1
|
Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome wide association study and genomic risk prediction of age related macular degeneration in Israel. Sci Rep 2024; 14:13034. [PMID: 38844476 DOI: 10.1038/s41598-024-63065-0] [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: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
The risk of developing age-related macular degeneration (AMD) is influenced by genetic background. In 2016, the International AMD Genomics Consortium (IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score (PRS) from these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish (AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study (GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Our discovery set recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary-statistics excluding our study and developed PRSs via clumping/thresholding or LDpred2. In our discovery set, 31/34 loci reported by IAMDGC were AMD-associated (P < 0.05). Of those, all effects were directionally consistent with IAMDGC and 11 loci had a P-value under Bonferroni-corrected threshold (0.05/34 = 0.0015). At a 5 × 10-5 threshold, we discovered four suggestive associations in FAM189A1, IGDCC4, C7orf50, and CNTNAP4. Only the FAM189A1 variant was AMD-associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS + covariates had an AUC of 0.82 (95% CI 0.79-0.85) and performed better than covariates-only model (P = 5.1 × 10-9). Therefore, previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
Collapse
Affiliation(s)
- Michelle Grunin
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Daria Triffon
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
| | - Gala Beykin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Elior Rahmani
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Regev Schweiger
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Genetics, University of Cambridge, CB21TN, Cambridge, UK
| | - Liran Tiosano
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Shira Hagbi-Levi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Batya Rinsky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Refael Munitz
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Eran Halperin
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel.
| | - Itay Chowers
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel.
| |
Collapse
|
2
|
Cebatoriene D, Vilkeviciute A, Gedvilaite G, Bruzaite A, Kriauciuniene L, Zaliuniene D, Liutkeviciene R. CFH (rs1061170, rs1410996), KDR (rs2071559, rs1870377) and KDR and CFH Serum Levels in AMD Development and Treatment Efficacy. Biomedicines 2024; 12:948. [PMID: 38790910 PMCID: PMC11117782 DOI: 10.3390/biomedicines12050948] [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: 03/15/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is a major global health problem as it is the leading cause of irreversible loss of central vision in the aging population. Av-vascular endothelial growth factor (anti-VEGF) therapies have been shown to be effective, but they do not respond optimally to all patients. OBJECTIVE This study investigates the genetic factors associated with susceptibility to AMD and response to treatment, focusing on key polymorphisms in the CFH (rs1061170, rs1410996) and KDR (rs2071559, rs1870377) genes and the association of CFH and KDR serum levels in patients with AMD. RESULTS A cohort of 255 patients with early AMD, 252 patients with exudative AMD, and 349 healthy controls underwent genotyping analysis, which revealed significant associations between CFH polymorphisms and the risk of exudative AMD. The CFH rs1061170 CC genotype was associated with an increased risk of early AMD (p = 0.046). For exudative AMD, the CFH rs1061170 TC + CC genotype increased odds (p < 0.001), while the rs1410996 GA + AA genotype decreased odds (p < 0.001). Haplotypes of CFH SNPs were associated with decreased odds of AMD. In terms of response to treatment, none of the SNPs were associated with the response to anti-VEGF treatment. We also found that both early and exudative AMD patients had lower CFH serum levels compared to the control group (p = 0.038 and p = 0.006, respectively). Exudative AMD patients with the CT genotype of CFH rs1061170 had lower CFH serum levels compared to the control group (p = 0.035). Exudative AMD patients with the GG genotype of CFH rs1410996 also had lower CFH serum levels compared to the control group (p = 0.021). CONCLUSIONS CFH polymorphisms influence susceptibility to AMD but do not correlate with a response to anti-VEGF therapy. Further research is imperative to fully evaluate the developmental significance, treatment efficacy, and predictive role in influencing susceptibility to anti-VEGF therapy for KDR and CFH.
Collapse
Affiliation(s)
- Dzastina Cebatoriene
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, LT-44307 Kaunas, Lithuania
| | - Alvita Vilkeviciute
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Greta Gedvilaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Akvile Bruzaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Loresa Kriauciuniene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Dalia Zaliuniene
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Rasa Liutkeviciene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| |
Collapse
|
3
|
Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome-wide association study and genomic risk prediction of age-related macular degeneration in Israel. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.06.23295126. [PMID: 37732190 PMCID: PMC10508791 DOI: 10.1101/2023.09.06.23295126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Purpose The risk of developing age-related macular degeneration(AMD) is influenced by genetic background. In 2016, International AMD Genomics Consortium(IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score(PRS) based on these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish(AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study(GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Methods For our discovery set, we recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped all individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary statistics excluding our study and developed PRSs via either clumping/thresholding or LDpred2. Results In our discovery set, 31/34 loci previously reported by the IAMDGC were AMD associated with P<0.05. Of those, all effects were directionally consistent with the IAMDGC and 11 loci had a p-value under Bonferroni-corrected threshold(0.05/34=0.0015). At a threshold of 5x10 -5 , we discovered four suggestive associations in FAM189A1 , IGDCC4 , C7orf50 , and CNTNAP4 . However, only the FAM189A1 variant was AMD associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS and other covariates had an AUC of 0.82(95%CI:0.79-0.85) and performed better than a covariates-only model(P=5.1x10 -9 ). Conclusions Previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
Collapse
|
4
|
Orozco LD, Owen LA, Hofmann J, Stockwell AD, Tao J, Haller S, Mukundan VT, Clarke C, Lund J, Sridhar A, Mayba O, Barr JL, Zavala RA, Graves EC, Zhang C, Husami N, Finley R, Au E, Lillvis JH, Farkas MH, Shakoor A, Sherva R, Kim IK, Kaminker JS, Townsend MJ, Farrer LA, Yaspan BL, Chen HH, DeAngelis MM. A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration. CELL GENOMICS 2023; 3:100302. [PMID: 37388919 PMCID: PMC10300496 DOI: 10.1016/j.xgen.2023.100302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/21/2023] [Accepted: 03/22/2023] [Indexed: 07/01/2023]
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease.
Collapse
Affiliation(s)
- Luz D. Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Leah A. Owen
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Jeffrey Hofmann
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Amy D. Stockwell
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Jianhua Tao
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Vineeth T. Mukundan
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jessica Lund
- Departments of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Akshayalakshmi Sridhar
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Oleg Mayba
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Richard Sherva
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua S. Kaminker
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Michael J. Townsend
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Lindsay A. Farrer
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Brian L. Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Margaret M. DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| |
Collapse
|