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Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration
Open accessAbstract
Genome-wide association studies (GWAS) have identified genetic variants at 34 loci contributing to age-related macular degeneration (AMD)1-3. We generated transcriptional profiles of postmortem retinas from 453 controls and cases at distinct stages of AMD and integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at more than 9 million common SNPs for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets 4,5. Cis-eQTL analysis identified 10,474 genes under genetic regulation, including 4,541 eQTLs detected only in the retina. Integrated analysis of AMD-GWAS with eQTLs ascertained likely target genes at six reported loci. Using transcriptome-wide association analysis (TWAS), we identified three additional genes, RLBP1, HIC1 and PARP12, after Bonferroni correction. Our studies expand the genetic landscape of AMD and establish the Eye Genotype Expression (EyeGEx) database as a resource for post-GWAS interpretation of multifactorial ocular traits.
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“In the retina, S2R is expressed in several cell types including the retinal pigment epithelium cells, photoreceptors, and retinal ganglion cells [70,71,72,73,74].”
From Sigma-2 Receptors—From Basic Biology to Therapeutic Target: A Focus on Age-Related Degenerative Diseases (2023) · cites this paper as [72]
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“In recent years, TWASs have been widely applied to complex diseases, such as schizophrenia, Parkinson’s disease, and prostate cancer (Gusev et al., 2018; Mancuso et al., 2018; Ratnapriya et al., 2019).”
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Brain–heart–eye axis revealed by multi-organ imaging genetics and proteomics
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“For example, distinct ageassociated transcriptional signatures are present in specific cell types in the eye, including the human retina [27,28] and Drosophila photoreceptors [4].”
BackgroundMultiome-wide Association Studies: Novel Approaches for Understanding Diseases
Shao, M., Chen, K., Zhang, S., Tian, M., Shen, Y., Cao, C., & Gu, N. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae077 · Cited by 14
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Genomic determinants of biological age estimated by deep learning applied to retinal images
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Self-citationMachine Learning Prediction of Non-Coding Variant Impact in Human Retinal cis -Regulatory Elements
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“12,13 14–16 However, due to the incomplete characterization of the non-coding genome, as well as the current limitations of some GWAS and eQTL analyses, it remains a challenge to systematically interpret the impact of individual variants within CREs.”
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Macular structural integrity estimates are associated with Parkinson’s disease genetic risk
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“Recent large-scale transcriptome-wide association studies have shed light on novel genes associated with age-related macular degeneration [21].”
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Self-citationEpistatic interactions of genetic loci associated with age-related macular degeneration
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“Alleles of the S1R and S2R genes have been associated with neural system diseases such as amyotrophic lateral sclerosis [12] and age-related macular degeneration (AMD) [13,14].”
BackgroundNew Technologies to Study Functional Genomics of Age-Related Macular Degeneration
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“To date, studies on AMD genetics have mostly focused on investigating cis-eQTLs (Ratnapriya et al., 2019; Han et al., 2020; Orozco et al., 2020) so it would be interesting to perform trans-eQTL studies in the future.”
BackgroundInfluentialGWAS-by-subtraction reveals an IOP-independent component of primary open angle glaucoma
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“For SNPs signi fi cantly associated with the non-IOP-dependent component of POAG in the discovery sample, variants annotation was based on the Genome Reference Consortium Human genome build 37 derived from the University of California Santa Cruz (UCSC) Genome resource 79 . eQTL mapping was performed using EyeGEx 80 , e…”
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Differentiation versus dysfunction: thyroid hormone, deiodinases and retinal photoreceptors
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“Raw RNA-Seq reads were processed as described earlier 13 .”
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Genetic and molecular biomarkers for geographic atrophy
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“The rs10033900 variant is associated with reduced CFI and PLA2G12A expression levels in the retina (Ratnapriya et al., 2019).”
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“The ‘NEI cohort’ included matched retinal RNAseq and genotype data for 404 donors (15,16) .”
BackgroundSelf-citationThe role of lipid metabolism disorder in the progression and treatment of ocular vascular diseases
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“The expression levels of four ORs in different normal tissues and immune cells derived from peripheral blood were acquired from three datasets: the HPA RNA-seq dataset [28, 29] (https:// www. prote inatl as. org/), the Monaco dataset [30], and the Consensus dataset [28, 29, 31].”
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“We obtained the DEG results from another AMD-related dataset, GSE115828 [39, 40], from the GEO; genes with P < 0.05 in this dataset were overlapped with the above results.”
ResultInfluentialMalka, S., Biswas, P., Berry, A. M., Sangermano, R., Ullah, M., Lin, S., D’Antonio, M., Jestin, A., Jiao, X., Quinodoz, M., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.07.020 · Cited by 7
“48,51 It is likely that the photoreceptor cells are more sensitive to the reduction of gene expression, and therefore the TMEM216 c. (cid:1) 69G > A or G > T variants leading to such gene expression reduction, rather than complete loss of expression, cause specific dysfunction of photoreceptors.”
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“T compare gene expressio lev ls in the RPE cells of pati nts with dry AMD, a published transcriptome databa e (GSE115828) was used [46].”
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“Bonferroni correction [28] was applied for multiple comparison testing.”
MethodGenome-wide association identifies novel ROP risk loci in a multiethnic cohort
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“To investigate the relationship between association signals and gene expression, we evaluated whether top ROP SNPs identi fi ed from GWAS are related to eQTL in the genotype-tissue speci fi c expression databases, EyeGEx 30 , by far the largest reference tissue bank for gene expression and regulation in the human retina.”
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“GERA data came from a grant,”
Guymer, R. H., Silva, R., Ghadessi, M., Leal, S., Gashaw, I., Damask, A., Paulding, C., & Rittenhouse, K. D. (2024) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.65.8.17 · Cited by 6
“…staining of the human retina shows moderate positivity for ANO2 in the outer plexiform layer of the retina, according to the Human Protein Atlas 35 based on data from the Eye Genotype Expression database, 36 with mRNA expression enhanced in photoreceptor cells and microglial cells.”
Villaplana-Velasco, A., Perrot, N., Huang, Y., Chong, M., Trucco, E., Mookiah, M. R. K., Nelson, W., Petch, J., Gerstein, H. C., Raina, P., et al. (2025) · Science Advances · doi:10.1126/sciadv.adu1985 · Cited by 7
“Of the eight MR significant biomarkers, three (IgG–Fc RecIIb, PON2, and IL-16) were expressed in retinal tissue and associated with open chromatin regions and related to immune and metabolic networks (table S20) ( 23 ).”
Structural framework to address variant-gene relationship in primary open-angle glaucoma
Singh, N., Kizhatil, K., Duraikkannu, D., Choquet, H., & Nair, K. S. (2024) · Vision Research · doi:10.1016/j.visres.2024.108505 · Cited by 7
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Chimeric Antigen Receptor T Cell Therapy in Acute Myeloid Leukemia: Trials and Tribulations
Garg, S., Wei Min, N. I., Griffin, J. D., & Sattler, M. (2023) · Hematology Reports · doi:10.3390/hematolrep15040063 · Cited by 8
“The expression of these antigens at the transcript level in different tissues (Figure 3A; data from the human proteome atlas [64] and GTEx consortium [65], downloaded from proteinatlas.org and prepared using iDEP [66]) shows potential antigen distribution in normal cells.”
BackgroundDu, Y., Kong, N., & Zhang, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.726599 · Cited by 6
“Ratnapriya et al. (2019) have found potential causal genes in six AMD GWAS loci from human retinal samples.”
BackgroundPower analysis of transcriptome-wide association study: implications for practical protocol choicePreprint
Cao, C., Ding, B., Li, Q., Kwok, D., Wu, J., & Long, Q. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.19.211151 · Cited by 6
“Since then, TWAS has achieved significant success in identifying the genetic basis of complex traits [21-27] and became a popular method in practice.”
BackgroundXie, W., Chen, S., Luo, H., Kong, C., & Wang, D. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1361445 · Cited by 6
Li, X., Tian, Y., Qiu, L., Lou, S., Zhu, G., Gao, Y., Ma, L., & Pan, Y. (2022) · Cells · doi:10.3390/cells11203281 · Cited by 5
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“RNA‐seq data A total of 177 bulk RNA-seq datasets from human retinas of non-visually impaired retinal post-mortem donors were retrieved from two different sources: the first one (hereafter labelled as TIGEM) contains data from 50 human retina samples [8], and the second dataset (hereafter labelled as NEI) contains 127…”
BackgroundMethodLi, J., Shen, H., & Guo, L. (2024) · Cellular Signalling · doi:10.1016/j.cellsig.2024.111069 · Cited by 6
Yang, H., Huang, H., & Pu, K. (2025) · Scientific Reports · doi:10.1038/s41598-025-89246-z · Cited by 6
Qi, G., Zheng, Y., Lin, F., Huang, X., Duan, L., You, Y., Liu, H., Wang, Y., Xu, H., & Chen, G. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13370 · Cited by 5
Boolean implication analysis of single-cell data predicts retinal cell type markers
Subramanian, R., & Sahoo, D. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04915-4 · Cited by 5
Augmented Reality Electronic Glasses Prototype to Improve Vision in Older Adults
Ocares-Cunyarachi, L., Santisteban, A. S., & Andrade–Arenas, L. (2020) · International Journal of Advanced Computer Science and Applications · doi:10.14569/ijacsa.2020.0111185 · Cited by 5
“The disease causes lesions in the central portion of the retina and in the macula which is responsible for the central vision necessary for reading or driving [17].”
BackgroundGuo, S., Liu, X., Cheng, X., Jiang, Y., Ji, S., Liang, Q., Koval, A., Li, Y., Owen, L. A., Kim, I. K., et al. (2024) · Genome Research · doi:10.1101/gr.278822.123 · Cited by 5
A proteogenomic atlas of the human neural retina
Riepe, T. V., Stemerdink, M., Salz, R., Rey, A. D., de Bruijn, S. E., Boonen, E., Tomkiewicz, T. Z., Kwint, M., Gloerich, J., Wessels, H. J. C. T., et al. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1451024 · Cited by 5
eQTL analysis: A bridge from genome to mechanism
Jia, Z., Xu, J., Ma, Y., Wei, S., Sun, C., Chen, X., Kang, J., Chen, H., Zhang, C., Dong, Y., et al. (2025) · Genes & Diseases · doi:10.1016/j.gendis.2025.101850 · Cited by 5
“93 Several other eQTL databases, such as Blood eQTL Browser, 94 EyeGEx, 95 and ImmuNexUT, 96 have been widely used.”
Yuan, J., Zhang, Y., Yao, Y., Li, S., Liang, J., Dai, W., Yang, J., Liu, M., Zhang, Q., Zhou, Y., et al. (2026) · Science Advances · doi:10.1126/sciadv.adw7768 · Cited by 4
“(ii) cis-eQTL mapping mapped SNPs to genes based on significant cis-eQTL associations (FDR ≤ 0.05) from three resources [EyeGEx ( 68 ), GTEx v8 ( 69 ), and BIOS QTL browser ( 70 )].”
InfluentialContribution of the STING in macrophages to the pulmonary inflammation and fibrosis
Wan, X., Zhao, H., Wu, B., Lu, Y., & Xiao, Y. (2026) · International Immunopharmacology · doi:10.1016/j.intimp.2026.116257 · Cited by 4
A systematic review on age-related macular degeneration: New insights from multi-omics studies
Castro-Fernández, D. C., Cañizo-Outeiriño, A., Cuartero‐Martínez, A., Gil‐Martínez, M., Mondelo‐García, C., González‐Barcia, M., Álvarez-Barrios, A., & Fernández‐Ferreiro, A. (2026) · Survey of Ophthalmology · doi:10.1016/j.survophthal.2026.02.001 · Cited by 4
Syntaxin 3B: A SNARE Protein Required for Vision
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“…of T14 phosphorylation for syntaxin 3B activation was first proposed ten years ago by Janz and colleagues [23]. syntaxin 3B activation was fi rst proposed ten years ago by Janz and colleagues [23 This per-ceptive interpretation was based, in part, on the observations that syntaxin 3B lacking its…”
BackgroundDey, P. N., Singh, N., Zelinger, L., Batz, Z. A., Nellissery, J. K., White, N. D., Qian, H., Li, T., Fariss, R. N., Dong, L., et al. (2024) · Human Molecular Genetics · doi:10.1093/hmg/ddae161 · Cited by 4
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“Additionally, to explore retina-specific eQTLs and sQTLs, we utilized the EyeGEx dataset 12 in FUMA to search for relevant associations.”
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Improving retinal vascular endothelial cell tropism through rational rAAV capsid design
Periasamy, R., Patel, D. D., Boye, S. L., Boye, S. L., & Lipinski, D. M. (2023) · PLoS ONE · doi:10.1371/journal.pone.0285370 · Cited by 5
“the inability to efficiently mediate gene transfer to the affected MVECs has severely limited 67 progress towards the development of a long-lasting gene therapy[6, 7].”
BackgroundZhong, C., Wu, C. H., Lin, Y., & Lin, D. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1180500 · Cited by 4
“This approach is based on the concept that a GWAS variant in some tissues affects expression at a nearby gene and that both the gene and tissue might play a role in the disease mechanism (Gamazon et al., 2015; Ratnapriya et al., 2019).”
BackgroundMethodPozo‐Valero, M. D., Almoallem, B., Rey, A. D., Mahieu, Q., Heetvelde, M. V., Jeddawi, L., Bauwens, M., & Baere, E. B. W. D. (2024) · Clinical Genetics · doi:10.1111/cge.14517 · Cited by 4
SLC16A8 is a causal contributor to age-related macular degeneration risk
Nouri, N., Hannon, B. G., Stockwell, A., Truong, T., Kang, G. J., Browder, K. C., Malato, Y., Sène, A., Everen, S. A. V., Wykoff, C. C., et al. (2024) · npj Genomic Medicine · doi:10.1038/s41525-024-00442-8 · Cited by 4
“The locus containing this gene has been seen in common variant AMD GWAS 5,6 , however co-localization studies for the lead GWAS SNP have not beenabletoidentifythecausalgeneatthelocus 8,9 .”
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Integrating external controls in case–control studies improves power for rare‐variant tests
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“However, its association with AMD has been reported through a study based on retina eQTL data (Ratnapriya et al., 2019).”
BackgroundIntegrative multi-omics database (iMOMdb) of Asian pregnant women
Pan, H., Tan, P. F., Lim, I. Y., Huan, J., Teh, A. L., Chen, L., Gong, M., Tin, F., Mir, S. A., Narasimhan, K., et al. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac079 · Cited by 5
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“, angiogenesis, extracellular matrix remodeling, inflammation, and immune responses) were perturbed in retinal pigment epithelium (RPE) cells (15, 16).”
BackgroundLi, J., Li, L., Li, W., Wang, Z., Gao, F., Hu, F., Zhang, S., Qu, S., Huang, J., Wang, L.-S., et al. (2020) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.1218 · Cited by 4
“We also checked data in GTEx's ophthalmic data set (Ratnapriya et al., 2019), rs129882 shows significant association between variant and DBH's expression in retina (p = .0144297) (Figure 3).”
MethodOcular genetics in the genomics age
Walter, M. A., Rezaie, T., Hufnagel, R. B., & Arno, G. (2020) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.31844 · Cited by 4
“In a recent study, over 4,000 eQTLs were detected in postmortem retinas from individuals with AMD compared to those from unaffected donors (Ratnapriya et al., 2019).”
BackgroundMolecular and genetic landscapes of retina and brain microglia in neurodegenerative diseasesPreprint
Ma, K., & Ratnapriya, R. (2025) · Genome Research · doi:10.1101/gr.280554.125 · Cited by 4
“…et al. 2022), they are likely to be enriched in the cis -regulatory elements (CREs), such as promoter, enhancer, and silencer elements of the disease-relevant tissues and cell types, and exert their effects through gene expression regulation (Albert and Kruglyak 2015; Ratnapriya et al. 2019, 2025).”
Self-citationGenome-Wide Association Study to Identify Genetic Variants Associated With Diabetic Maculopathy
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“…generated using the (1) Combined Annotation-Dependent Depletion (CADD) 25 scores, (2) RegulomeDB rank, 26 (3) expression quantitative trait locus (eQTL) mapping using Genotype-Tissue Expression database (GTEx database version 8) and the EyeGEx database 27 at the false discovery rate (FDR) < 0.05.”
InfluentialHong, S. E., Choi, M., & Lee, J. (2025) · Molecules and Cells · doi:10.1016/j.mocell.2025.100256 · Cited by 3
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The Role of Gene Expression Regulation on Genetic Risk of Age-Related Macular Degeneration
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Shared whole environmental etiology between Alzheimer’s disease and age-related macular degeneration
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“Identifying common genetic features between AD and AMD can help in the development of precision medicine approaches tailored to individuals based on their genetic pro fi les 9 .”
BackgroundLi, J., Nagasaka, Y., Shen, H., Zhou, X., Ma, J., Trevisan-Silva, D., Sherman, N. E., Ambati, J., Gelfand, B. D., & Guo, L. (2025) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2025.102460 · Cited by 3
“While there is no perfect murine model for mimicking human AMD, the oxidant (NaIO 3 )-induced model is widely acknowledged for inducing damage to the RPE and subsequent loss of photoreceptors.”
Metadata
- Authors
- Ratnapriya, R., Sosina, O. A., Starostik, M. R., Kwicklis, M., Kapphahn, R. J., Fritsche, L. G., Walton, A., Arvanitis, M., Gieser, L., Pietraszkiewicz, A., Montezuma, S. R., Chew, E. Y., Battle, A., Abecasis, G. R., Ferrington, D. A., Chatterjee, N., & Swaroop, A.
- Affiliations
- National Institutes of Health (US)
- University of Minnesota (US)
- University of Michigan (US)
- Johns Hopkins University (US)
- Corresponding author
- Ferrington, Deborah A.
- Chatterjee, Nilanjan
- Swaroop, Anand
- ORCID
- Venue
- Nature Genetics
- Published
- 2019-02-11
- Volume
- 51
- Issue
- 4
- Pages
- 606-610
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6441365
- OpenAlex
- W2914762802
- Cited by
- 312
- References
- 56
- Citations by year
- 2026: 47 · 2025: 49 · 2024: 46 · 2023: 40 · 2022: 35 · 2021: 36 · 2020: 46 · 2019: 13
- FWCI
- 31.89
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-05-08)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Minnesota Lions Eye Bank
- University of Minnesota
- National Institutes of Health
- National Human Genome Research Institute (T32HG000040)
- National Eye Institute (ZIAEY000475, Z01EY000450, R01EY026012, ZIAEY000474, ZIAEY000450, R01EY028554)
- Topics
- Health Sciences › Medicine › Ophthalmology › Retinal Diseases and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Ophthalmology › Retinal Development and Disorders
- Keywords
- age-related macular degeneration, retinal transcriptome, expression quantitative trait loci, transcriptome-wide association study, cis-eQTL, RLBP1, HIC1, PARP12, non-coding RNA, ocular genetics
- MeSH terms
- Gene Expression Regulation, Genotype, Humans, Macular Degeneration, Phenotype, Retina, Case-Control Studies, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Genome-Wide Association Study, Transcriptome
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