Cited by 325Retinal Diseases and TreatmentsGenetic Associations and EpidemiologyRetinal Development and Disorders

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Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration

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Ratnapriya, Rinki, Sosina, Olukayode A., Starostik, Margaret R., Kwicklis, Madeline, Kapphahn, Rebecca J., Fritsche, Lars G., Walton, Ashley, Arvanitis, Marios, Gieser, Linn, Pietraszkiewicz, Alexandra, Montezuma, Sandra R., Chew, Emily Y., Battle, Alexis, Abecasis, Gonçalo R., Ferrington, Deborah A., Chatterjee, Nilanjan, Swaroop, Anand·2019·Nature Genetics

DOI 10.1038/s41588-019-0351-9PMC PMC6441365

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Abstract

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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Background
HTRA1 rs11528744, BCRA1 rs9928736, and B3GLCT rs4381465 are associated with age-related macular degeneration in a Chinese population
Huang, G. P., Li, H., Lai, S., Xiao, J., Wang, L., Xu, H., Lei, C., Zhang, J., Yu, M., Shuai, P., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.997840 · Cited by 1
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Fletcher, E. L., Pébay, A., Rutar, M., Kakavand, K., Wang, A. Y., Vessey, K. A., Jobling, A. I., & Greferath, U. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-809324-5.24191-6
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Method
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“Encoding a component of the BLOC1 protein complex required for the biogenesis and function of the 172 endosomal-lysosomal system, BLOC1S1 was previously hypothesized to play a role in synaptic 173 function.(24) BLOC1S1’s putative function as a transporter between endosomes and lysosomes, and the 174 observation that a…”
Background
Understanding retinal diseases with genotypic and transcriptomic data analysis
Manda, S. A. P. (2021) · Minerva Access (University of Melbourne)
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“SGC without semi-supervised cluster improvement) and SGC with three pipelines (WGCNA, CoExpNets, CEMiTool) on 12 gene expression datasets: 4 DNA-microarray datasets [18, 48, 47, 5] and 8 RNA-sequencing datasets [43, 29, 24, 9, 41, 35, 36, 42].”
Method
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Usoltseva, A. S., Litwin, C., Lee, M., Hill, C., Cai, J., & Chen, Y. (2024) · The FASEB Journal · doi:10.1096/fj.202400981r
“Dysregulated lipid metabolism has been linked to the pathogenesis of AMD, 1,57–59 and therefore, we examined additional markers of AMD, with a particular focus on inflammatory markers, in frozen sections of posterior eyes.”
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Additional file 2 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26721990
Additional file 7 of Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Ruiz-Ceja, K. A., Capasso, D., Pinelli, M., Prete, E. D., Carrella, D., di Bernardo, D., & Banfi, S. (2023) · Figshare · doi:10.6084/m9.figshare.22655475
Additional file 6 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722002
Additional file 1 of Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease
Rey, A. D., Pozo‐Valero, M. D., Bouckaert, M., Wood, K., den Broeck, F. V., Varela, M. D., Thomas, H. B., Heetvelde, M. V., Bruyne, M. D., de Sompele, S. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26664214
Additional file 3 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26721993
Additional file 4 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26721996
Additional file 10 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722014
Additional file 7 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722005
Additional file 2 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.24647311
Additional file 3 of Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease
Rey, A. D., Pozo‐Valero, M. D., Bouckaert, M., Wood, K., den Broeck, F. V., Varela, M. D., Thomas, H. B., Heetvelde, M. V., Bruyne, M. D., de Sompele, S. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26664226
Additional file 1 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24647213
Additional file 9 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722011
Additional file 1 of Boolean implication analysis of single-cell data predicts retinal cell type markers
Subramanian, R., & Sahoo, D. (2022) · Figshare · doi:10.6084/m9.figshare.21151415
Additional file 5 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26721999
Additional file 2 of Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease
Rey, A. D., Pozo‐Valero, M. D., Bouckaert, M., Wood, K., den Broeck, F. V., Varela, M. D., Thomas, H. B., Heetvelde, M. V., Bruyne, M. D., de Sompele, S. V., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26664217
Additional file 3 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26645521
Additional file 1 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26721987
Additional file 8 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722008
Additional file 11 of Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
D’haene, E., López-Soriano, V., Martínez‐García, P. M., Kalayanamontri, S., Rey, A. D., Sousa‐Ortega, A., Naranjo, S., de Sompele, S. V., Vantomme, L., Mahieu, Q., et al. (2024) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.6084/m9.figshare.26722017
Network-phenotype key gene screening (NPKG) identifies therapeutically relevant targets for neurodegenerative diseases
Diao, Y., Li, J., Gao, C., Fang, H., & Mao, S. (2026) · Genes & Diseases · doi:10.1016/j.gendis.2026.102033
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Gangappa, K., Duraikkannu, D., Advani, J., Labelle‐Dumais, C., Uludag, E. B., Singh, N., Koli, S., Jiang, C., Kuo, Y., Ishikawa, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.11.697334
“54 The expression of these transcription factors was further checked in single cell RNAseq data from human retina and transcription factors with average log expression > 1 in Müller cells was further considered ( Table S8) .”
Self-citation
Synergistic Effects of Urban Air Pollution Mixtures on AMD Pathogenesis: Subtype-Specific Molecular Signatures and Predictive Modeling
Chen, M. (2026) · Aerosol and Air Quality Research · doi:10.1007/s44408-026-00111-8
Single-cell quantitative trait loci analyses identify expression changes in macular degeneration risk genesPreprint
Voigt, A. P., Mullin, N. K., Mulfaul, K., Lozano, L. P., Navratil, E., Flamme‐Wiese, M. J., Lavine, J. A., Fingert, J. H., Tucker, B. A., Stone, E. M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.30.714946
“In addition to identifying genetic variants implicated in gene expression regulation, we next identified genes enriched in different AMD states by performing a pseudobulk differential expression analysis between control cells and each of early dry AMD, geographic atrophy, and MNV donors ( SI Files 2-4 ).”
Influential

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: Ratnapriya, Rinki
Sosina, Olukayode A.
Starostik, Margaret R.
Fritsche, Lars G.
Arvanitis, Marios
Pietraszkiewicz, Alexandra
Montezuma, Sandra R.
Chew, Emily Y.
Battle, Alexis
Abecasis, Gonçalo R.
Ferrington, Deborah A.
Chatterjee, Nilanjan
Swaroop, Anand
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2019-02-11
Volume: 51
Issue: 4
Pages: 606-610
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/s41588-019-0351-9
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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Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration

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