been identified for glaucoma, a large portion of its heritability is still unexplained. Here we describe the foundation of the Genetics of GLaucoma Evaluation in the AMish (GGLEAM) study to investigate the genetic architecture of glaucoma in the Ohio Amish, which exhibits lower genetic and environmental heterogeneity compared to the general population. To date, we have enrolled 81 Amish individuals in our study from Holmes County, Ohio. As a part of our enrollment process, 62 GGLEAM study participants (42 glaucoma-affected and 20 unaffected individuals) received comprehensive eye examinations and glaucoma evaluations. Using the data from the Anabaptist Genealogy Database, we found that 80 of the GGLEAM study participants were related to one another through a large, multigenerational pedigree containing 1586 people. We plan to integrate the health and kinship data obtained for the GGLEAM study to interrogate glaucoma genetics and pathophysiology in this unique population.
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Affiliation(s)
- Andrea R. Waksmunski
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Tyler G. Kinzy
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Reneé A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Jane Sewell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Sarada Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Sherri Miller
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA;
| | - Louis R. Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Jonathan M. Skarie
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
- Ohio Eye Associates, Mansfield, OH 44906, USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jessica N. Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; (A.R.W.); (Y.E.S.); (T.G.K.); (R.A.L.); (J.S.); (D.F.); (S.F.); (S.M.); (J.M.S.); (J.L.H.)
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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