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Kwong A, Zawistowski M, Fritsche LG, Zhan X, Bragg-Gresham J, Branham KE, Advani J, Othman M, Ratnapriya R, Teslovich TM, Stambolian D, Chew EY, Abecasis GR, Swaroop A. Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration. Hum Mol Genet 2024; 33:374-385. [PMID: 37934784 PMCID: PMC10840384 DOI: 10.1093/hmg/ddad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.
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Affiliation(s)
- Alan Kwong
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Xiaowei Zhan
- Southwestern Medical Center, University of Texas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Jennifer Bragg-Gresham
- Kidney Epidemiology and Cost Center, Department of Internal Medicine-Nephrology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Jayshree Advani
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Tanya M Teslovich
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania Medical School, 51 N. 39th Street, Philadelphia, PA 19104, United States
| | - Emily Y Chew
- Division of Epidemiology and Clinical Application, National Eye Institute, National Institutes of Health, 10 Center Drive Building 10-CRC, Bethesda, MD 20892, United States
| | - Gonçalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
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Alteration of gene expression in mice after glaucoma filtration surgery. Sci Rep 2020; 10:15036. [PMID: 32929145 PMCID: PMC7490364 DOI: 10.1038/s41598-020-72036-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/24/2020] [Indexed: 12/01/2022] Open
Abstract
To clarify the early alterations of gene expression using a mouse model of glaucoma filtration surgery, we carried out microarray expression analysis. Using BALB/c mice, a filtration surgery model was made by incision of the limbal conjunctiva, followed by the insertion of a 33G needle tip into the anterior chamber, and 11-0 nylon sutures. Subgroups of mice were treated intraoperatively with 0.4 mg/ml mitomycin-C (MMC). At day 3 after surgery the bleb was maintained. The bleb region tissue was sampled 3 days after the filtration surgery, and gene expression analysis was carried out using a mouse Agilent 8 × 60 K array. We found 755 hyperexpressed transcripts in the bleb region compared to control conjunctiva. The hyperexpressed transcripts included epithelial cell metaplasia-related (Il1b, Krt16, Sprr1b), inflammation-related (Ccl2, Il6) and wound healing-related (Lox, Timp1) genes. We also found downregulation of a goblet cell marker gene (Gp2) in the bleb conjunctiva. MMC treatment suppressed elastin (Eln) gene expression and enhanced keratinization-related gene expression (Krt1, Lor) in the bleb region. Our results suggest the importance of epithelial wound healing after filtration surgery, and this filtration surgery model will be a useful tool for further pathophysiological analysis.
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Wan W, Cao L, Kalionis B, Murthi P, Xia S, Guan Y. Iron Deposition Leads to Hyperphosphorylation of Tau and Disruption of Insulin Signaling. Front Neurol 2019; 10:607. [PMID: 31275224 PMCID: PMC6593079 DOI: 10.3389/fneur.2019.00607] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/22/2019] [Indexed: 12/22/2022] Open
Abstract
Iron deposition in the brain is an early issue in Alzheimer's disease (AD). However, the pathogenesis of iron-induced pathological changes in AD remains elusive. Insulin resistance in brains is an essential feature of AD. Previous studies determined that insulin resistance is involved in the development of pathologies in AD. Tau pathology is one of most important hallmarks in AD and is associated with the impairment of cognition and clinical grades of the disease. In the present study, we observed that ferrous (Fe2+) chloride led to aberrant phosphorylation of tau, and decreased tyrosine phosphorylation levels of insulin receptor β (IRβ), insulin signal substrate 1 (IRS-1) and phosphoinositide 3-kinase p85α (PI3K p85α), in primary cultured neurons. In the in vivo studies using mice with supplemented dietary iron, learning and memory was impaired. As well, hyperphosphorylation of tau and disrupted insulin signaling in the brain was induced in iron-overloaded mice. Furthermore, in our in vitro work we identified the activation of insulin signaling following exogenous supplementation of insulin. This was further attenuated by iron-induced hyperphosphorylation of tau in primary neurons. Together, these data suggest that dysfunctional insulin signaling participates in iron-induced abnormal phosphorylation of tau in AD. Our study highlights the promising role of insulin signaling in pathological lesions induced by iron overloading.
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Affiliation(s)
- Wenbin Wan
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lan Cao
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bill Kalionis
- Department of Maternal-Fetal Medicine, Pregnancy Research Centre, University of Melbourne, Parkville, VIC, Australia.,Department of Obstetrics and Gynecology, Royal Women's Hospital, Parkville, VIC, Australia
| | - Padma Murthi
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
| | - Shijin Xia
- Shanghai Institute of Geriatrics, Huadong Hospital, Fudan University, Shanghai, China
| | - Yangtai Guan
- Department of Neurology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Rancic A, Filipovic N, Marin Lovric J, Mardesic S, Saraga-Babic M, Vukojevic K. Neuronal differentiation in the early human retinogenesis. Acta Histochem 2017; 119:264-272. [PMID: 28216069 DOI: 10.1016/j.acthis.2017.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 11/28/2022]
Abstract
AIM Our study investigates the differentiation of retinal stem cells towards different neuronal subtypes during the critical period of human eye development. METHODS Expression of the neuronal marker neurofilament 200 (NF200), tyrosine hydroxilase (TH) and choline acetyltransferase (ChAT) was seen by immunofluorescence in the 5th-12th - week stage of development in the human eye. Data was analysed by Mann-Whitney, Kruskal-Wallis and Dunn's post hoc tests. RESULTS NF200, TH and ChAT cells appeared in the 5th/6th week and gradually increased during further development. The proportion of TH positive areas were distributed similarly to NF200, with a higher proportion in the outer neuroblastic layer. The proportion of a ChAT positive surface was highest in the 5th/6th - week whilst from the 7th week onwards, its proportion became higher in the optic nerve and inner neuroblastic layers than in the outer layer, where a decrease of ChAT positive areas were seen. CONCLUSIONS Our study indicates a high differentiation potential of early retinal cells, which decreased with the advancement of development. The observed great variety of retinal phenotypic expressions results from a large scale of influences, taking place at different developmental stages.
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Affiliation(s)
- Anita Rancic
- Department of Ophthalmology, University Hospital Centre Split, Spinciceva 1, 21000, Split, Croatia
| | - Natalija Filipovic
- Laboratory for Early Human Development, Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia
| | - Josipa Marin Lovric
- Department of Ophthalmology, University Hospital Centre Split, Spinciceva 1, 21000, Split, Croatia
| | - Snjezana Mardesic
- Laboratory for Early Human Development, Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia
| | - Mirna Saraga-Babic
- Laboratory for Early Human Development, Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia
| | - Katarina Vukojevic
- Laboratory for Early Human Development, Department of Anatomy, Histology and Embryology, School of Medicine, University of Split, Soltanska 2, 21000, Split, Croatia.
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Wan W, Jin L, Wang Z, Wang L, Fei G, Ye F, Pan X, Wang C, Zhong C. Iron Deposition Leads to Neuronal α-Synuclein Pathology by Inducing Autophagy Dysfunction. Front Neurol 2017; 8:1. [PMID: 28138322 PMCID: PMC5237641 DOI: 10.3389/fneur.2017.00001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022] Open
Abstract
Growing evidence has indicated that iron deposition in the substantia nigra plays an important role in Parkinson’s disease (PD). However, the underlying mechanism is still elusive. Using primary dopaminergic neurons and SH-SY5Y cells cultured in vitro, we observed that iron loading increased α-synuclein and reactive oxygen species (ROS) levels in these cells but did not affect the intracellular α-synuclein mRNA levels. Furthermore, iron loading significantly downregulated Beclin-1 levels and decreased the ratio of microtubule-associated protein 1 light chain 3 isoforms (LC3 II/LC3 I). However, a significant change in the levels of autophagy-related gene 5 (Atg5) was not observed in either neurons or SH-SY5Y cells after iron treatment. After treatment with rapamycin, the iron loading-induced increase in the α-synuclein level was significantly reversed and ROS generation was alleviated in both cultured neurons and SH-SY5Y cells. These results indicate that the inhibition of autophagy is critical for the pathological alterations in α-synuclein induced by iron loading. Moreover, treatment with vitamin E did not affect the increase in the α-synuclein levels but significantly eliminated the iron-induced ROS production. Together, our study shows that autophagy dysfunction contributes to iron-induced α-synuclein pathology.
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Affiliation(s)
- Wenbin Wan
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Lirong Jin
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Zigao Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Neurology, Jingshan Hospital, Fudan University, Shanghai, China
| | - Lingyan Wang
- Experimental Research Center, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Guoqiang Fei
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Fanlong Ye
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Xiaoli Pan
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Changpeng Wang
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Chunjiu Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University , Shanghai , China
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Retinal output changes qualitatively with every change in ambient illuminance. Nat Neurosci 2014; 18:66-74. [PMID: 25485757 PMCID: PMC4338531 DOI: 10.1038/nn.3891] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/28/2014] [Indexed: 12/20/2022]
Abstract
The collective activity pattern of retinal ganglion cells, the retinal code, underlies higher visual processing. How does the ambient illuminance of the visual scene influence this retinal output? We recorded from isolated mouse and pig retina and from mouse dLGN in-vivo at up to seven ambient light levels covering the scotopic to photopic regimes. Across each luminance transition, the majority of ganglion cells exhibited qualitative response changes, while maintaining stable responses within each luminance. Strikingly, we commonly observed the appearance and disappearance of ON responses in OFF cells and vice versa. Such qualitative response changes occurred for a variety of stimuli, including full-field and localized contrast steps, and naturalistic movies. Our results suggest that the retinal code is not fixed but varies with every change of ambient luminance. This finding raises new questions about signal processing within the retina and has intriguing implications for visual processing in higher brain areas.
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