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Rylee A. Zavala

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Shwani T, Zhang C, Owen LA, Shakoor A, Vitale AT, Lillvis JH, Barr JL, Cromwell P, Finley R, Husami N, Au E, Zavala RA, Graves EC, Zhang SX, Farkas MH, Ammar DA, Allison KM, Tawfik A, Sherva RM, Li M, Stambolian D, Kim IK, Farrer LA, DeAngelis MM. Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration. Cells 2023;12:2668. [PMID: 38067097 PMCID: PMC10705168 DOI: 10.3390/cells12232668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open

Abstract

Age-related macular degeneration (AMD) is a leading cause of blindness, and elucidating its underlying disease mechanisms is vital to the development of appropriate therapeutics. 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 (60-94 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, RORα, 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.

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Affiliation(s)

Treefa Shwani 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Neuroscience Graduate Program, 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
Leah A. Owen 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.) 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
Akbar Shakoor Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
Albert T. Vitale Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
Parker Cromwell 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
Sarah X. 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) 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
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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Neuroscience Graduate Program, 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 Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
David A. Ammar Lion’s Eye Institute for Transplant & Research, Tampa, FL 33605, USA;
Karen M. Allison Department of Ophthalmology, Flaum Eye Institute, University of Rochester, Rochester, NY 14642, USA;
Amany Tawfik Department of Foundational Medical Studies and Eye Research Center, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA; Eye Research Institute, Oakland University, Rochester, MI 48309, USA
Richard M. Sherva Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
Mingyao Li Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
Dwight Stambolian Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
Ivana K. Kim Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA;
Lindsay A. Farrer Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
Margaret M. DeAngelis 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; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.) Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.) Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA Department of Biochemistry, 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

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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 Genom 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] [What about the content of this article? (0)] [Affiliation(s)] [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]

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

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