1
|
Clarke B, Holtkamp E, Öztürk H, Mück M, Wahlberg M, Meyer K, Munzlinger F, Brechtmann F, Hölzlwimmer FR, Lindner J, Chen Z, Gagneur J, Stegle O. Integration of variant annotations using deep set networks boosts rare variant association testing. Nat Genet 2024:10.1038/s41588-024-01919-z. [PMID: 39322779 DOI: 10.1038/s41588-024-01919-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/20/2024] [Indexed: 09/27/2024]
Abstract
Rare genetic variants can have strong effects on phenotypes, yet accounting for rare variants in genetic analyses is statistically challenging due to the limited number of allele carriers and the burden of multiple testing. While rich variant annotations promise to enable well-powered rare variant association tests, methods integrating variant annotations in a data-driven manner are lacking. Here we propose deep rare variant association testing (DeepRVAT), a model based on set neural networks that learns a trait-agnostic gene impairment score from rare variant annotations and phenotypes, enabling both gene discovery and trait prediction. On 34 quantitative and 63 binary traits, using whole-exome-sequencing data from UK Biobank, we find that DeepRVAT yields substantial gains in gene discoveries and improved detection of individuals at high genetic risk. Finally, we demonstrate how DeepRVAT enables calibrated and computationally efficient rare variant tests at biobank scale, aiding the discovery of genetic risk factors for human disease traits.
Collapse
Affiliation(s)
- Brian Clarke
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- AI Health Innovation Cluster, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Eva Holtkamp
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association-Munich School for Data Science (MUDS), Munich, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Hakime Öztürk
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Mück
- AI Health Innovation Cluster, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magnus Wahlberg
- AI Health Innovation Cluster, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kayla Meyer
- AI Health Innovation Cluster, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Munzlinger
- AI Health Innovation Cluster, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Brechtmann
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Florian R Hölzlwimmer
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Jonas Lindner
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Zhifen Chen
- Department of Cardiology, Deutsches Herzzentrum München, Technical University Munich, Munich, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Munich Center for Machine Learning, Munich, Germany.
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany.
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| |
Collapse
|
2
|
Paquay S, Duraffourd J, Bury M, Heremans IP, Caligiore F, Gerin I, Stroobant V, Jacobs J, Pinon A, Graff J, Vertommen D, Van Schaftingen E, Dewulf JP, Bommer GT. ACAD10 and ACAD11 allow entry of 4-hydroxy fatty acids into β-oxidation. Cell Mol Life Sci 2024; 81:367. [PMID: 39174697 PMCID: PMC11342911 DOI: 10.1007/s00018-024-05397-8] [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: 04/27/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024]
Abstract
Hydroxylated fatty acids are important intermediates in lipid metabolism and signaling. Surprisingly, the metabolism of 4-hydroxy fatty acids remains largely unexplored. We found that both ACAD10 and ACAD11 unite two enzymatic activities to introduce these metabolites into mitochondrial and peroxisomal β-oxidation, respectively. First, they phosphorylate 4-hydroxyacyl-CoAs via a kinase domain, followed by an elimination of the phosphate to form enoyl-CoAs catalyzed by an acyl-CoA dehydrogenase (ACAD) domain. Studies in knockout cell lines revealed that ACAD10 preferentially metabolizes shorter chain 4-hydroxy fatty acids than ACAD11 (i.e. 6 carbons versus 10 carbons). Yet, recombinant proteins showed comparable activity on the corresponding 4-hydroxyacyl-CoAs. This suggests that the localization of ACAD10 and ACAD11 to mitochondria and peroxisomes, respectively, might influence their physiological substrate spectrum. Interestingly, we observed that ACAD10 is cleaved internally during its maturation generating a C-terminal part consisting of the ACAD domain, and an N-terminal part comprising the kinase domain and a haloacid dehalogenase (HAD) domain. HAD domains often exhibit phosphatase activity, but negligible activity was observed in the case of ACAD10. Yet, inactivation of a presumptive key residue in this domain significantly increased the kinase activity, suggesting that this domain might have acquired a regulatory function to prevent accumulation of the phospho-hydroxyacyl-CoA intermediate. Taken together, our work reveals that 4-hydroxy fatty acids enter mitochondrial and peroxisomal fatty acid β-oxidation via two enzymes with an overlapping substrate repertoire.
Collapse
Affiliation(s)
- Stéphanie Paquay
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- Department of Pediatric Neurology and Metabolic Diseases, Cliniques Universitaires St. Luc, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Julia Duraffourd
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Marina Bury
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Isaac P Heremans
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Francesco Caligiore
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Isabelle Gerin
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | | | - Jean Jacobs
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Aymeric Pinon
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Julie Graff
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute & MASSPROT Platform, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Emile Van Schaftingen
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Joseph P Dewulf
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- Department of Laboratory Medicine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Guido T Bommer
- Metabolic Research Group, de Duve Institute & WELRI, Université Catholique de Louvain, 1200, Brussels, Belgium.
- WELBIO Department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium.
| |
Collapse
|
3
|
Al-Saei O, Malka S, Owen N, Aliyev E, Vempalli FR, Ocieczek P, Al-Khathlan B, Fakhro K, Moosajee M. Increasing the diagnostic yield of childhood glaucoma cases recruited into the 100,000 Genomes Project. BMC Genomics 2024; 25:484. [PMID: 38755526 PMCID: PMC11097485 DOI: 10.1186/s12864-024-10353-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Childhood glaucoma (CG) encompasses a heterogeneous group of genetic eye disorders that is responsible for approximately 5% of childhood blindness worldwide. Understanding the molecular aetiology is key to improving diagnosis, prognosis and unlocking the potential for optimising clinical management. In this study, we investigated 86 CG cases from 78 unrelated families of diverse ethnic backgrounds, recruited into the Genomics England 100,000 Genomes Project (GE100KGP) rare disease cohort, to improve the genetic diagnostic yield. Using the Genomics England/Genomic Medicine Centres (GE/GMC) diagnostic pipeline, 13 unrelated families were solved (13/78, 17%). Further interrogation using an expanded gene panel yielded a molecular diagnosis in 7 more unrelated families (7/78, 9%). This analysis effectively raises the total number of solved CG families in the GE100KGP to 26% (20/78 families). Twenty-five percent (5/20) of the solved families had primary congenital glaucoma (PCG), while 75% (15/20) had secondary CG; 53% of this group had non-acquired ocular anomalies (including iris hypoplasia, megalocornea, ectopia pupillae, retinal dystrophy, and refractive errors) and 47% had non-acquired systemic diseases such as cardiac abnormalities, hearing impairment, and developmental delay. CYP1B1 was the most frequently implicated gene, accounting for 55% (11/20) of the solved families. We identified two novel likely pathogenic variants in the TEK gene, in addition to one novel pathogenic copy number variant (CNV) in FOXC1. Variants that passed undetected in the GE100KGP diagnostic pipeline were likely due to limitations of the tiering process, the use of smaller gene panels during analysis, and the prioritisation of coding SNVs and indels over larger structural variants, CNVs, and non-coding variants.
Collapse
Affiliation(s)
- Omayma Al-Saei
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | | | - Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Zhou X, He Y, Xu T, Wu Z, Guo W, Xu X, Liu Y, Zhang Y, Shang H, Huang L, Yao Z, Li Z, Su L, Li Z, Feng T, Zhang S, Monteiro O, Cunha RA, Huang ZL, Zhang K, Li Y, Cai X, Qu J, Chen JF. 40 Hz light flickering promotes sleep through cortical adenosine signaling. Cell Res 2024; 34:214-231. [PMID: 38332199 PMCID: PMC10907382 DOI: 10.1038/s41422-023-00920-1] [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: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024] Open
Abstract
Flickering light stimulation has emerged as a promising non-invasive neuromodulation strategy to alleviate neuropsychiatric disorders. However, the lack of a neurochemical underpinning has hampered its therapeutic development. Here, we demonstrate that light flickering triggered an immediate and sustained increase (up to 3 h after flickering) in extracellular adenosine levels in the primary visual cortex (V1) and other brain regions, as a function of light frequency and intensity, with maximal effects observed at 40 Hz frequency and 4000 lux. We uncovered cortical (glutamatergic and GABAergic) neurons, rather than astrocytes, as the cellular source, the intracellular adenosine generation from AMPK-associated energy metabolism pathways (but not SAM-transmethylation or salvage purine pathways), and adenosine efflux mediated by equilibrative nucleoside transporter-2 (ENT2) as the molecular pathway responsible for extracellular adenosine generation. Importantly, 40 Hz (but not 20 and 80 Hz) light flickering for 30 min enhanced non-rapid eye movement (non-REM) and REM sleep for 2-3 h in mice. This somnogenic effect was abolished by ablation of V1 (but not superior colliculus) neurons and by genetic deletion of the gene encoding ENT2 (but not ENT1), but recaptured by chemogenetic inhibition of V1 neurons and by focal infusion of adenosine into V1 in a dose-dependent manner. Lastly, 40 Hz light flickering for 30 min also promoted sleep in children with insomnia by decreasing sleep onset latency, increasing total sleep time, and reducing waking after sleep onset. Collectively, our findings establish the ENT2-mediated adenosine signaling in V1 as the neurochemical basis for 40 Hz flickering-induced sleep and unravel a novel and non-invasive treatment for insomnia, a condition that affects 20% of the world population.
Collapse
Affiliation(s)
- Xuzhao Zhou
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yan He
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tao Xu
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhaofa Wu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Wei Guo
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xi Xu
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuntao Liu
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Zhang
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huiping Shang
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Libin Huang
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhimo Yao
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zewen Li
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lingya Su
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhihui Li
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tao Feng
- Key Laboratory of Biomedical Engineering of Ministry of Education, Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shaomin Zhang
- Key Laboratory of Biomedical Engineering of Ministry of Education, Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, Zhejiang, China
| | - Olivia Monteiro
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Rodrigo A Cunha
- CNC-Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Zhi-Li Huang
- Department of Pharmacology, School of Basic Medical Sciences; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Kang Zhang
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau, China.
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xiaohong Cai
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Jia Qu
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Jiang-Fan Chen
- The Eye and Brain Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health), School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| |
Collapse
|
6
|
Pandino I, Giammaria S, Zingale GA, Roberti G, Michelessi M, Coletta M, Manni G, Agnifili L, Vercellin AV, Harris A, Oddone F, Sbardella D. Ubiquitin proteasome system and glaucoma: A survey of genetics and molecular biology studies supporting a link with pathogenic and therapeutic relevance. Mol Aspects Med 2023; 94:101226. [PMID: 37950974 DOI: 10.1016/j.mam.2023.101226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 11/13/2023]
Abstract
Glaucoma represents a group of progressive neurodegenerative diseases characterized by the loss of retinal ganglion cells (RGCs) and their axons with subsequent visual field impairment. The disease develops through largely uncharacterized molecular mechanisms, that are likely to occur in different localized cell types, either in the anterior (e.g., trabecular meshwork cells) or posterior (e.g., Muller glia, retinal ganglion cells) segments of the eye. Genomic and preclinical studies suggest that glaucoma pathogenesis may develop through altered ubiquitin (Ub) signaling. Ubiquitin conjugation, referred to as ubiquitylation, is a major post-synthetic modification catalyzed by E1-E2-E3 enzymes, that profoundly regulates the turnover, trafficking and biological activity of the targeted protein. The development of new technologies, including proteomics workflows, allows the biology of ubiquitin signaling to be described in health and disease. This post-translational modification is emerging as a key role player in neurodegeneration, gaining relevance for novel therapeutic options, such as in the case of Proteolysis Targeting Chimeras technology. Although scientific evidence supports a link between Ub and glaucoma, their relationship is still not well-understood. Therefore, this review provides a detailed research-oriented discussion on current evidence of Ub signaling in glaucoma. A review of genomic and genetic data is provided followed by an in-depth discussion of experimental data on ASB10, parkin and optineurin, which are proteins that play a key role in Ub signaling and have been associated with glaucoma.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Gianluca Manni
- IRCCS Fondazione Bietti, Rome, Italy; DSCMT University of Tor Vergata, Rome, Italy
| | - Luca Agnifili
- Ophthalmology Clinic, Department of Medicine and Aging Science, University "G. D'Annunzio" of Chieti-Pescara, Italy
| | | | - Alon Harris
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | |
Collapse
|
7
|
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: 3.0] [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.
Collapse
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
| |
Collapse
|
8
|
Causal Association between Iritis or Uveitis and Glaucoma: A Two-Sample Mendelian Randomisation Study. Genes (Basel) 2023; 14:genes14030642. [PMID: 36980914 PMCID: PMC10048342 DOI: 10.3390/genes14030642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Recent studies have suggested an association between iritis or uveitis and glaucoma. This study investigated the causal relationship between glaucoma and iritis and uveitis as exposures in a multi-ethnic population. Single-nucleotide polymorphisms associated with exposures to iritis and uveitis from the genome-wide association study (GWAS) data of Biobank Japan (BBJ) and the meta-analysis data from BBJ and UK Biobank (UKB) were used as instrumental variables (IVs). The GWAS dataset for glaucoma was extracted from the meta-analysis data (n = 240,302) of Genetic Epidemiology Research in Adult Health and Aging and UKB. The casual estimates were assessed with a two-sample Mendelian randomisation (MR) test using the inverse-variance-weighted (IVW) method, weighted median method, MR–Egger method, and MR-Pleiotropy Residual Sum and Outlier test. The IVW method revealed a significant causal association between iritis and glaucoma using IVs (p < 5.0 × 10−8) from the East Asian population (n = 2) (odds ratio [OR] = 1.01, p = 0.017), a significant association between iritis exposures (p < 5.0 × 10−8) in the multi-ethnic population (n = 11) (OR = 1.04, p = 0.001), and a significant causal association between uveitis exposures (n = 10 with p < 5.0 × 10−8) and glaucoma in the multi-ethnic population (OR = 1.04, p = 0.001). Iritis and uveitis had causal effects on glaucoma risk based on IVs from the multi-ethnic population. These findings imply that the current classifications of uveitic glaucoma and open-angle glaucoma overlap, indicating the need for further investigating these complex relationships.
Collapse
|