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We identified differentially expressed genes (DEGs) and differentially spliced genes (DSGs) across the clinical stages of AMD in disease-affected tissue, the macular retina pigment epithelium (RPE)\/choroid and the macular neural retina within the same eye. We utilized 27 deeply phenotyped donor eyes (recovered within a 6 h postmortem interval time) from Caucasian donors (60\u201394 years) using a standardized published protocol. Significant findings were then validated in an independent set of well-characterized donor eyes (n = 85). There was limited overlap between DEGs and DSGs, suggesting distinct mechanisms at play in AMD pathophysiology. A greater number of previously reported AMD loci overlapped with DSGs compared to DEGs between disease states, and no DEG overlap with previously reported loci was found in the macular retina between disease states. Additionally, we explored allele-specific expression (ASE) in coding regions of previously reported AMD risk loci, uncovering a significant imbalance in C3 rs2230199 and CFH rs1061170 in the macular RPE\/choroid for normal eyes and intermediate AMD (iAMD), and for CFH rs1061147 in the macular RPE\/choroid for normal eyes and iAMD, and separately neovascular AMD (NEO). Only significant DEGs\/DSGs from the macular RPE\/choroid were found to overlap between disease states. STAT1, validated between the iAMD vs. normal comparison, and AGTPBP1, BBS5, CERKL, FGFBP2, KIFC3, ROR\u03b1, and ZNF292, validated between the NEO vs. normal comparison, revealed an intricate regulatory network with transcription factors and miRNAs identifying potential upstream and downstream regulators. Findings regarding the complement genes C3 and CFH suggest that coding variants at these loci may influence AMD development via an imbalance of gene expression in a tissue-specific manner. Our study provides crucial insights into the multifaceted genomic underpinnings of AMD (i.e., tissue-specific gene expression changes, potential splice variation, and allelic imbalance), which may open new avenues for AMD diagnostics and therapies specific to iAMD and NEO.<\/jats:p>","DOI":"10.3390\/cells12232668","type":"journal-article","created":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T01:48:45Z","timestamp":1700531325000},"page":"2668","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration"],"prefix":"10.3390","volume":"12","author":[{"given":"Treefa","family":"Shwani","sequence":"first","affiliation":[{"name":"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"},{"name":"Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Zhang","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3802-3868","authenticated-orcid":false,"given":"Leah A.","family":"Owen","sequence":"additional","affiliation":[{"name":"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"},{"name":"Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"},{"name":"Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"},{"name":"Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akbar","family":"Shakoor","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert T.","family":"Vitale","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parker","family":"Cromwell","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Finley","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadine","family":"Husami","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Au","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rylee A.","family":"Zavala","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elijah C.","family":"Graves","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, 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Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA"},{"name":"Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA"},{"name":"Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-7192","authenticated-orcid":false,"given":"David A.","family":"Ammar","sequence":"additional","affiliation":[{"name":"Lion\u2019s Eye Institute for Transplant & Research, Tampa, FL 33605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen M.","family":"Allison","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Flaum Eye Institute, University of Rochester, Rochester, NY 14642, 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dwight","family":"Stambolian","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivana K.","family":"Kim","sequence":"additional","affiliation":[{"name":"Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5533-4225","authenticated-orcid":false,"given":"Lindsay A.","family":"Farrer","sequence":"additional","affiliation":[{"name":"Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3731-142X","authenticated-orcid":false,"given":"Margaret M.","family":"DeAngelis","sequence":"additional","affiliation":[{"name":"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"},{"name":"Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA"},{"name":"Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"},{"name":"Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA"},{"name":"Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA"},{"name":"Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA"},{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Chew, E.Y., and Swaroop, A. (2021). Age-Related Macular Degeneration, Springer International Publishing.","DOI":"10.1007\/978-3-030-66014-7"},{"key":"ref_2","first-page":"e39624","article-title":"Age-Related Macular Degeneration: An Exponentially Emerging Imminent Threat of Visual Impairment and Irreversible Blindness","volume":"15","author":"Chaudhuri","year":"2023","journal-title":"Cureus"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1186\/s12967-023-03937-7","article-title":"Emerging therapeutic strategies for unmet need in neovascular age-related macular degeneration","volume":"21","author":"Khachigian","year":"2023","journal-title":"J. Transl. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"917","DOI":"10.2147\/OPTH.S231913","article-title":"Neovascular Age-Related Macular Degeneration (nAMD): A Review of Emerging Treatment Options","volume":"16","author":"Tan","year":"2022","journal-title":"Clin. Ophthalmol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"25158414221083363","DOI":"10.1177\/25158414221083363","article-title":"Quantitative assessment of retinal fluid in neovascular age-related macular degeneration under anti-VEGF therapy","volume":"14","author":"Reiter","year":"2022","journal-title":"Ther. Adv. Ophthalmol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Age-Related Eye Disease Study Research Group (2001). A randomized, placebo-controlled, clinical trial of high-dose supplementation with vitamins C and E, beta carotene, and zinc for age-related macular degeneration and vision loss: AREDS report no. 8. Arch. Ophthalmol., 119, 1417\u20131436.","DOI":"10.1001\/archopht.119.10.1417"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1038\/ng.3448","article-title":"A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants","volume":"48","author":"Fritsche","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/s41588-019-0351-9","article-title":"Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration","volume":"51","author":"Ratnapriya","year":"2019","journal-title":"Nat. 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