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1
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Wei P, Gao S, Han G. Evidence for Genetic Causal Association Between the Gut Microbiome, Derived Metabolites, and Age-Related Macular Degeneration: A Mediation Mendelian Randomization Analysis. Biomedicines 2025; 13:639. [PMID: 40149615 PMCID: PMC11940807 DOI: 10.3390/biomedicines13030639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 02/25/2025] [Accepted: 03/03/2025] [Indexed: 03/29/2025] Open
Abstract
Background/Objectives: Despite substantial research, the causal relationships between gut microbiota (GM) and age-related macular degeneration (AMD) remain unclear. We aimed to explore these causal associations using Mendelian randomization (MR) and elucidate the potential mechanisms mediated by blood metabolites. Methods: We utilized the 211 GM dataset (n = 18,340) provided by the MiBioGen consortium. AMD outcome data were sourced from the MRC Integrated Epidemiology Unit (IEU) OpenGWAS Project. We performed bidirectional MR, two mediation analyses, and two-step MR to assess the causal links between GM and different stages of AMD (early, dry, and wet). Results: Our findings indicate that the Bacteroidales S24.7 group and genus Dorea are associated with an increased risk of early AMD, while Ruminococcaceae UCG011 and Parasutterella are linked to a higher risk of dry AMD. Conversely, Lachnospiraceae UCG004 and Anaerotruncus are protective against dry AMD. In the case of wet AMD, Intestinimonas and Sellimonas increase risk, whereas Anaerotruncus and Rikenellaceae RC9 reduce it. Additionally, various blood metabolites were implicated: valine, arabinose, creatine, lysine, alanine, and apolipoprotein A1 were associated with early AMD; glutamine and hyodeoxycholate-with a reduced risk of dry AMD; and androsterone sulfate, epiandrosterone sulfate, and lipopolysaccharide-with a reduced risk of wet AMD. Notably, the association between family Oxalobacteraceae and early AMD was mediated by valine, accounting for 19.1% of the association. Conclusions: This study establishes causal links between specific gut microbiota and AMD, mediated by blood metabolites, thereby enhancing our understanding of the gut-retina axis in AMD pathophysiology.
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Affiliation(s)
- Pinghui Wei
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin 300020, China; (P.W.); (S.G.)
- Nankai University Eye Institute, Nankai University Affiliated Eye Hospital, Nankai University, Tianjin 300071, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin 300020, China
| | - Shan Gao
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin 300020, China; (P.W.); (S.G.)
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Guoge Han
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin 300020, China; (P.W.); (S.G.)
- Nankai University Eye Institute, Nankai University Affiliated Eye Hospital, Nankai University, Tianjin 300071, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin 300020, China
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2
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Dey PN, Singh N, Zelinger L, Batz Z, Nellissery J, White Carreiro ND, Qian H, Li T, Fariss RN, Dong L, Swaroop A. Loss of paired immunoglobin-like type 2 receptor B gene associated with age-related macular degeneration impairs photoreceptor function in mouse retina. Hum Mol Genet 2025; 34:64-76. [PMID: 39532089 PMCID: PMC12034095 DOI: 10.1093/hmg/ddae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 10/10/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024] Open
Abstract
Genome-wide association studies have uncovered mostly non-coding variants at over 60 genetic loci linked to susceptibility for age-related macular degeneration (AMD). To ascertain the causal gene at the PILRB/PILRA locus, we used a CRISPR strategy to produce germline deletions in the mouse paired immunoglobin-like type 2 receptor (Pilr) genes that encode highly related activating (PILRB) and inhibitory (PILRA) receptors. We show that a combined loss of Pilrb1 and Pilrb2, but not Pilra, leads to an early but relatively stationary defect as the electroretinography (ERG) amplitudes of Pilrb1/2-/- mice exhibit a marked reduction as early as postnatal day 15 and do not show additional significant decrease at 3 and 12-months. No alterations are evident in Müller glia, microglia, bipolar, amacrine and horizontal cells based on immunohistochemistry using cell-type specific markers. PILRB immunostaining is specifically detected at the proximal part of photoreceptor outer segment. Reduced expression of select calcium-regulated phototransduction and synapse-associated proteins, including GCAP1 and 2, PDE6b, AIPL1, PSD95, and CTBP1 indicates dysregulation of calcium homeostasis as a possible mechanism of retinal phenotype in Pilrb1/2-/- mice. Our studies suggest a novel function of PILRB in retinal photoreceptors and an association of PILRB, but not PILRA, with AMD pathogenesis.
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Affiliation(s)
- Partha Narayan Dey
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Nivedita Singh
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Lina Zelinger
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Zachary Batz
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Jacob Nellissery
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Noor D White Carreiro
- Biological Imaging Core, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Haohua Qian
- Visual Function Core Facility, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Tiansen Li
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Robert N Fariss
- Biological Imaging Core, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, United States
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3
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Singh M, Negi R, Alka, Vinayagam R, Kang SG, Shukla P. Age-Related Macular Degeneration (AMD): Pathophysiology, Drug Targeting Approaches, and Recent Developments in Nanotherapeutics. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:1647. [PMID: 39459435 PMCID: PMC11509623 DOI: 10.3390/medicina60101647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/26/2024] [Accepted: 10/06/2024] [Indexed: 10/28/2024]
Abstract
The most prevalent reason for vision impairment in aging inhabitants is age-related macular degeneration (AMD), a posterior ocular disease with a poor understanding of the anatomic, genetic, and pathophysiological progression of the disease. Recently, new insights exploring the role of atrophic changes in the retinal pigment epithelium, extracellular drusen deposits, lysosomal lipofuscin, and various genes have been investigated in the progression of AMD. Hence, this review explores the incidence and risk factors for AMD, such as oxidative stress, inflammation, the complement system, and the involvement of bioactive lipids and their role in angiogenesis. In addition to intravitreal anti-vascular endothelial growth factor (VEGF) therapy and other therapeutic interventions such as oral kinase inhibitors, photodynamic, gene, and antioxidant therapy, as well as their benefits and drawbacks as AMD treatment options, strategic drug delivery methods, including drug delivery routes with a focus on intravitreal pharmacokinetics, are investigated. Further, the recent advancements in nanoformulations such as polymeric and lipid nanocarriers, liposomes, etc., intended for ocular drug delivery with pros and cons are too summarized. Therefore, the purpose of this review is to give new researchers an understanding of AMD pathophysiology, with an emphasis on angiogenesis, inflammation, the function of bioactive lipids, and therapy options. Additionally, drug delivery options that focus on the development of drug delivery system(s) via several routes of delivery can aid in the advancement of therapeutic choices.
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Affiliation(s)
- Mahendra Singh
- Department of Biotechnology, Institute of Biotechnology, School of Life and Applied Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Riyakshi Negi
- Department of Pharmaceutical Sciences, School of Heath Sciences and Technology, UPES, Dehradun 246008, India; (R.N.); (A.)
| | - Alka
- Department of Pharmaceutical Sciences, School of Heath Sciences and Technology, UPES, Dehradun 246008, India; (R.N.); (A.)
| | - Ramachandran Vinayagam
- Department of Biotechnology, Institute of Biotechnology, School of Life and Applied Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, School of Life and Applied Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Prashant Shukla
- Department of Pharmaceutical Sciences, School of Heath Sciences and Technology, UPES, Dehradun 246008, India; (R.N.); (A.)
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4
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Advani J, Mehta PA, Hamel AR, Mehrotra S, Kiel C, Strunz T, Corso-Díaz X, Kwicklis M, van Asten F, Ratnapriya R, Chew EY, Hernandez DG, Montezuma SR, Ferrington DA, Weber BHF, Segrè AV, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. Nat Commun 2024; 15:1972. [PMID: 38438351 PMCID: PMC10912779 DOI: 10.1038/s41467-024-46063-8] [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: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
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Affiliation(s)
- Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Kiel
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
- Doheny Eye Institute, Pasadena, CA, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Kwong A, Zawistowski M, Fritsche LG, Zhan X, Bragg-Gresham J, Branham KE, Advani J, Othman M, Ratnapriya R, Teslovich TM, Stambolian D, Chew EY, Abecasis GR, Swaroop A. Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration. Hum Mol Genet 2024; 33:374-385. [PMID: 37934784 PMCID: PMC10840384 DOI: 10.1093/hmg/ddad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.
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Affiliation(s)
- Alan Kwong
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Xiaowei Zhan
- Southwestern Medical Center, University of Texas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Jennifer Bragg-Gresham
- Kidney Epidemiology and Cost Center, Department of Internal Medicine-Nephrology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Jayshree Advani
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Tanya M Teslovich
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania Medical School, 51 N. 39th Street, Philadelphia, PA 19104, United States
| | - Emily Y Chew
- Division of Epidemiology and Clinical Application, National Eye Institute, National Institutes of Health, 10 Center Drive Building 10-CRC, Bethesda, MD 20892, United States
| | - Gonçalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
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6
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Advani J, Corso-Diaz X, Kwicklis M, van Asten F, Ratnapriya R, Mehta P, Hamel A, Mahrotra S, Segrè A, Kiel C, Strunz T, Weber B, Chew E, Hernandez D, Montezuma S, Ferrington D, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. RESEARCH SQUARE 2023:rs.3.rs-3011096. [PMID: 37398472 PMCID: PMC10312909 DOI: 10.21203/rs.3.rs-3011096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype-environment interaction in retina.
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Affiliation(s)
| | | | | | | | | | - Puja Mehta
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Andrew Hamel
- Department of Ophthalmology, Massachusetts Eye and Ear
| | | | | | | | | | | | - Emily Chew
- National Eye Institute/National Institutes of Health
| | | | | | | | - Anand Swaroop
- National Eye Institute, National Institutes of Health
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