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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] [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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Owen LA, Zhang C, Shirer K, Carroll L, Wood B, Szczotka K, Cornia C, Stubben C, Fung C, Yost CC, Katikaneni LD, DeAngelis MM, Comstock J. Placental Inflammation Significantly Correlates with Reduced Risk for Retinopathy of Prematurity. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1776-1788. [PMID: 36822266 PMCID: PMC10616712 DOI: 10.1016/j.ajpath.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
Retinopathy of prematurity (ROP), a blinding condition affecting preterm infants, is an interruption of retinal vascular maturation that is incomplete when born preterm. Although ROP demonstrates delayed onset following preterm birth, representing a window for therapeutic intervention, there are no curative or preventative measures available for this condition. The in utero environment, including placental function, is increasingly recognized for contributions to preterm infant disease risk. The current study identified a protective association between acute placental inflammation and preterm infant ROP development using logistic regression, with the most significant association found for infants without gestational exposure to maternal preeclampsia and those with earlier preterm birth. Expression analysis of proteins with described ROP risk associations demonstrated significantly decreased placental high temperature requirement A serine peptidase-1 (HTRA-1) and fatty acid binding protein 4 protein expression in infants with acute placental inflammation compared with those without. Within the postnatal peripheral circulation, HTRA-1 and vascular endothelial growth factor-A demonstrated inverse longitudinal trends for infants born in the presence of, compared with absence of, acute placental inflammation. An agnostic approach, including whole transcriptome and differential methylation placental analysis, further identify novel mediators and pathways that may underly protection. Taken together, these data build on emerging literature showing a protective association between acute placental inflammation and ROP development and identify novel mechanisms that may inform postnatal risk associations in preterm infants.
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Affiliation(s)
- Leah A Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah; Department of Population Health Sciences, University of Utah, Salt Lake City, Utah; Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah; Department of Ophthalmology, University at Buffalo/State University of New York, Buffalo, New York.
| | - Charles Zhang
- Department of Ophthalmology, University at Buffalo/State University of New York, Buffalo, New York
| | - Kinsey Shirer
- Department of Ophthalmology, Medical University of South Carolina, Charleston, South Carolina
| | - Lara Carroll
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Blair Wood
- Retina Associates of Utah, Salt Lake City, Utah
| | - Kathryn Szczotka
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Colette Cornia
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah
| | - Christopher Stubben
- Department of Bioinformatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Camille Fung
- Division of Neonatology, Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Christian C Yost
- Division of Neonatology, Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Lakshmi D Katikaneni
- Division of Neonatology, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina
| | - Margaret M DeAngelis
- Department of Ophthalmology, University at Buffalo/State University of New York, Buffalo, New York; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York, Buffalo, New York; Department of Neuroscience, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York, Buffalo, New York; Department of Genetics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York, Buffalo, New York; Bioinformatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York, Buffalo, New York.
| | - Jessica Comstock
- Department of Pathology, University of Utah, Salt Lake City, Utah
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Ren C, Yu J. Potential gene identification and pathway crosstalk analysis of age-related macular degeneration. Front Genet 2022; 13:992328. [PMID: 36147504 PMCID: PMC9486309 DOI: 10.3389/fgene.2022.992328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022] Open
Abstract
Age-related macular degeneration (AMD), the most prevalent visual disorder among the elderly, is confirmed as a multifactorial disease. Studies demonstrated that genetic factors play an essential role in its pathogenesis. Our study aimed to make a relatively comprehensive study about biological functions of AMD related genes and crosstalk of their enriched pathways. 1691 AMD genetic studies were reviewed, GO enrichment and pathway crosstalk analyses were conducted to elucidate the biological features of these genes and to demonstrate the pathways that these genes participate. Moreover, we identified novel AMD-specific genes using shortest path algorithm in the context of human interactome. We retrieved 176 significantly AMD-related genes. GO results showed that the most significant term in each of these three GO categories was: signaling receptor binding (PBH = 4.835 × 10−7), response to oxygen-containing compound (PBH = 2.764 × 10−21), and extracellular space (PBH = 2.081 × 10−19). The pathway enrichment analysis showed that complement pathway is the most enriched. The pathway crosstalk study showed that the pathways could be divided into two main modules. These two modules were connected by cytokine-cytokine receptor interaction pathway. 42 unique genes potentially participating AMD development were obtained. The aberrant expression of the mRNA of FASN and LRP1 were validated in AMD cell and mouse models. Collectively, our study carried out a comprehensive analysis based on genetic association study of AMD and put forward several evidence-based genes for future study of AMD.
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Expression of Pro-Angiogenic Markers Is Enhanced by Blue Light in Human RPE Cells. Antioxidants (Basel) 2020; 9:antiox9111154. [PMID: 33233546 PMCID: PMC7699675 DOI: 10.3390/antiox9111154] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
Inherited retinal dystrophies are characterized by photoreceptor death. Oxidative stress usually occurs, increasing vision loss, and oxidative damage is often reported in retinitis pigmentosa (RP). More than 300 genes have been reported as RP causing. In contrast, choroidal neovascularization (CNV) only occasionally develops in the late stages of RP. We herein study the regulation of RP causative genes that are likely linked to CNV onset under oxidative conditions. We studied how the endogenous adduct N-retinylidene-N-retinylethanolamine (A2E) affects the expression of angiogenic markers in human retinal pigment epithelium (H-RPE) cells and a possible correlation with RP-causing genes. H-RPE cells were exposed to A2E and blue light for 3 and 6h. By transcriptome analysis, genes differentially expressed between A2E-treated cells and untreated ones were detected. The quantification of differential gene expression was performed by the Limma R package. Enrichment pathway analysis by the FunRich tool and gene prioritization by ToppGene allowed us to identify dysregulated genes involved in angiogenesis and linked to RP development. Two RP causative genes, AHR and ROM1, can be associated with an increased risk of CNV development. Genetic analysis of RP patients affected by CNV will confirm this hypothesis.
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Predictive genetics for AMD: Hype and hopes for genetics-based strategies for treatment and prevention. Exp Eye Res 2019; 191:107894. [PMID: 31862397 DOI: 10.1016/j.exer.2019.107894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/14/2019] [Accepted: 12/04/2019] [Indexed: 01/18/2023]
Abstract
Age-related macular degeneration (AMD) is a complex disease with multiple genetic and environmental risk factors. In the age of molecular genetics, many investigators have established a link between genes and development or progression of the disease. This later evolved to determine whether phenotypic features of AMD have distinct genetic profiles. Molecular genetics have subsequently been introduced as factors in risk assessment models, increasing the predictive value of these tools. Models seek to predict either development or progression of disease, and different AMD-related genes aid our understanding of these respective features. Several investigators have attempted to link molecular genetics with treatment response, but results and their clinical significance vary. Ocular and systemic biomarkers may interact with established genes, promising future routes of ongoing clinical assessment. Our understanding of AMD molecular genetics is not yet sufficient to recommend routine testing, despite its utility in the research setting. Clinicians must be wary of misusing population-based risk models from genetic and biomarker associations, as they are not necessarily relevant for individual counseling. This review addresses the known uses of predictive genetics, and suggests future directions.
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Williams LB, Javed A, Sabri A, Morgan DJ, Huff CD, Grigg JR, Heng XT, Khng AJ, Hollink IHIM, Morrison MA, Owen LA, Anderson K, Kinard K, Greenlees R, Novacic D, Nida Sen H, Zein WM, Rodgers GM, Vitale AT, Haider NB, Hillmer AM, Ng PC, Shankaracharya, Cheng A, Zheng L, Gillies MC, van Slegtenhorst M, van Hagen PM, Missotten TOAR, Farley GL, Polo M, Malatack J, Curtin J, Martin F, Arbuckle S, Alexander SI, Chircop M, Davila S, Digre KB, Jamieson RV, DeAngelis MM. ALPK1 missense pathogenic variant in five families leads to ROSAH syndrome, an ocular multisystem autosomal dominant disorder. Genet Med 2019; 21:2103-2115. [PMID: 30967659 PMCID: PMC6752478 DOI: 10.1038/s41436-019-0476-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/25/2019] [Indexed: 01/07/2023] Open
Abstract
Purpose To identify the molecular cause in five unrelated families with a distinct autosomal dominant ocular systemic disorder we called ROSAH syndrome due to clinical features of retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and migraine headache. Methods Independent discovery exome and genome sequencing in families 1, 2, and 3, and confirmation in families 4 and 5. Expression of wild-type messenger RNA and protein in human and mouse tissues and cell lines. Ciliary assays in fibroblasts from affected and unaffected family members. Results We found the heterozygous missense variant in the ɑ-kinase gene, ALPK1, (c.710C>T, [p.Thr237Met]), segregated with disease in all five families. All patients shared the ROSAH phenotype with additional low-grade ocular inflammation, pancytopenia, recurrent infections, and mild renal impairment in some. ALPK1 was notably expressed in retina, retinal pigment epithelium, and optic nerve, with immunofluorescence indicating localization to the basal body of the connecting cilium of the photoreceptors, and presence in the sweat glands. Immunocytofluorescence revealed expression at the centrioles and spindle poles during metaphase, and at the base of the primary cilium. Affected family member fibroblasts demonstrated defective ciliogenesis. Conclusion Heterozygosity for ALPK1, p.Thr237Met leads to ROSAH syndrome, an autosomal dominant ocular systemic disorder.
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Affiliation(s)
- Lloyd B Williams
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Asif Javed
- Genome Institute of Singapore, Singapore, Singapore.,School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Amin Sabri
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Denise J Morgan
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Chad D Huff
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Grigg
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia.,Discipline of Ophthalmology, University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Margaux A Morrison
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Leah A Owen
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Krista Kinard
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rebecca Greenlees
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Danica Novacic
- National Institutes of Health, National Human Genome Research Institute, Undiagnosed Diseases Network, Bethesda, MD, USA
| | - H Nida Sen
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wadih M Zein
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - George M Rodgers
- Department of Hematology, Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Albert T Vitale
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute/Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | | | - Pauline C Ng
- Genome Institute of Singapore, Singapore, Singapore
| | - Shankaracharya
- Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anson Cheng
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Linda Zheng
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
| | - Mark C Gillies
- Discipline of Ophthalmology, University of Sydney, Sydney, NSW, Australia
| | | | | | | | | | - Michael Polo
- Drs. Farley, Polo and Ho, Colonial Heights, VA, USA
| | - James Malatack
- Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
| | - Julie Curtin
- Department of Haematology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Frank Martin
- Department of Ophthalmology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Susan Arbuckle
- Department of Pathology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Stephen I Alexander
- Department of Nephrology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Megan Chircop
- Cell Cycle Unit, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | - Sonia Davila
- Genome Institute of Singapore, Singapore, Singapore
| | - Kathleen B Digre
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Save Sight Institute, University of Sydney, Sydney, NSW, Australia. .,Disciplines of Genomic Medicine, and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia. .,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia.
| | - Margaret M DeAngelis
- Department of Ophthalmology and Visual Sciences, John A Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT, USA. .,Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.
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Owen LA, Shakoor A, Morgan DJ, Hejazi AA, McEntire MW, Brown JJ, Farrer LA, Kim I, Vitale A, DeAngelis MM. The Utah Protocol for Postmortem Eye Phenotyping and Molecular Biochemical Analysis. Invest Ophthalmol Vis Sci 2019; 60:1204-1212. [PMID: 30924847 PMCID: PMC6440527 DOI: 10.1167/iovs.18-24254] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022] Open
Abstract
Purpose Current understanding of local disease pathophysiology in AMD is limited. Analysis of the human disease-affected tissue is most informative, as gene expression, expressed quantitative trait loci, microenvironmental, and epigenetic changes can be tissue, cell type, and location specific. Development of a novel translational treatment and prevention strategies particularly for earlier forms of AMD are needed, although access to human ocular tissue analysis is challenging. We present a standardized protocol to study rapidly processed postmortem donor eyes for molecular biochemical and genomic studies. Methods We partnered with the Utah Lions Eye Bank to obtain donor human eyes, blood, and vitreous, within 6 hours postmortem. Phenotypic analysis was performed using spectral-domain optical coherence tomography (SD-OCT) and color fundus photography. Macular and extramacular tissues were immediately isolated, and the neural retina and retinal pigment epithelium/choroid from each specimen were separated and preserved. Ocular disease phenotype was analyzed using clinically relevant grading criteria by a group of four ophthalmologists incorporating data from SD-OCT retinal images, fundus photographs, and medical records. Results The use of multimodal imaging leads to greater resolution of retinal pathology, allowing greater phenotypic rigor for both interobserver phenotype and known clinical diagnoses. Further, our analysis resulted in excellent quality RNA, which demonstrated appropriate tissue segregation. Conclusions The Utah protocol is a standardized methodology for analysis of disease mechanisms in AMD. It uniquely allows for simultaneous rigorous phenotypic, molecular biochemical, and genomic analysis of both systemic and local tissues. This better enables the development of disease biomarkers and therapeutic interventions.
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Affiliation(s)
- Leah A. Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
| | - Denise J. Morgan
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
| | - Andre A. Hejazi
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
| | | | - Jared J. Brown
- Utah Lions Eye Bank, Salt Lake City, Utah, United States
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States
| | - Ivana Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Albert Vitale
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
| | - Margaret M. DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, Utah, United States
- Department of Population Health Sciences, University of Utah, School of Medicine, Salt Lake City, Utah, United States
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8
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Chirco KR, Lewis CJ, Scheetz TE, Johnston RM, Tucker BA, Stone EM, Fingert JH, Mullins RF. Evaluation of sFLT1 protein levels in human eyes with the FLT1 rs9943922 polymorphism. Ophthalmic Genet 2017; 39:68-72. [PMID: 28949775 DOI: 10.1080/13816810.2017.1369550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE Age-related macular degeneration (AMD) is a devastating disease characterized by central vision impairment in individuals with advanced age. Neovascular AMD is a form of end-stage disease in which choroidal vessel outgrowth occurs beneath the retina. While many hypotheses have been raised as to what triggers the formation of pathological choroidal neovascular membranes, the exact mechanism for their initiation remains unresolved. Polymorphisms in the FLT1 gene have previously been associated with neovascular AMD risk, including the rs9943922 single nucleotide polymorphism (SNP). Here, we aimed to determine the association between the high-risk FLT1 genotype and FLT1 protein levels in human retina or retinal pigment epithelium (RPE)/choroid tissue. METHODS Retina and RPE/choroid tissue from 10 human donor eyes was selected from a collection of eyes genotyped for the rs9943922 SNP. Differences in soluble and membrane bound FLT1 protein levels were assessed for retina versus RPE/choroid donor tissue using ELISA and Western blotting analyses. Genotype-associated changes in FLT1 protein levels were also evaluated. RESULTS We found soluble FLT1 levels in the RPE/choroid tissue to be approximately three times higher than that of the retina (p < 0.001), while both samples have similar levels of the membrane bound form. When tissue with the rs9943922 SNP was compared with controls, no significant genotypic differences in FLT1 protein levels were observed. CONCLUSIONS Based on these data, we conclude that the rs9943922 SNP in the FLT1 gene does not result in a large difference in FLT1 protein levels, regardless of whether it is the soluble or the membrane bound form.
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Affiliation(s)
- Kathleen R Chirco
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Carly J Lewis
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Todd E Scheetz
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Rebecca M Johnston
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Budd A Tucker
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Edwin M Stone
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - John H Fingert
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
| | - Robert F Mullins
- a The Stephen A. Wynn Institute for Vision Research and the Department of Ophthalmology and Visual Sciences , The University of Iowa , Iowa City , Iowa , USA
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9
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Kersten E, Paun CC, Schellevis RL, Hoyng CB, Delcourt C, Lengyel I, Peto T, Ueffing M, Klaver CCW, Dammeier S, den Hollander AI, de Jong EK. Systemic and ocular fluid compounds as potential biomarkers in age-related macular degeneration. Surv Ophthalmol 2017; 63:9-39. [PMID: 28522341 DOI: 10.1016/j.survophthal.2017.05.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 12/15/2022]
Abstract
Biomarkers can help unravel mechanisms of disease and identify new targets for therapy. They can also be useful in clinical practice for monitoring disease progression, evaluation of treatment efficacy, and risk assessment in multifactorial diseases, such as age-related macular degeneration (AMD). AMD is a highly prevalent progressive retinal disorder for which multiple genetic and environmental risk factors have been described, but the exact etiology is not yet fully understood. Many compounds have been evaluated for their association with AMD. We performed an extensive literature review of all compounds measured in serum, plasma, vitreous, aqueous humor, and urine of AMD patients. Over 3600 articles were screened, resulting in more than 100 different compounds analyzed in AMD studies, involved in neovascularization, immunity, lipid metabolism, extracellular matrix, oxidative stress, diet, hormones, and comorbidities (such as kidney disease). For each compound, we provide a short description of its function and discuss the results of the studies in relation to its usefulness as AMD biomarker. In addition, biomarkers identified by hypothesis-free techniques, including metabolomics, proteomics, and epigenomics, are covered. In summary, compounds belonging to the oxidative stress pathway, the complement system, and lipid metabolism are the most promising biomarker candidates for AMD. We hope that this comprehensive survey of the literature on systemic and ocular fluid compounds as potential biomarkers in AMD will provide a stepping stone for future research and possible implementation in clinical practice.
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Affiliation(s)
- Eveline Kersten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Constantin C Paun
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rosa L Schellevis
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cécile Delcourt
- Université de Bordeaux, ISPED, Bordeaux, France; INSERM, U1219-Bordeaux Population Health Research Center, Bordeaux, France
| | - Imre Lengyel
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Tunde Peto
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Marius Ueffing
- Department for Ophthalmology and Medical Bioanalytics Centre Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sascha Dammeier
- Department for Ophthalmology and Medical Bioanalytics Centre Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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10
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Olivares AM, Jelcick AS, Reinecke J, Leehy B, Haider A, Morrison MA, Cheng L, Chen DF, DeAngelis MM, Haider NB. Multimodal Regulation Orchestrates Normal and Complex Disease States in the Retina. Sci Rep 2017; 7:690. [PMID: 28386079 PMCID: PMC5429617 DOI: 10.1038/s41598-017-00788-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Regulation of biological processes occurs through complex, synergistic mechanisms. In this study, we discovered the synergistic orchestration of multiple mechanisms regulating the normal and diseased state (age related macular degeneration, AMD) in the retina. We uncovered gene networks with overlapping feedback loops that are modulated by nuclear hormone receptors (NHR), miRNAs, and epigenetic factors. We utilized a comprehensive filtering and pathway analysis strategy comparing miRNA and microarray data between three mouse models and human donor eyes (normal and AMD). The mouse models lack key NHRS (Nr2e3, RORA) or epigenetic (Ezh2) factors. Fifty-four total miRNAs were differentially expressed, potentially targeting over 150 genes in 18 major representative networks including angiogenesis, metabolism, and immunity. We identified sixty-eight genes and 5 miRNAS directly regulated by NR2E3 and/or RORA. After a comprehensive analysis, we discovered multimodal regulation by miRNA, NHRs, and epigenetic factors of three miRNAs (miR-466, miR1187, and miR-710) and two genes (Ell2 and Entpd1) that are also associated with AMD. These studies provide insight into the complex, dynamic modulation of gene networks as well as their impact on human disease, and provide novel data for the development of innovative and more effective therapeutics.
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Affiliation(s)
- A M Olivares
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - A S Jelcick
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - J Reinecke
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - B Leehy
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - A Haider
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - M A Morrison
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - L Cheng
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - D F Chen
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - M M DeAngelis
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - N B Haider
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America.
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11
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Paradowska-Gorycka A, Sowinska A, Pawlik A, Malinowski D, Stypinska B, Haladyj E, Romanowska-Prochnicka K, Olesinska M. FLT-1 gene polymorphisms and protein expression profile in rheumatoid arthritis. PLoS One 2017; 12:e0172018. [PMID: 28323906 PMCID: PMC5360214 DOI: 10.1371/journal.pone.0172018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/29/2017] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Inflammation and angiogenesis are a significant element of pathogenesis in rheumatoid arthritis (RA). The FLT-1- triggering factor for production of proinflammatory cytokines-might contributes to inflammation in patients with RA. Association of the FLT-1 polymorphisms with different "angiogenic diseases" suggests that it may be a novel genetic risk factor also for RA. The aim of the study was to identify FLT-1 genetic variants and their possible association with sFLT-1 levels, susceptibility to and severity of RA. METHODS The FLT-1 gene polymorphisms were genotyped for 471 RA patients and 684 healthy individuals. Correlation analysis was performed with clinical parameters, cardiovascular disease (CVD) and anti-citrullinated peptide/protein antibody (ACPA) presence. The sFLT-1 serum levels were evaluated. RESULTS The FLT-1 gene polymorphisms showed no significant differences in the proportion of cases and controls. Furthermore, the FLT-1 rs2296188 T/C polymorphism was associated with ACPA-positive RA. Overall, rs9943922 T/C and rs2296283 G/A are in almost completed linkage disequilibrium (LD) with D' = 0.97 and r2 = 0.83. The FLT-1 rs7324510 A allele has shown association with VAS score (p = 0.035), DAS-28 score (p = 0.013) and ExRA presence (p = 0.027). Moreover, other clinical parameters were also higher in RA patients with this allele. In addition, FLT-1 genetic variants conferred higher sFLT-1 levels in RA patients compared to controls. CONCLUSION FLT-1 rs7324510 C/A variant may be a new genetic risk factor for severity of RA. Examined factor highly predispose to more severe disease activity as well as higher sFLT-1 levels in RA.
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Affiliation(s)
- Agnieszka Paradowska-Gorycka
- Department of Biochemistry and Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Anna Sowinska
- Department of Computer Science and Statistics, Poznan University of Medical Sciences, Poznan, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Damian Malinowski
- Department of Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Barbara Stypinska
- Department of Biochemistry and Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Ewa Haladyj
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Katarzyna Romanowska-Prochnicka
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
- Department of Pathophysiology, Warsaw Medical University, Warsaw, Poland
| | - Marzena Olesinska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
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12
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Fulton J, Mazumder B, Whitchurch JB, Monteiro CJ, Collins HM, Chan CM, Clemente MP, Hernandez-Quiles M, Stewart EA, Amoaku WM, Moran PM, Mongan NP, Persson JL, Ali S, Heery DM. Heterodimers of photoreceptor-specific nuclear receptor (PNR/NR2E3) and peroxisome proliferator-activated receptor-γ (PPARγ) are disrupted by retinal disease-associated mutations. Cell Death Dis 2017; 8:e2677. [PMID: 28300834 PMCID: PMC5386588 DOI: 10.1038/cddis.2017.98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/30/2022]
Abstract
Photoreceptor-specific nuclear receptor (PNR/NR2E3) and Tailless homolog (TLX/NR2E1) are human orthologs of the NR2E group, a subgroup of phylogenetically related members of the nuclear receptor (NR) superfamily of transcription factors. We assessed the ability of these NRs to form heterodimers with other members of the human NRs representing all major subgroups. The TLX ligand-binding domain (LBD) did not appear to form homodimers or interact directly with any other NR tested. The PNR LBD was able to form homodimers, but also exhibited robust interactions with the LBDs of peroxisome proliferator-activated receptor-γ (PPARγ)/NR1C3 and thyroid hormone receptor b (TRb) TRβ/NR1A2. The binding of PNR to PPARγ was specific for this paralog, as no interaction was observed with the LBDs of PPARα/NR1C1 or PPARδ/NR1C2. In support of these findings, PPARγ and PNR were found to be co-expressed in human retinal tissue extracts and could be co-immunoprecipitated as a native complex. Selected sequence variants in the PNR LBD associated with human retinopathies, or a mutation in the dimerization region of PPARγ LBD associated with familial partial lipodystrophy type 3, were found to disrupt PNR/PPARγ complex formation. Wild-type PNR, but not a PNR309G mutant, was able to repress PPARγ-mediated transcription in reporter assays. In summary, our results reveal novel heterodimer interactions in the NR superfamily, suggesting previously unknown functional interactions of PNR with PPARγ and TRβ that have potential importance in retinal development and disease.
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Affiliation(s)
- Joel Fulton
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Bismoy Mazumder
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | | | | | - Chun M Chan
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | | | - Elizabeth A Stewart
- Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Winfried M Amoaku
- Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Paula M Moran
- School of Psychology, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Jenny L Persson
- Division of Experimental Cancer Research, Department of Translational Medicine, Lund University, Clinical Research Centre, Malmö, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - David M Heery
- School of Pharmacy, University of Nottingham, Nottingham, UK
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13
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Lee CJ, Lee JY, Oum CY, Youn JC, Kang SM, Choi D, Jang Y, Park S, Jee SH, Lee SH. The Effect of FLT1 Variant on Long-Term Cardiovascular Outcomes: Validation of a Locus Identified in a Previous Genome-Wide Association Study. PLoS One 2016; 11:e0164705. [PMID: 27736948 PMCID: PMC5063388 DOI: 10.1371/journal.pone.0164705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/29/2016] [Indexed: 11/18/2022] Open
Abstract
Background Data on genetic variants that can predict follow-up cardiovascular events are highly limited, particularly for Asians. The aim of this study was to validate the effects of two variants in FLT1 and 9p21 on long-term cardiovascular outcomes in high-risk Korean patients. Methods We examined the prognostic values of the rs9508025 and rs1333049 variants that were found to be associated with coronary artery disease (CAD) risk in a previous Korean genome-wide association study. A total of 2693 patients (mean age: 55.2 years; male: 55.2%) with CAD or its risk factors at baseline were enrolled and followed for major adverse cardiac events (MACE). Results During the mean follow-up of 8.8 years, 15.4% of the patients experienced MACE. Kaplan-Meier curves showed that MACE-free survival was different according to the genotype of rs9508025 (log rank p = 0.02), whereas rs1333049 genotype did not correlate with the prognosis. Multivariate Cox proportional hazard analysis showed that C-allele of rs9508025 was significantly associated with a high rate of MACE, while rs1333049 was not. Further analyses demonstrated that the association of the rs9508025 variant with MACE was mainly due to its relation to coronary revascularization, which was also associated with the rs1333049 variant. In an additional analysis, rs9508025 was found to be an independent determinant of the outcome only in the subgroup with history of CAD. Conclusions rs9508025 in FLT1 was significantly associated with long-term cardiovascular events, particularly in patients with prior CAD. The association of rs1333049 in 9p21 was not significant.
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Affiliation(s)
- Chan Joo Lee
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Ji-Young Lee
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Chi-Yoon Oum
- Department of Biostatistics and Computing, the Graduate School, Yonsei University, Seoul, Korea
| | - Jong-Chan Youn
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Seok-Min Kang
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Donghoon Choi
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Yangsoo Jang
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
| | - Sungha Park
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
- * E-mail: (SHL); (SHJ); (SP)
| | - Sun Ha Jee
- Institute of Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
- * E-mail: (SHL); (SHJ); (SP)
| | - Sang-Hak Lee
- Division of Cardiology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute and Cardiovascular Genome Center, Yonsei College of Medicine, Seoul, Korea
- * E-mail: (SHL); (SHJ); (SP)
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14
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Xiang W, Zhuang W, Chi H, Sheng X, Zhang W, Xue Z, Pan B, Liu Y. Evaluating VEGFR1 genetic polymorphisms as a predisposition to AMD in a cohort from northern China. Ophthalmic Genet 2016; 37:388-393. [PMID: 26914796 DOI: 10.3109/13816810.2015.1107597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE The association among genetic variants in VEGFR1 and a predisposition to age-related macular degeneration (AMD) in a northern cohort from China was evaluated. METHODS A retrospective case-control correlation study was conducted on 432 cases and 906 gender-and ethnicity-matched controls. Whole DNA was isolated from peripheral blood samples after the individuals underwent detailed eye examinations. Eight single nucleotide polymorphisms (SNPs) in VEGFR1 genes were genotyped for all individuals using a MALDI-TOF technique. The distribution of genotypes was analyzed for Hardy-Weinberg equilibrium and the relationships among the genotype and allele frequencies with AMD were evaluated by age-adjusted logistic regression analysis. The measurement of linkage disequilibrium (LD) was carried out by Haploview 4.2. Bonferroni testing was employed to correct for multiple comparisons. RESULTS Among the SNPs genotyped, p values of six SNPs were less than 0.05 between AMD cases and unaffected controls. However, after Bonferroni correction, the genotype and allele distributions of only two SNPs, rs9554322 and rs9582036 differed significantly between the controls and AMD patients. Further, the rs9554322 CC genotype conferred strong susceptibility to AMD (OR = 6.057, 95% CI: 3.099-11.839). Rs9943922 was also found to be significantly associated with AMD in the distributions for the genotype and allele recessive model (p = 0.004). The specific haplotype CA of rs9582036 and rs9554320 was associated with AMD (p = 0.035), but the correlation did not remain after correction. CONCLUSIONS The SNPs rs9554322, rs9582036 and rs9943922 were correlated with AMD. Gene variants in VEGFR1 were linked to a pronounced emerging risk for AMD in a population in northern China.
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Affiliation(s)
- Wei Xiang
- a Department of Ophthalmology , Ningxia Medical University , Yinchuan , China
| | - Wenjuan Zhuang
- b Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region , Yinchuan , China
| | - Hao Chi
- a Department of Ophthalmology , Ningxia Medical University , Yinchuan , China
| | - Xunlun Sheng
- b Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region , Yinchuan , China
| | - Wen Zhang
- a Department of Ophthalmology , Ningxia Medical University , Yinchuan , China
| | - Zhongqi Xue
- a Department of Ophthalmology , Ningxia Medical University , Yinchuan , China
| | - Bo Pan
- b Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region , Yinchuan , China
| | - Yang Liu
- b Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region , Yinchuan , China
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