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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]
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.
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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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Zhang C, Reynolds AL, Beiter A, Lillvis JH, Reynolds JD. Effect of Low-dose Intravitreal Bevacizumab and Ranibizumab on Regression and Late Reactivation in Retinopathy of Prematurity in the Treatment-Naïve Eyes. Ophthalmol Retina 2022; 6:328-330. [PMID: 34968757 DOI: 10.1016/j.oret.2021.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, University at Buffalo, Buffalo, New York
| | - Andrew L Reynolds
- Department of Ophthalmology, Ross Eye Institute, University at Buffalo, Buffalo, New York.
| | - Andrew Beiter
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia
| | - John H Lillvis
- Department of Ophthalmology, Ross Eye Institute, University at Buffalo, Buffalo, New York
| | - James D Reynolds
- Department of Ophthalmology, Ross Eye Institute, University at Buffalo, Buffalo, New York
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Zhang C, Owen LA, Lillvis JH, Zhang SX, Kim IK, DeAngelis MM. AMD Genomics: Non-Coding RNAs as Biomarkers and Therapeutic Targets. J Clin Med 2022; 11:jcm11061484. [PMID: 35329812 PMCID: PMC8954267 DOI: 10.3390/jcm11061484] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 12/04/2022] Open
Abstract
Age-related macular degeneration (AMD) is a progressive neurodegenerative disease that is the world’s leading cause of blindness in the aging population. Although the clinical stages and forms of AMD have been elucidated, more specific prognostic tools are required to determine when patients with early and intermediate AMD will progress into the advanced stages of AMD. Another challenge in the field has been the appropriate development of therapies for intermediate AMD and advanced atrophic AMD. After numerous negative clinical trials, an anti-C5 agent and anti-C3 agent have recently shown promising results in phase 3 clinical trials, in terms of slowing the growth of geographic atrophy, an advanced form of AMD. Interestingly, both drugs appear to be associated with an increased incidence of wet AMD, another advanced form of the disease, and will require frequent intravitreal injections. Certainly, there remains a need for other therapeutic agents with the potential to prevent progression to advanced stages of the disease. Investigation of the role and clinical utility of non-coding RNAs (ncRNAs) is a major advancement in biology that has only been minimally applied to AMD. In the following review, we discuss the clinical relevance of ncRNAs in AMD as both biomarkers and therapeutic targets.
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Affiliation(s)
- 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; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
| | - 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; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- 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
| | - 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; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - 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; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- Department of Biochemistry, 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
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Correspondence: (I.K.K.); (M.M.D.)
| | - 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; (C.Z.); (L.A.O.); (J.H.L.); (S.X.Z.)
- 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
- 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
- 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
- Correspondence: (I.K.K.); (M.M.D.)
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Lillvis JH, Lillvis DF, Towle-Miller LM, Wilding GE, Kuo DZ. Association of state vision screening requirements with parent-reported vision testing in young children. J AAPOS 2020; 24:291.e1-291.e6. [PMID: 33007448 DOI: 10.1016/j.jaapos.2020.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To examine the relationship between state school vision screening requirements and the likelihood that children 3-5 years of age receive vision testing. METHODS We obtained nationally representative data from the 2016 National Survey of Children's Health on children ages 3-5 (n = 7,567) and used available sources to compile state policies that mandate childhood vision testing. We calculated the rates of parent-reported vision testing for each state and fit logistic regression models using survey-based estimation methods with nationally representative weights. Our models controlled for factors such as age, sex, race/ethnicity, and insurance coverage. Additional analyses added comorbidities that may lead to an eye care provider referral. RESULTS Parent-reported vision testing rates by state ranged from 41% to 84%. A significant association was found between the presence of state-level vision screening requirements and parent-reported vision testing, which remained after controlling for comorbidities (aOR = 1.374; P = 0.016). Of these comorbidities, arthritis, blindness, and very low birth weight were associated with a higher rate of vision screening (all P < 0.05). CONCLUSIONS The presence of a state-level school vision screening requirement is associated with increased parent-reported vision testing in children 3-5 years of age. This suggests that state policy may ensure timely screening for amblyopia and other sight-threatening complications.
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Affiliation(s)
- John H Lillvis
- Ross Eye Institute, University at Buffalo Jacobs School of Medicine, Buffalo, New York.
| | - Denise F Lillvis
- Department of Family Medicine, University at Buffalo Jacobs School of Medicine, Buffalo, New York
| | - Lorin M Towle-Miller
- Department of Biostatistics, University at Buffalo School of Public Health and Health Professions, Buffalo, New York
| | - Gregory E Wilding
- Department of Biostatistics, University at Buffalo School of Public Health and Health Professions, Buffalo, New York
| | - Dennis Z Kuo
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine, Buffalo, New York
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Hinterseher I, Schworer CM, Lillvis JH, Stahl E, Erdman R, Gatalica Z, Tromp G, Kuivaniemi H. Immunohistochemical analysis of the natural killer cell cytotoxicity pathway in human abdominal aortic aneurysms. Int J Mol Sci 2015; 16:11196-212. [PMID: 25993291 PMCID: PMC4463696 DOI: 10.3390/ijms160511196] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 12/18/2022] Open
Abstract
Our previous analysis using genome-wide microarray expression data revealed extreme overrepresentation of immune related genes belonging the Natural Killer (NK) Cell Mediated Cytotoxicity pathway (hsa04650) in human abdominal aortic aneurysm (AAA). We followed up the microarray studies by immunohistochemical analyses using antibodies against nine members of the NK pathway (VAV1, VAV3, PLCG1, PLCG2, HCST, TYROBP, PTK2B, TNFA, and GZMB) and aortic tissue samples from AAA repair operations (n = 6) and control aortae (n = 8) from age-, sex- and ethnicity-matched donors from autopsies. The results confirmed the microarray results. Two different members of the NK pathway, HCST and GRZB, which act at different steps in the NK-pathway, were actively transcribed and translated into proteins in the same cells in the AAA tissue demonstrated by double staining. Furthermore, double staining with antibodies against CD68 or CD8 together with HCST, TYROBP, PTK2B or PLCG2 revealed that CD68 and CD8 positive cells expressed proteins of the NK-pathway but were not the only inflammatory cells involved in the NK-pathway in the AAA tissue. The results provide strong evidence that the NK Cell Mediated Cytotoxicity Pathway is activated in human AAA and valuable insight for future studies to dissect the pathogenesis of human AAA.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adult
- Aged
- Aged, 80 and over
- Antigens, CD/metabolism
- Antigens, Differentiation, Myelomonocytic/metabolism
- Aorta, Abdominal/metabolism
- Aorta, Abdominal/pathology
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/pathology
- CD8 Antigens/metabolism
- Female
- Focal Adhesion Kinase 2/genetics
- Focal Adhesion Kinase 2/metabolism
- Humans
- Immunohistochemistry
- Killer Cells, Natural/cytology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Male
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Phospholipase C gamma/metabolism
- Proto-Oncogene Proteins c-vav/genetics
- Proto-Oncogene Proteins c-vav/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Transcriptome
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Affiliation(s)
- Irene Hinterseher
- Department of General, Visceral, Vascular and Thoracic Surgery, Charité Universitätsmedizin, Campus Mitte, 10117 Berlin, Germany.
| | - Charles M Schworer
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - John H Lillvis
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA.
| | - Elizabeth Stahl
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - Robert Erdman
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | | | - Gerard Tromp
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - Helena Kuivaniemi
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
- Department of Surgery, Temple University School of Medicine, Philadelphia, PA 19140, USA.
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7
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Pahl MC, Erdman R, Kuivaniemi H, Lillvis JH, Elmore JR, Tromp G. Transcriptional (ChIP-Chip) Analysis of ELF1, ETS2, RUNX1 and STAT5 in Human Abdominal Aortic Aneurysm. Int J Mol Sci 2015; 16:11229-58. [PMID: 25993293 PMCID: PMC4463698 DOI: 10.3390/ijms160511229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 12/31/2014] [Indexed: 01/22/2023] Open
Abstract
We investigated transcriptional control of gene expression in human abdominal aortic aneurysm (AAA). We previously identified 3274 differentially expressed genes in human AAA tissue compared to non-aneurysmal controls. Four expressed transcription factors (ELF1, ETS2, STAT5 and RUNX1) were selected for genome-wide chromatin immunoprecipitation. Transcription factor binding was enriched in 4760 distinct genes (FDR < 0.05), of which 713 were differentially expressed in AAA. Functional classification using Gene Ontology (GO), KEGG, and Network Analysis revealed enrichment in several biological processes including “leukocyte migration” (FDR = 3.09 × 10−05) and “intracellular protein kinase cascade” (FDR = 6.48 × 10−05). In the control aorta, the most significant GO categories differed from those in the AAA samples and included “cytoskeleton organization” (FDR = 1.24 × 10−06) and “small GTPase mediated signal transduction” (FDR = 1.24 × 10−06). Genes up-regulated in AAA tissue showed a highly significant enrichment for GO categories “leukocyte migration” (FDR = 1.62 × 10−11), “activation of immune response” (FDR = 8.44 × 10−11), “T cell activation” (FDR = 4.14 × 10−10) and “regulation of lymphocyte activation” (FDR = 2.45 × 10−09), whereas the down-regulated genes were enriched in GO categories “cytoskeleton organization” (FDR = 7.84 × 10−05), “muscle cell development” (FDR = 1.00 × 10−04), and “organ morphogenesis” (FDR = 3.00 × 10−04). Quantitative PCR assays confirmed a sub-set of the transcription factor binding sites including those in MTMR11, DUSP10, ITGAM, MARCH1, HDAC8, MMP14, MAGI1, THBD and SPOCK1.
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Affiliation(s)
- Matthew C Pahl
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - Robert Erdman
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - Helena Kuivaniemi
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
- Department of Surgery, Temple University School of Medicine, Philadelphia, PA 19140, USA.
| | - John H Lillvis
- Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI 48202, USA.
| | - James R Elmore
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA 17822, USA.
| | - Gerard Tromp
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
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8
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Ryer EJ, Ronning KE, Erdman R, Schworer CM, Elmore JR, Peeler TC, Nevius CD, Lillvis JH, Garvin RP, Franklin DP, Kuivaniemi H, Tromp G. The potential role of DNA methylation in abdominal aortic aneurysms. Int J Mol Sci 2015; 16:11259-75. [PMID: 25993294 PMCID: PMC4463699 DOI: 10.3390/ijms160511259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/19/2015] [Indexed: 12/14/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is a complex disorder that has a significant impact on the aging population. While both genetic and environmental risk factors have been implicated in AAA formation, the precise genetic markers involved and the factors influencing their expression remain an area of ongoing investigation. DNA methylation has been previously used to study gene silencing in other inflammatory disorders and since AAA has an extensive inflammatory component, we sought to examine the genome-wide DNA methylation profiles in mononuclear blood cells of AAA cases and matched non-AAA controls. To this end, we collected blood samples and isolated mononuclear cells for DNA and RNA extraction from four all male groups: AAA smokers (n = 11), AAA non-smokers (n = 9), control smokers (n = 10) and control non-smokers (n = 11). Methylation data were obtained using the Illumina 450k Human Methylation Bead Chip and analyzed using the R language and multiple Bioconductor packages. Principal component analysis and linear analysis of CpG island subsets identified four regions with significant differences in methylation with respect to AAA: kelch-like family member 35 (KLHL35), calponin 2 (CNN2), serpin peptidase inhibitor clade B (ovalbumin) member 9 (SERPINB9), and adenylate cyclase 10 pseudogene 1 (ADCY10P1). Follow-up studies included RT-PCR and immunostaining for CNN2 and SERPINB9. These findings are novel and suggest DNA methylation may play a role in AAA pathobiology.
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Affiliation(s)
- Evan J Ryer
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA 17822, USA.
| | - Kaitryn E Ronning
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
- Department of Biology, Susquehanna University, Selinsgrove, PA 17870, USA.
| | - Robert Erdman
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - Charles M Schworer
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - James R Elmore
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA 17822, USA.
| | - Thomas C Peeler
- Department of Biology, Susquehanna University, Selinsgrove, PA 17870, USA.
| | - Christopher D Nevius
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
| | - John H Lillvis
- Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI 48202, USA.
| | - Robert P Garvin
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA 17822, USA.
| | - David P Franklin
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, PA 17822, USA.
| | - Helena Kuivaniemi
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
- Department of Surgery, Temple University School of Medicine, Philadelphia, PA 19140, USA.
| | - Gerard Tromp
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822, USA.
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9
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Hinterseher I, Erdman R, Elmore JR, Stahl E, Pahl MC, Derr K, Golden A, Lillvis JH, Cindric MC, Jackson K, Bowen WD, Schworer CM, Chernousov MA, Franklin DP, Gray JL, Garvin RP, Gatalica Z, Carey DJ, Tromp G, Kuivaniemi H. Novel pathways in the pathobiology of human abdominal aortic aneurysms. Pathobiology 2012; 80:1-10. [PMID: 22797469 PMCID: PMC3782105 DOI: 10.1159/000339303] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/23/2012] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES Abdominal aortic aneurysm (AAA), a dilatation of the infrarenal aorta, typically affects males >65 years. The pathobiological mechanisms of human AAA are poorly understood. The goal of this study was to identify novel pathways involved in the development of AAAs. METHODS A custom-designed 'AAA-chip' was used to assay 43 of the differentially expressed genes identified in a previously published microarray study between AAA (n = 15) and control (n = 15) infrarenal abdominal aorta. Protein analyses were performed on selected genes. RESULTS Altogether 38 of the 43 genes on the 'AAA-chip' showed significantly different expression. Novel validated genes in AAA pathobiology included ADCY7, ARL4C, BLNK, FOSB, GATM, LYZ, MFGE8, PRUNE2, PTPRC, SMTN, TMODI and TPM2. These genes represent a wide range of biological functions, such as calcium signaling, development and differentiation, as well as cell adhesion not previously implicated in AAA pathobiology. Protein analyses for GATM, CD4, CXCR4, BLNK, PLEK, LYZ, FOSB, DUSP6, ITGA5 and PTPRC confirmed the mRNA findings. CONCLUSION The results provide new directions for future research into AAA pathogenesis to study the role of novel genes confirmed here. New treatments and diagnostic tools for AAA could potentially be identified by studying these novel pathways.
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Affiliation(s)
- Irene Hinterseher
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
- Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, Dresden, Germany
| | - Robert Erdman
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - James R Elmore
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Elizabeth Stahl
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Matthew C Pahl
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Kimberly Derr
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Alicia Golden
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - John H Lillvis
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Matthew C Cindric
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Kathryn Jackson
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - William D Bowen
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Charles M Schworer
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Michael A Chernousov
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - David P Franklin
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | - John L Gray
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Robert P Garvin
- Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, Pennsylvania, USA
| | | | - David J Carey
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Gerard Tromp
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Helena Kuivaniemi
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
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10
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Lillvis JH, Erdman R, Schworer CM, Golden A, Derr K, Gatalica Z, Cox LA, Shen J, Vander Heide RS, Lenk GM, Hlavaty L, Li L, Elmore JR, Franklin DP, Gray JL, Garvin RP, Carey DJ, Lancaster WD, Tromp G, Kuivaniemi H. Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms. BMC Physiol 2011; 11:9. [PMID: 21627813 PMCID: PMC3125234 DOI: 10.1186/1472-6793-11-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 05/31/2011] [Indexed: 12/19/2022]
Abstract
BACKGROUND The infrarenal abdominal aorta exhibits increased disease susceptibility relative to other aortic regions. Allograft studies exchanging thoracic and abdominal segments showed that regional susceptibility is maintained regardless of location, suggesting substantial roles for embryological origin, tissue composition and site-specific gene expression. RESULTS We analyzed gene expression with microarrays in baboon aortas, and found that members of the HOX gene family exhibited spatial expression differences. HOXA4 was chosen for further study, since it had decreased expression in the abdominal compared to the thoracic aorta. Western blot analysis from 24 human aortas demonstrated significantly higher HOXA4 protein levels in thoracic compared to abdominal tissues (P < 0.001). Immunohistochemical staining for HOXA4 showed nuclear and perinuclear staining in endothelial and smooth muscle cells in aorta. The HOXA4 transcript levels were significantly decreased in human abdominal aortic aneurysms (AAAs) compared to age-matched non-aneurysmal controls (P < 0.00004). Cultured human aortic endothelial and smooth muscle cells stimulated with INF-γ (an important inflammatory cytokine in AAA pathogenesis) showed decreased levels of HOXA4 protein (P < 0.0007). CONCLUSIONS Our results demonstrated spatial variation in expression of HOXA4 in human aortas that persisted into adulthood and that downregulation of HOXA4 expression was associated with AAAs, an important aortic disease of the ageing population.
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Affiliation(s)
- John H Lillvis
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
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11
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Hinterseher I, Erdman R, Donoso LA, Vrabec TR, Schworer CM, Lillvis JH, Boddy AM, Derr K, Golden A, Bowen WD, Gatalica Z, Tapinos N, Elmore JR, Franklin DP, Gray JL, Garvin RP, Gerhard GS, Carey DJ, Tromp G, Kuivaniemi H. Role of complement cascade in abdominal aortic aneurysms. Arterioscler Thromb Vasc Biol 2011; 31:1653-60. [PMID: 21493888 DOI: 10.1161/atvbaha.111.227652] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The goal of this study was to investigate the role of complement cascade genes in the pathobiology of human abdominal aortic aneurysms (AAAs). METHODS AND RESULTS Results of a genome-wide microarray expression profiling revealed 3274 differentially expressed genes between aneurysmal and control aortic tissue. Interestingly, 13 genes in the complement cascade were significantly differentially expressed between AAA and the controls. In silico analysis of the promoters of the 13 complement cascade genes showed enrichment for transcription factor binding sites for signal transducer and activator of transcription (STAT)5A. Chromatin-immunoprecipitation experiments demonstrated binding of transcription factor STAT5A to the promoters of the majority of the complement cascade genes. Immunohistochemical analysis showed strong staining for C2 in AAA tissues. CONCLUSIONS These results provide strong evidence that the complement cascade plays a role in human AAA. Based on our microarray studies, the pathway is activated in AAA, particularly via the lectin and classical pathways. The overrepresented binding sites of transcription factor STAT5A in the complement cascade gene promoters suggest a role for STAT5A in the coordinated regulation of complement cascade gene expression.
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Affiliation(s)
- Irene Hinterseher
- Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, PA 17822-2610, USA
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12
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Lillvis JH, Kyo Y, Tromp G, Lenk GM, Li M, Lu Q, Igo RP, Sakalihasan N, Ferrell RE, Schworer CM, Gatalica Z, Land S, Kuivaniemi H. Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19. BMC Med Genet 2011; 12:14. [PMID: 21247474 PMCID: PMC3037298 DOI: 10.1186/1471-2350-12-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 01/19/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database. METHODS Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22) were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies. RESULTS Several SNPs were nominally associated with AAA (p < 0.05). The SNPs with most significant p-values were located near the CCAAT enhancer binding protein (CEBPG), peptidase D (PEPD), and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP) database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples. CONCLUSIONS Association testing of the functional positional candidate genes on the AAA1 locus on chromosome 19q13 demonstrated nominal association in three genes. PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.
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Affiliation(s)
- John H Lillvis
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
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13
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Lillvis JH, Lanfear DE. Progress toward genetic tailoring of heart failure therapy. Curr Opin Mol Ther 2010; 12:294-304. [PMID: 20521218 PMCID: PMC3048822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Heart failure (HF) is a modern epidemic and a heterogeneous disorder with many therapeutic options. While the average response to each individual treatment is favorable, significant interindividual variation exists in the response to HF therapeutics. As a result, the optimal regimen for an individual patient or subgroup of patients is elusive, with current treatment being mainly empirical. Pharmacogenetic customization of HF therapy may provide an important opportunity to improve the treatment of HF. Common genetic variations exist in genes related to most classes of HF drugs, many of which have known functional consequences for or established relationships with drug response. This review summarizes the current understanding of the pharmacogenetics of HF therapeutics, including angiotensin-converting enzyme inhibitors and beta-blockers, and focuses on recent advances and medium-term expectations for the field.
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Affiliation(s)
- John H Lillvis
- Wayne State University, Center for Molecular Medicine and Genetics, 540 East Canfield, Detroit, MI 48201, USA
| | - David E Lanfear
- Henry Ford Hospital, Heart and Vascular Institute, Section of Advanced Heart Failure and Cardiac Transplantation, 2799 West Grand Boulevard, Detroit, MI 48202, USA
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14
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Boddy AM, Lenk GM, Lillvis JH, Nischan J, Kyo Y, Kuivaniemi H. Basic research studies to understand aneurysm disease. Drug News Perspect 2008; 21:142-148. [PMID: 18560612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Abdominal aortic aneurysm (AAA) is a complex multifactorial disease with life-threatening implications. Aneurysms typically have no signs or symptoms, and rupture of AAA has a high mortality rate. Multiple environmental and genetic risk factors are involved in aneurysm formation and progression making it a complicated disease to study. Little is understood about the mechanisms in disease initiation, thus there are currently no therapeutic approaches to prevent AAA, leaving patients with surgery as their only option. Ongoing research into the genetic components of AAA using a candidate gene approach has been overall unsuccessful. A more promising approach to study complex diseases involves genome-wide techniques such as DNA linkage analysis, genetic association studies and microarray expression profiling. Furthermore, studies involving inhibition of AAA progression, rather than formation, have a potentially promising outcome. Targeting biological pathways in AAA pathogenesis may benefit patients by slowing the growth and possibly preventing the rupture of AAA. Critical pathways involved in AAA pathogenesis include immunological processes, such as T-cell and natural killer cell pathways, oxidative stress, depletion of vascular smooth muscle cells through the process of apoptosis and the destruction of the extracellular matrix by matrix metalloproteinases.
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Affiliation(s)
- Amy M Boddy
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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