1
|
Zhang X, Wang S, Liu S, Du Z, Wu G, Liang Y, Huang Y, Shang X, Hu Y, Zhu Z, Sun W, Zhang X, Yu H. Epidemiologic association and shared genetic architecture between cataract and hearing difficulties among middle-aged and older adults. Hum Genomics 2024; 18:39. [PMID: 38632618 PMCID: PMC11022469 DOI: 10.1186/s40246-024-00601-z] [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: 08/06/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Age-related cataract and hearing difficulties are major sensory disorders that often co-exist in the global-wide elderly and have a tangible influence on the quality of life. However, the epidemiologic association between cataract and hearing difficulties remains unexplored, while little is known about whether the two share their genetic etiology. We first investigated the clinical association between cataract and hearing difficulties using the UK Biobank covering 502,543 individuals. Both unmatched analysis (adjusted for confounders) and a matched analysis (one control matched for each patient with cataract according to confounding factors) were undertaken and confirmed that cataract was associated with hearing difficulties (OR, 2.12; 95% CI, 1.98-2.27; OR, 2.03; 95% CI, 1.86-2.23, respectively). Furthermore, we explored and quantified the shared genetic architecture of these two complex sensory disorders at the common variant level using the bivariate causal mixture model (MiXeR) and conditional/conjunctional false discovery rate method based on the largest available genome-wide association studies of cataract (N = 585,243) and hearing difficulties (N = 323,978). Despite detecting only a negligible genetic correlation, we observe polygenic overlap between cataract and hearing difficulties and identify 6 shared loci with mixed directions of effects. Follow-up analysis of the shared loci implicates candidate genes QKI, STK17A, TYR, NSF, and TCF4 likely contribute to the pathophysiology of cataracts and hearing difficulties. In conclusion, this study demonstrates the presence of epidemiologic association between cataract and hearing difficulties and provides new insights into the shared genetic architecture of these two disorders at the common variant level.
Collapse
Affiliation(s)
- Xiayin Zhang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shan Wang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shunming Liu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Du
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanrong Wu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yingying Liang
- Department of Ophthalmology, Guangzhou First people's Hospital, Guangzhou, China
| | - Yu Huang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xianwen Shang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yijun Hu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuoting Zhu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, East Melbourne, Australia
| | - Wei Sun
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Xueli Zhang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Honghua Yu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, China.
| |
Collapse
|
2
|
Reyes LP, Reyes TC, Dueñas Z, Duran D, Perdomo S, Avila MY. Expression of oxysterols in human lenses: Implications of the sterol pathway in age-related cataracts. J Steroid Biochem Mol Biol 2023; 225:106200. [PMID: 36272497 DOI: 10.1016/j.jsbmb.2022.106200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Lanosterol, an oxysterol molecule, has been proposed to help maintain lens transparency by inhibiting the formation of protein aggregates. This sterol is produced by the enzyme lanosterol synthase and is part of a metabolic pathway that forms cholesterol as a final step. Abnormalities in lanosterol synthase are responsible for congenital cataracts. The αA-crystallin protein, which acts as a molecular chaperone to lanosterol synthase, has been reported to have anti-protein aggregation, anti-inflammatory and anti-apoptotic properties. In this work, we evaluated the correlation of lanosterol synthase and αA-crystallin in human cataractous lenses with the grade of opacity, as well as the expression of lanosterol synthase, farnesyl DPP, geranyl synthase and squalene epoxidase genes. Lanosterol synthase and αA-crystallin were overexpressed in cataractous lenses as well as farnesyl-DP synthase, squalene epoxidase, lanosterol synthase and geranyl synthase genes in cataratous lenses in comparison with normal lenses. Our data confirm that lanosterol synthase and the sterol pathway are upregulated in cataractous lenses. This argues for a functional role of the oxysterol pathway and its products as an important mediator in the pathogenesis of human cataracts.
Collapse
Affiliation(s)
- Laura P Reyes
- Department of Ophthalmology, School of Medicine, Universidad Nacional de Colombia, Colombia
| | - Tatiana C Reyes
- Department of Ophthalmology, School of Medicine, Universidad Nacional de Colombia, Colombia; Department of Physiology, School of Medicine, Universidad Nacional de Colombia, Colombia
| | - Zulma Dueñas
- Department of Physiology, School of Medicine, Universidad Nacional de Colombia, Colombia
| | - Diego Duran
- Department of Ophthalmology, School of Medicine, Universidad Nacional de Colombia, Colombia
| | | | - Marcel Y Avila
- Department of Ophthalmology, School of Medicine, Universidad Nacional de Colombia, Colombia.
| |
Collapse
|
3
|
Rift Valley Fever Virus Infects the Posterior Segment of the Eye and Induces Inflammation in a Rat Model of Ocular Disease. J Virol 2022; 96:e0111222. [PMID: 36194021 PMCID: PMC9599513 DOI: 10.1128/jvi.01112-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
People infected with the mosquito-borne Rift Valley fever virus (RVFV) can suffer from eye-related problems resulting in ongoing vision issues or even permanent blindness. Despite ocular disease being the most frequently reported severe outcome, it is vastly understudied compared to other disease outcomes caused by RVFV. Ocular manifestations of RVFV include blurred vision, uveitis, and retinitis. When an infected individual develops macular or paramacular lesions, there is a 50% chance of permanent vision loss in one or both eyes. The cause of blinding ocular pathology remains unknown in part due to the lack of a tractable animal model. Using 3 relevant exposure routes, both subcutaneous (SC) and aerosol inoculation of Sprague Dawley rats led to RVFV infection of the eye. Surprisingly, direct inoculation of the conjunctiva did not result in successful ocular infection. The posterior segment of the eye, including the optic nerve, choroid, ciliary body, and retina, were all positive for RVFV antigen in SC-infected rats, and live virus was isolated from the eyes. Proinflammatory cytokines and increased leukocyte counts were also found in the eyes of infected rats. Additionally, human ocular cell lines were permissive for Lrp1-dependent RVFV infection. This study experimentally defines viral tropism of RVFV in the posterior segment of the rat eye and characterizes virally-mediated ocular inflammation, providing a foundation for evaluation of vaccines and therapeutics to protect against adverse ocular outcomes. IMPORTANCE Rift Valley fever virus (RVFV) infection leads to eye damage in humans in up to 10% of reported cases. Permanent blindness occurs in 50% of individuals with significant retinal scarring. Despite the prevalence and severity of this outcome, very little is known about the mechanisms of pathogenesis. We addressed this gap by developing a rodent model of ocular disease. Subcutaneous infection of Sprague Dawley rats resulted in infection of the uvea, retina, and optic nerve along with the induction of inflammation within the posterior eye. Infection of human ocular cells induced inflammatory responses and required host entry factors for RVFV infection similar to rodents. This work provides evidence of how RVFV infects the eye, and this information can be applied to help mitigate the devastating outcomes of RVF ocular disease through vaccines or treatments.
Collapse
|
4
|
Lu A, Duan P, Xie J, Gao H, Chen M, Gong Y, Li J, Xu H. Recent progress and research trend of anti-cataract pharmacology therapy: A bibliometric analysis and literature review. Eur J Pharmacol 2022; 934:175299. [PMID: 36181780 DOI: 10.1016/j.ejphar.2022.175299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
Abstract
Cataract is the leading cause of blindness worldwide. Cataract phacoemulsification combined with intraocular lens implantation causes great burden to global healthcare, especially for low- and middle-income countries. Such burden would be significantly relieved if cataracts can effectively be treated or delayed by non-surgical means. Excitingly, novel drugs have been developed to treat cataracts in recent decades. For example, oxysterols are found to be able to innovatively reverse lens clouding, novel nanotechnology-loaded drugs improve anti-cataract pharmacological effect, and traditional Chinese medicine demonstrates promising therapeutic effects against cataracts. In the present review, we performed bibliometric analysis to provide an overview perspective regarding the research status, hot topics, and academic trends in the field of anti-cataract pharmacology therapy. We further reviewed the curative effects and molecular mechanisms of anti-cataract drugs such as lanosterol, metformin, resveratrol and curcumin, and prospected the possibility of their clinical application in future.
Collapse
Affiliation(s)
- Ao Lu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China; The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Ping Duan
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Jing Xie
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Hui Gao
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Mengmeng Chen
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yu Gong
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Jiawen Li
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, China.
| | - Haiwei Xu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China; Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China.
| |
Collapse
|
5
|
Brown C, Agosta P, McKee C, Walker K, Mazzella M, Alamri A, Svinarich D, Chaudhry GR. Human primitive mesenchymal stem cell-derived retinal progenitor cells improved neuroprotection, neurogenesis, and vision in rd12 mouse model of retinitis pigmentosa. Stem Cell Res Ther 2022; 13:148. [PMID: 35395806 PMCID: PMC8994263 DOI: 10.1186/s13287-022-02828-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/20/2022] [Indexed: 01/05/2023] Open
Abstract
Background Currently, there is no treatment for retinal degenerative diseases (RDD) such as retinitis pigmentosa (RP). Stem cell-based therapies could provide promising opportunities to repair the damaged retina and restore vision. Thus far, primarily adult mesenchymal stem cells (MSCs) have been investigated in preclinical and clinical studies, and the results have not been convincing. We applied a new approach in which primitive (p) MSC-derived retinal progenitor cells (RPCs) were examined to treat retinal degeneration in an rd12 mouse model of RP. Methods Well-characterized pMSCs and RPCs labeled with PKH26 were intravitreally injected into rd12 mice. The vision and retinal function of transplanted animals were analyzed using electroretinography. Animals were killed 4 and 8 weeks after cell transplantation for histological, immunological, molecular, and transcriptomic analyses of the retina. Results Transplanted RPCs significantly improved vision and retinal thickness as well as function in rd12 mice. pMSCs and RPCs homed to distinct retinal layers. pMSCs homed to the retinal pigment epithelium, and RPCs migrated to the neural layers of the retina, where they improved the thickness of the respective layers and expressed cell-specific markers. RPCs induced anti-inflammatory and neuroprotective responses as well as upregulated the expression of genes involved in neurogenesis. The transcriptomic analysis showed that RPCs promoted neurogenesis and functional recovery of the retina through inhibition of BMP and activation of JAK/STAT and MAPK signaling pathways. Conclusions Our study demonstrated that RPCs countered inflammation, provided retinal protection, and promoted neurogenesis resulting in improved retinal structure and physiological function in rd12 mice. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02828-w.
Collapse
Affiliation(s)
- Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA
| | - Patrina Agosta
- Ascension Providence Hospital, Southfield, MI, 48075, USA
| | - Christina McKee
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA
| | - Keegan Walker
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA
| | - Matteo Mazzella
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA
| | - Ali Alamri
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA.,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA
| | | | - G Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA. .,OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI, 48309, USA.
| |
Collapse
|
6
|
Abstract
The eye presents a unique opportunity for complement component 3 (C3) therapeutics. Drugs can be delivered directly to specific parts of the eye, and growing evidence has established a pivotal role for C3 in age-related macular degeneration (AMD). Emerging data show that C3 may be important to the pathophysiology of other eye diseases as well. This article will discuss the location of C3 expression in the eye as well as the preclinical and clinical data regarding C3's functions in AMD. We will provide a comprehensive review of developing C3 inhibitors for the eye, including the Phase 2 and 3 data for the C3 inhibitor pegcetacoplan as a treatment for the geographic atrophy of AMD. Developing evidence also points toward C3 as a therapeutic target for stages of AMD preceding geographic atrophy. We will also discuss data illuminating C3's relationship to other eye diseases, such as Stargardt disease, diabetic retinopathy, and glaucoma. In addition to being a converging point and centerpiece of the complement cascade, C3 has broad effects as a multifaceted controller of opsonophagocytosis, microglia/macrophage recruitment, and downstream terminal pathway activity. C3 is a crucial player in the pathophysiology of AMD but also seems to have importance in other diseases that are major causes of blindness. Directions for further investigation will be highlighted, as culminating evidence suggests that we may be approaching an era of C3 therapeutics for the eye.
Collapse
Affiliation(s)
- Benjamin J Kim
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Tianyu Liu
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - John D Lambris
- Department of Laboratory Medicine and Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
7
|
Youkilis JC, Bassnett S. Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye. Exp Eye Res 2021; 213:108811. [PMID: 34717927 PMCID: PMC8860325 DOI: 10.1016/j.exer.2021.108811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/08/2021] [Accepted: 10/24/2021] [Indexed: 12/12/2022]
Abstract
The ciliary epithelium plays a central role in ocular homeostasis but cells of the pigmented and non-pigmented layers are difficult to isolate physically and study. Here we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptional signatures of cells harvested from the ciliary body and contiguous tissues. Microdissected tissue was dissociated by collagenase digestion and the transcriptomes of individual cells were obtained using a droplet-based scRNA-seq approach. In situ hybridization was used to verify the expression patterns of selected differentially-expressed genes. High quality transcriptomes were obtained from 10,024 cells and unsupervised clustering distinguished 22 cell types. Although efforts were made to specifically isolate the ciliary body, approximately half of the sequenced cells were derived from the adjacent retina. Cluster identities were assigned using expression of canonical markers or cluster-specific genes. The transcriptional signature of cells in the PCE and NPCE were distinct from each other and from cells in contiguous tissues. PCE cell transcriptomes were characterized by genes involved in melanin synthesis and transport proteins such as Slc4a4. Among the most differentially expressed genes in NPCE cells were those encoding members of the Zic family of transcription factors (Zic1, 2, 4), collagen XVIII (Col18a1), and corticotrophin-releasing hormone-binding protein (Crhbp). The ocular melanocyte population was distinguished by expression of the gap junction genes Gjb2 and Gjb6. Two fibroblast signatures were detected in the ciliary body preparation and shown by in situ hybridization to correspond to uveal and scleral populations. This cell atlas for the ciliary body and contiguous layers represents a useful resource that may facilitate studies into the development of the ciliary epithelium, the production of the aqueous and vitreous humors, and the synthesis of the ciliary zonule.
Collapse
Affiliation(s)
- J C Youkilis
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - S Bassnett
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
8
|
Dong S, Boyle AP. Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome. Nucleic Acids Res 2021; 50:e6. [PMID: 34648033 PMCID: PMC8754628 DOI: 10.1093/nar/gkab924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the functional consequences of genetic variation in the non-coding regions of the human genome remains a challenge. We introduce h ere a computational tool, TURF, to prioritize regulatory variants with tissue-specific function by leveraging evidence from functional genomics experiments, including over 3000 functional genomics datasets from the ENCODE project provided in the RegulomeDB database. TURF is able to generate prediction scores at both organism and tissue/organ-specific levels for any non-coding variant on the genome. We present that TURF has an overall top performance in prediction by using validated variants from MPRA experiments. We also demonstrate how TURF can pick out the regulatory variants with tissue-specific function over a candidate list from associate studies. Furthermore, we found that various GWAS traits showed the enrichment of regulatory variants predicted by TURF scores in the trait-relevant organs, which indicates that these variants can be a valuable source for future studies.
Collapse
Affiliation(s)
- Shengcheng Dong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alan P Boyle
- To whom correspondence should be addressed. Tel: +1 734 763 7382; Fax: +1 734 763 7382;
| |
Collapse
|
9
|
Ligocki AJ, Fury W, Gutierrez C, Adler C, Yang T, Ni M, Bai Y, Wei Y, Lehmann GL, Romano C. Molecular characteristics and spatial distribution of adult human corneal cell subtypes. Sci Rep 2021; 11:16323. [PMID: 34381080 PMCID: PMC8357950 DOI: 10.1038/s41598-021-94933-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.
Collapse
Affiliation(s)
- Ann J Ligocki
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Tao Yang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yu Bai
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | - Carmelo Romano
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
| |
Collapse
|
10
|
Zhou H, Li Y, Yang Y, Liu S, Yang Z. Lanosterol reduces the aggregation propensity of ultraviolet-damaged human γD-crystallins: a molecular dynamics study. Phys Chem Chem Phys 2021; 23:13696-13704. [PMID: 34128026 DOI: 10.1039/d1cp00132a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ultraviolet (UV) radiation-induced oxidation of tryptophan (Trp) to kynurenine (KN) (TRP > KN) in human γD-crystallins (HγD-Crys) promotes the conversion of proteins into partially unfolded species that act as important precursors for sequential large-scale aggregation. Herein, we report that lanosterol shows protective activity to the structure of the TRP > KN mutant HγD-Crys, particularly its N-terminal domain (N-td), by using all-atom molecular dynamics simulations. The Trp68 > KN mutation significantly destabilizes the originally highly stable "Tyr55-Trp68-Tyr62" cluster, thereby causing loop2, where the mutation occurs, to become very flexible. The large fluctuation of loop2 induces cracks, which appear on the protein surface, resulting in the intrusion of water molecules into the hydrophobic core of the N-td. This event eventually triggers the unfolding of the N-td. However, lanosterol can suppress the large fluctuation of loop2 to protect the structural stability of the mutant N-td, thus reducing the aggregation propensity of the TRP > KN mutant HγD-Crys. This structure protective activity of lanosterol arises from its capability to preferentially bind to the hydrophobic regions near loop2. Thus, lanosterol acts as a "water blocker" to prevent the invasion of solvent molecules into the hydrophobic core. These findings provide some valuable insights into the development of potential lanosterol-based drugs for cataract prevention and treatment.
Collapse
Affiliation(s)
- Hong Zhou
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Youyun Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Ying Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Shengtang Liu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | - Zaixing Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| |
Collapse
|
11
|
Noreikiene K, Ozerov M, Ahmad F, Kõiv T, Kahar S, Gross R, Sepp M, Pellizzone A, Vesterinen EJ, Kisand V, Vasemägi A. Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding. Parasit Vectors 2020; 13:433. [PMID: 32859251 PMCID: PMC7456052 DOI: 10.1186/s13071-020-04306-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/16/2020] [Indexed: 01/09/2023] Open
Abstract
Background Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses. Methods We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach. Results Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned to Tylodelphys clavata. Conclusions High intraspecific diversity of T. clavata indicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.![]()
Collapse
Affiliation(s)
- Kristina Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia.
| | - Mikhail Ozerov
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893, Drottningholm, Sweden.,Biodiversity Unit, University of Turku, 20014, Turku, Finland
| | - Freed Ahmad
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Toomas Kõiv
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51006, Tartu, Estonia
| | - Siim Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia
| | - Riho Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia
| | - Margot Sepp
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51006, Tartu, Estonia
| | - Antonia Pellizzone
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | - Eero J Vesterinen
- Biodiversity Unit, University of Turku, 20014, Turku, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, 75651, Uppsala, Sweden
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Anti Vasemägi
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006, Tartu, Estonia. .,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893, Drottningholm, Sweden.
| |
Collapse
|
12
|
van Zyl T, Yan W, McAdams A, Peng YR, Shekhar K, Regev A, Juric D, Sanes JR. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. Proc Natl Acad Sci U S A 2020; 117:10339-10349. [PMID: 32341164 PMCID: PMC7229661 DOI: 10.1073/pnas.2001250117] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells; lowering IOP is the only proven treatment strategy to delay disease progression. The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations. Drainage occurs through two pathways in the anterior segment of the eye called conventional and uveoscleral. To gain insights into the cell types that comprise these pathways, we used high-throughput single-cell RNA sequencing (scRNAseq). From ∼24,000 single-cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa), and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident. Finally, we identified the cell types that express genes implicated in glaucoma in all five species. Together, our results provide foundations for investigating the pathogenesis of glaucoma and for using model systems to assess mechanisms and potential interventions.
Collapse
Affiliation(s)
- Tavé van Zyl
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114;
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Alexi McAdams
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Yi-Rong Peng
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Karthik Shekhar
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Aviv Regev
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Dejan Juric
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital Cancer Center, Boston, MA 02114
| | - Joshua R Sanes
- Center for Brain Science, Harvard University, Cambridge, MA 02138;
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| |
Collapse
|
13
|
Zhou H, Yang Z, Tian X, Chen L, Lee S, Huynh T, Ge C, Zhou R. Lanosterol Disrupts the Aggregation of Amyloid-β Peptides. ACS Chem Neurosci 2019; 10:4051-4060. [PMID: 31369236 DOI: 10.1021/acschemneuro.9b00285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lanosterol, an amphipathic molecule, was discovered only very recently to effectively hinder the aggregation of lens proteins and dissolve the extremely stable fibrillar aggregates in cataracts. Here, we combined computational and experimental approaches to study how lanosterol disrupts the aggregation of another important peptide, amyloid-β (Aβ) peptide, associated with the Alzheimer's Disease (AD). Molecular dynamics simulations using the core amyloidogenic segment (KLVFFA) of Aβ peptide revealed that lanosterol exhibits at least two types of inhibition mechanism on the self-assembly of Aβ peptides. First, lanosterol entangles with peptides and forms a hydrophobic core with residues Phe-19 and Phe-20 in particular. Second, it interferes with the steric zipper interaction at the β-sheet-β-sheet interface. These simulation data suggest that lanosterol induces the unfolding of the Aβ peptide and the separation of the β-sheet layers. This predicted inhibition effect of lanosterol was then confirmed by an in vitro ThT fluorescence assay and AFM imaging. The cell toxicity assay also showed that the treatment of lanosterol indeed mitigates the cytotoxicity of the Aβ peptide in PC-12 cells. Moreover, lanosterol shows a stronger suppression effect on Aβ peptides' aggregation than cholesterol because of its higher hydrophobicity. This result establishes a foundation for the development of lanosterol-based potential therapies for AD and other protein conformational diseases.
Collapse
Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Xin Tian
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Lei Chen
- East District of Suzhou Municipal Hospital, Suzhou, Jiangsu 215001, China
| | - Sangyun Lee
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Tien Huynh
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Cuicui Ge
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu 215123, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
14
|
Gao X, Nannini DR, Corrao K, Torres M, Chen YDI, Fan BJ, Wiggs JL, Taylor KD, Gauderman WJ, Rotter JI, Varma R. Genome-wide association study identifies WNT7B as a novel locus for central corneal thickness in Latinos. Hum Mol Genet 2018; 25:5035-5045. [PMID: 28171582 DOI: 10.1093/hmg/ddw319] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/18/2016] [Accepted: 09/12/2016] [Indexed: 01/16/2023] Open
Abstract
The cornea is the outermost layer of the eye and is a vital component of focusing incoming light on the retina. Central corneal thickness (CCT) is now recognized to have a significant role in ocular health and is a risk factor for various ocular diseases, such as keratoconus and primary open angle glaucoma. Most previous genetic studies utilized European and Asian subjects to identify genetic loci associated with CCT. Minority populations, such as Latinos, may aid in identifying additional loci and improve our understanding of the genetic architecture of CCT. In this study, we conducted a genome-wide association study (GWAS) in Latinos, a traditionally understudied population in genetic research, to further identify loci contributing to CCT. Study participants were genotyped using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). All study participants were 40 years of age and older. We assessed the association between individual single nucleotide polymorphisms (SNPs) and CCT using linear regression, adjusting for age, gender and principal components of genetic ancestry. To expand genomic coverage and to interrogate additional SNPs, we imputed SNPs from the 1000 Genomes Project reference panels. We identified a novel SNP, rs10453441 (P = 6.01E-09), in an intron of WNT7B that is associated with CCT. Furthermore, WNT7B is expressed in the human cornea. We also replicated 11 previously reported loci, including IBTK, RXRA-COL5A1, COL5A1, FOXO1, LRRK1 and ZNF469 (P < 1.25E-3). These findings provide further insight into the genetic architecture of CCT and illustrate that the use of minority groups in GWAS will help identify additional loci.
Collapse
Affiliation(s)
- Xiaoyi Gao
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Drew R Nannini
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Kristen Corrao
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Mina Torres
- USC Roski Eye Institute, Department of Ophthalmology, University of Southern California, Los Angeles, CA, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, CA, USA
| | - Bao J Fan
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | | | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, CA, USA
| | - Rohit Varma
- USC Roski Eye Institute, Department of Ophthalmology, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
15
|
Liu Y, Allingham RR. Major review: Molecular genetics of primary open-angle glaucoma. Exp Eye Res 2017; 160:62-84. [PMID: 28499933 DOI: 10.1016/j.exer.2017.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/07/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common type, is a complex inherited disorder that is characterized by progressive retinal ganglion cell death, optic nerve head excavation, and visual field loss. The discovery of a large, and growing, number of genetic and chromosomal loci has been shown to contribute to POAG risk, which carry implications for disease pathogenesis. Differential gene expression analyses in glaucoma-affected tissues as well as animal models of POAG are enhancing our mechanistic understanding in this common, blinding disorder. In this review we summarize recent developments in POAG genetics and molecular genetics research.
Collapse
Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States; James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States; Duke - National University of Singapore (Duke-NUS), Singapore.
| |
Collapse
|
16
|
Abstract
The human lens is comprised largely of crystallin proteins assembled into a highly ordered, interactive macro-structure essential for lens transparency and refractive index. Any disruption of intra- or inter-protein interactions will alter this delicate structure, exposing hydrophobic surfaces, with consequent protein aggregation and cataract formation. Cataracts are the most common cause of blindness worldwide, affecting tens of millions of people, and currently the only treatment is surgical removal of cataractous lenses. The precise mechanisms by which lens proteins both prevent aggregation and maintain lens transparency are largely unknown. Lanosterol is an amphipathic molecule enriched in the lens. It is synthesized by lanosterol synthase (LSS) in a key cyclization reaction of a cholesterol synthesis pathway. Here we identify two distinct homozygous LSS missense mutations (W581R and G588S) in two families with extensive congenital cataracts. Both of these mutations affect highly conserved amino acid residues and impair key catalytic functions of LSS. Engineered expression of wild-type, but not mutant, LSS prevents intracellular protein aggregation of various cataract-causing mutant crystallins. Treatment by lanosterol, but not cholesterol, significantly decreased preformed protein aggregates both in vitro and in cell-transfection experiments. We further show that lanosterol treatment could reduce cataract severity and increase transparency in dissected rabbit cataractous lenses in vitro and cataract severity in vivo in dogs. Our study identifies lanosterol as a key molecule in the prevention of lens protein aggregation and points to a novel strategy for cataract prevention and treatment.
Collapse
|
17
|
Serum and aqueous xanthine oxidase levels, and mRNA expression in anterior lens epithelial cells in pseudoexfoliation. Graefes Arch Clin Exp Ophthalmol 2015; 253:1161-7. [PMID: 25957764 DOI: 10.1007/s00417-015-3043-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 04/18/2015] [Accepted: 04/29/2015] [Indexed: 01/26/2023] Open
Abstract
PURPOSE The aim of this study was to determine serum and aqueous xanthine oxidase (XO) levels, and mRNA expression in anterior lens epithelial cells in pseudoexfoliation (PEX). METHODS In this prospective study, serum, aqueous and anterior lens capsules were taken from 21 patients with PEX and 23 normal subjects who had undergone routine cataract surgery. Serum and aqueous XO levels were analyzed using the colorimetric method. mRNA expression of XO in anterior lens epithelial cells was evaluated using reverse transcription polymerase chain reaction analysis. RESULTS Serum XO levels (means ± standard deviations) were 207.0 ± 86.1 IU/mL and 240.6 ± 114.1 IU/mL in the normal and PEX groups, respectively (p = 0.310). Aqueous XO levels (means ± standard deviations) were 65.5 ± 54.3 IU/mL in the normal group and 130.5 ± 117.4 IU/mL in the PEX group (p = 0.028). There was a 2.9 fold decrease in mRNA expression in anterior lens epithelial cells of PEX, which is significantly lower than the normal group (p = 0.01). CONCLUSIONS Higher aqueous XO levels lacking associated different serum XO suggests higher oxidative stress in the aqueous. Higher aqueous XO levels in PEX with decreased mRNA expression in anterior lens epithelial cells indicate possible overexpression of XO in other structures related to the aqueous.
Collapse
|
18
|
Takamiya M, Weger BD, Schindler S, Beil T, Yang L, Armant O, Ferg M, Schlunck G, Reinhard T, Dickmeis T, Rastegar S, Strähle U. Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber. PLoS One 2015; 10:e0117645. [PMID: 25692557 PMCID: PMC4334901 DOI: 10.1371/journal.pone.0117645] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/29/2014] [Indexed: 11/19/2022] Open
Abstract
The cornea is a central component of the camera eye of vertebrates and even slight corneal disturbances severely affect vision. The transcription factor PAX6 is required for normal eye development, namely the proper separation of the lens from the developing cornea and the formation of the iris and anterior chamber. Human PAX6 mutations are associated with severe ocular disorders such as aniridia, Peters anomaly and chronic limbal stem cell insufficiency. To develop the zebrafish as a model for corneal disease, we first performed transcriptome and in situ expression analysis to identify marker genes to characterise the cornea in normal and pathological conditions. We show that, at 7 days post fertilisation (dpf), the zebrafish cornea expresses the majority of marker genes (67/84 tested genes) found also expressed in the cornea of juvenile and adult stages. We also characterised homozygous pax6b mutants. Mutant embryos have a thick cornea, iris hypoplasia, a shallow anterior chamber and a small lens. Ultrastructure analysis revealed a disrupted corneal endothelium. pax6b mutants show loss of corneal epithelial gene expression including regulatory genes (sox3, tfap2a, foxc1a and pitx2). In contrast, several genes (pitx2, ctnnb2, dcn and fabp7a) were ectopically expressed in the malformed corneal endothelium. Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme.
Collapse
Affiliation(s)
- Masanari Takamiya
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Benjamin D. Weger
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Simone Schindler
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Tanja Beil
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Lixin Yang
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Olivier Armant
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Günther Schlunck
- Eye Center, Freiburg University Medical Center, Killianstr. 5, 79106 Freiburg, Germany
| | - Thomas Reinhard
- Eye Center, Freiburg University Medical Center, Killianstr. 5, 79106 Freiburg, Germany
| | - Thomas Dickmeis
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Sepand Rastegar
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany
- * E-mail:
| |
Collapse
|
19
|
Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Exp Eye Res 2014; 129:93-106. [PMID: 25446321 DOI: 10.1016/j.exer.2014.11.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/31/2014] [Accepted: 11/04/2014] [Indexed: 12/27/2022]
Abstract
Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes.
Collapse
|
20
|
Osthoff M, Brown KD, Kong DC, Daniell M, Eisen DP. Activation of the lectin pathway of complement in experimental human keratitis with Pseudomonas aeruginosa. Mol Vis 2014; 20:38-45. [PMID: 24426774 PMCID: PMC3888499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/02/2014] [Indexed: 11/16/2022] Open
Abstract
PURPOSE Pseudomonas aeruginosa (P. aeruginosa) microbial keratitis (MK) is a sight-threatening disease. Previous animal studies have identified an important contribution of the complement system to the clearance of P. aeruginosa infection of the cornea. Mannose-binding lectin (MBL), a pattern recognition receptor of the lectin pathway of complement, has been implicated in the host defense against P. aeruginosa. However, studies addressing the role of the lectin pathway in P. aeruginosa MK are lacking. Hence, we sought to determine the activity of the lectin pathway in human MK caused by P. aeruginosa. METHODS Primary human corneal epithelial cells (HCECs) from cadaveric donors were exposed to two different P. aeruginosa strains. Gene expression of interleukin (IL)-6, IL-8, MBL, and other complement proteins was determined by reverse transcription-polymerase chain reaction (RT-PCR) and MBL synthesis by enzyme-linked immunosorbent assay and intracellular flow cytometry. RESULTS MBL gene expression was not detected in unchallenged HCECs. Exposure of HCECs to P. aeruginosa resulted in rapid induction of the transcriptional expression of MBL, IL-6, and IL-8. In addition, expression of several complement proteins of the classical and lectin pathways, but not the alternative pathway, were upregulated after 5 h of challenge, including MBL-associated serine protease 1. However, MBL protein secretion was not detectable 18 h after challenge with P. aeruginosa. CONCLUSIONS MK due to P. aeruginosa triggers activation of MBL and the lectin pathway of complement. However, the physiologic relevance of this finding is unclear, as corresponding MBL oligomer production was not observed.
Collapse
Affiliation(s)
- Michael Osthoff
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville VIC, Australia,Department of Medicine, Royal Melbourne Hospital, University of Melbourne, VIC, Australia
| | - Karl D. Brown
- Centre for Eye Research Australia, East Melbourne VIC, Australia
| | - David C.M. Kong
- Centre for Medicine Use and Safety, Monash University, Parkville VIC, Australia
| | - Mark Daniell
- Centre for Eye Research Australia, East Melbourne VIC, Australia
| | - Damon P. Eisen
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville VIC, Australia,Department of Medicine, Royal Melbourne Hospital, University of Melbourne, VIC, Australia
| |
Collapse
|
21
|
Lim MN, Hussin NH, Othman A, Umapathy T, Gurbind S, Baharuddin P, Jamal R, Zakaria Z. Comparative global gene expression profile of human limbal stromal cells, bone marrow mesenchymal stromal cells, adipose-derived mesenchymal stromal cells and foreskin fibroblasts. ACTA ACUST UNITED AC 2014. [DOI: 10.7243/2054-717x-1-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
22
|
Rajkumar S, Vasavada AR, Praveen MR, Ananthan R, Reddy GB, Tripathi H, Ganatra DA, Arora AI, Patel AR. Exploration of molecular factors impairing superoxide dismutase isoforms activity in human senile cataractous lenses. Invest Ophthalmol Vis Sci 2013; 54:6224-33. [PMID: 23970468 DOI: 10.1167/iovs.13-11935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
PURPOSE To explore different molecular factors impairing the activities of superoxide dismutase (SOD) isoforms in senile cataractous lenses. METHODS Enzyme activity of SOD isoforms, levels of their corresponding cofactors copper (Cu), manganese (Mn), zinc (Zn), and expression of mRNA transcripts and proteins were determined in the lenses of human subjects with and without cataract. DNA from lens epithelium (LE) and peripheral blood was isolated. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) followed by sequencing was carried out to screen somatic mutations. The impact of intronic insertion/deletion (INDEL) variations on the splicing process and on the resultant transcript was evaluated. Genotyping of IVS4+42delG polymorphism of SOD1 gene was done by PCR-restriction fragment length polymorphism (RFLP). RESULTS A significant decrease in Cu/Zn- and Mn-SOD activity (P < 0.001) and in Cu/Zn-SOD transcript (P < 0.001) and its protein (P < 0.05) were found in cataractous lenses. No significant change in the level of copper (P = 0.36) and an increase in the level of manganese (P = 0.01) and zinc (P = 0.02) were observed in cataractous lenses. A significant positive correlation between the level of Cu/Zn-SOD activity and the levels of Cu (P = 0.003) and Zn (P = 0.005) was found in the cataractous lenses. DNA sequencing revealed three intronic INDEL variations in exon4 of SOD1 gene. Splice-junction analysis showed the potential of IVS4+42delG in creating a new cryptic acceptor site. If it is involved in alternate splicing, it could result in generation of SOD1 mRNA transcripts lacking exon4 region. Transcript analysis revealed the presence of complete SOD1 mRNA transcripts. Genotyping revealed the presence of IVS4+42delG polymorphism in all subjects. CONCLUSIONS The decrease in the activity of SOD1 isoform in cataractous lenses was associated with the decreased level of mRNA transcripts and their protein expression and was not associated with either modulation in the level of enzyme cofactors or with INDEL variations.
Collapse
Affiliation(s)
- Sankaranarayanan Rajkumar
- Department of Molecular Genetics and Biochemistry, Iladevi Cataract and IOL Research Centre, Memnagar, Ahmedabad, Gujarat, India
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Strzalka-Mrozik B, Prudlo L, Kimsa MW, Kimsa MC, Kapral M, Nita M, Mazurek U. Quantitative analysis of SOD2, ALDH1A1 and MGST1 messenger ribonucleic acid in anterior lens epithelium of patients with pseudoexfoliation syndrome. Mol Vis 2013; 19:1341-9. [PMID: 23805041 PMCID: PMC3692400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/10/2013] [Indexed: 11/06/2022] Open
Abstract
PURPOSE The aim of the study was to investigate the expression of selected genes encoding enzymes involved in the antioxidant defense system (superoxide dismutase 2, SOD2; aldehyde dehydrogenase 1, ALDH1A1; microsomal glutathione S-transferase 1, MGST1) in fragments of anterior lens capsules of patients with pseudoexfoliation syndrome (PEX). The specificity and sensitivity of these molecular markers for PEX development were also assessed. METHODS The study group consisted of 20 patients (9 women and 11 men) with diagnosed PEX and cataract. The control group included 23 patients (8 women and 15 men) who needed cataract surgery but did not have PEX. Quantification of SOD2, ALDH1A1, and MGST1 messenger ribonucleic acid (mRNA) was performed with quantitative real-time PCR. RESULTS SOD2, ALDH1A1, and MGST1 mRNAs were detected in all studied samples. The examined genes had statistically significant higher expression in the group of patients with PEX than in the control group (SOD2, p=0.0015; ALDH1A1, p=0.0001; MGST1, p=0.0001, Mann-Whitney U test). The areas under the curve (AUC) of SOD2, MGST1, and ALDH1A1 were 0.766, 0.818, and 0.957, respectively. CONCLUSIONS Differential expression of SOD2, ALDH1A1, and MGST1 genes in the anterior lens capsules of patients with PEX suggest that diseased tissue appears to respond to the previously reported oxidative stress. A possible role of ALDH1A1 mRNA level as a risk factor or marker for PEX needs further confirmation.
Collapse
Affiliation(s)
| | - Lilianna Prudlo
- Department of Ophthalmology, Medical University of Silesia, Katowice, Poland
| | - Malgorzata W. Kimsa
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| | - Magdalena C. Kimsa
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| | - Malgorzata Kapral
- Department of Biochemistry, Medical University of Silesia, Sosnowiec, Poland
| | - Malgorzata Nita
- Department of Ophthalmology, Medical University of Silesia, Katowice, Poland
| | - Urszula Mazurek
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| |
Collapse
|
24
|
Kim BJ, Sprehe N, Morganti A, Wordinger RJ, Clark AF. The effect of postmortem time on the RNA quality of human ocular tissues. Mol Vis 2013; 19:1290-5. [PMID: 23805035 PMCID: PMC3692406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/07/2013] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Profiling gene expression in human ocular tissues provides invaluable information for understanding ocular biology and investigating numerous ocular diseases. Accurate measurement of gene expression requires high-quality RNA, which often is a challenge with postmortem ocular tissues. METHODS We examined the effect of various death to preservation (DP) times on the RNA quality of ten different ocular tissues. We used 16 eyes from eight different human donors. The eyes were preserved immediately in RNAlater or preserved after initial storage at 4 °C to create a range of DP times from 2 to 48 h. Ten ocular tissues were dissected from each eye. After total RNA was extracted from each dissected ocular tissue, the RNA integrity number (RIN) was determined using an Agilent Bioanalyzer. RESULTS The RIN values from corneal and trabecular meshwork tissues were significantly (p<0.05) higher than those from the ciliary body at an earlier DP time (<6 h), but were not different among all tissues after 8 h. Interestingly, the RIN values from non-vascularized tissues were significantly (p=0.0002) higher than those from vascularized ocular tissues at early DP times (<6 h). The RIN value from the cornea was significantly (p<0.05) higher at short DP times compared to longer DP times. The RIN values from corneal tissues were significantly correlated to DP time according to regression analysis (p<0.05). CONCLUSIONS In this study, we determined RNA quality from postmortem ocular tissues with various DP times. Our results emphasize the need for rapid preservation and processing of postmortem human donor eye tissues, especially for vascularized ocular tissues.
Collapse
Affiliation(s)
- Byung-Jin Kim
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
| | | | | | - Robert J. Wordinger
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
| | - Abbot F. Clark
- Department of Cell Biology & Anatomy and The North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX
| |
Collapse
|
25
|
Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma. Nat Genet 2012; 44:1142-1146. [PMID: 22922875 DOI: 10.1038/ng.2390] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 08/01/2012] [Indexed: 01/11/2023]
Abstract
Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study including 1,854 PACG cases and 9,608 controls across 5 sample collections in Asia. Replication experiments were conducted in 1,917 PACG cases and 8,943 controls collected from a further 6 sample collections. We report significant associations at three new loci: rs11024102 in PLEKHA7 (per-allele odds ratio (OR)=1.22; P=5.33×10(-12)), rs3753841 in COL11A1 (per-allele OR=1.20; P=9.22×10(-10)) and rs1015213 located between PCMTD1 and ST18 on chromosome 8q (per-allele OR=1.50; P=3.29×10(-9)). Our findings, accumulated across these independent worldwide collections, suggest possible mechanisms explaining the pathogenesis of PACG.
Collapse
|
26
|
Wilson GR, Morton JD, Palmer DN, McEwan JC, Gately K, Anderson RM, Dodds KG. The locus for an inherited cataract in sheep maps to ovine chromosome 6. Mol Vis 2012; 18:1384-94. [PMID: 22690116 PMCID: PMC3370893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/28/2012] [Indexed: 11/04/2022] Open
Abstract
PURPOSE Cataracts are an important cause of blindness in humans but there are few large animal models available. One of these animal models is Ovine Heritable Cataract, a bilateral cortical cataract which develops after birth. This cataract has been used as a model for human cataracts in drug trials, but the gene responsible for the cataract trait is unknown. A genetic test for cataract would improve the efficiency of the model by predicting which animals would develop cataracts. Identifying the genetic basis of the cataract would indicate its relevance to human cataract. METHODS A genome scan was performed on 20 sheep chromosomes, representing 86% of the genome, to determine the position of the cataract locus. Additional microsatellite markers were tested on chromosome 6 using a larger pedigree. Fine mapping was performed using a breakpoint panel of 36 animals and novel microsatellite markers taken from the bovine genome assembly. All exons of the candidate gene nudix (nucleoside diphosphate linked moiety X)-type motif 9 (NUDT9) were sequenced in normal and affected sheep. RESULTS Significant linkage was found between cataract status and markers on chromosome 6. Linkage analysis on the larger pedigree showed the most likely position of the cataract locus was between 112.3 and 132.9 cM from the centromere. During fine mapping, NUDT9 was considered as a positional candidate for the cataract gene because it was located within the linked interval and is expressed in the lens. The gene was ruled out as the cataract gene after extensive genotype analysis, but a single nucleotide polymorphism (SNP) inside it provided a useful restriction fragment length polymorphism (RFLP) marker for further fine mapping. Twelve new markers were found and used to map the cataract locus to between 131.1 and 131.8 cM from the centromere. CONCLUSIONS A region of ovine chromosome 6 strongly linked to cataract has been identified, and a genetic test for cataract based on a SNP within this region has been developed. The best candidate gene within this region is AF4/FMR2 family, member 1 (AFF1), the mouse equivalent of which is associated with an inherited cataract.
Collapse
Affiliation(s)
- Gareth R.S. Wilson
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - James D. Morton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - David N. Palmer
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - John C. McEwan
- Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand
| | - Karl Gately
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | | | - Ken G. Dodds
- Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand
| |
Collapse
|
27
|
Lachke SA, Ho JWK, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci 2012; 53:1617-27. [PMID: 22323457 DOI: 10.1167/iovs.11-8839] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE To facilitate the identification of genes associated with cataract and other ocular defects, the authors developed and validated a computational tool termed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE uses a mouse embryonic lens gene expression data set as a bioinformatics filter to select candidate genes from human or mouse genomic regions implicated in disease and to prioritize them for further mutational and functional analyses. METHODS Microarray gene expression profiles were obtained for microdissected embryonic mouse lens at three key developmental time points in the transition from the embryonic day (E)10.5 stage of lens placode invagination to E12.5 lens primary fiber cell differentiation. Differentially regulated genes were identified by in silico comparison of lens gene expression profiles with those of whole embryo body (WB) lacking ocular tissue. RESULTS Gene set analysis demonstrated that this strategy effectively removes highly expressed but nonspecific housekeeping genes from lens tissue expression profiles, allowing identification of less highly expressed lens disease-associated genes. Among 24 previously mapped human genomic intervals containing genes associated with isolated congenital cataract, the mutant gene is ranked within the top two iSyTE-selected candidates in approximately 88% of cases. Finally, in situ hybridization confirmed lens expression of several novel iSyTE-identified genes. CONCLUSIONS iSyTE is a publicly available Web resource that can be used to prioritize candidate genes within mapped genomic intervals associated with congenital cataract for further investigation. Extension of this approach to other ocular tissue components will facilitate eye disease gene discovery.
Collapse
Affiliation(s)
- Salil A Lachke
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard edical School, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Baas DC, Ho L, Tanck MW, Fritsche LG, Merriam JE, van het Slot R, Koeleman BP, Gorgels TG, van Duijn CM, Uitterlinden AG, de Jong PT, Hofman A, ten Brink JB, Vingerling JR, Klaver CC, Dean M, Weber BHF, Allikmets R, Hageman GS, Bergen AA. Multicenter cohort association study of SLC2A1 single nucleotide polymorphisms and age-related macular degeneration. Mol Vis 2012; 18:657-74. [PMID: 22509097 PMCID: PMC3324365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 03/14/2012] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Age-related macular degeneration (AMD) is a major cause of blindness in older adults and has a genetically complex background. This study examines the potential association between single nucleotide polymorphisms (SNPs) in the glucose transporter 1 (SLC2A1) gene and AMD. SLC2A1 regulates the bioavailability of glucose in the retinal pigment epithelium (RPE), which might influence oxidative stress-mediated AMD pathology. METHODS Twenty-two SNPs spanning the SLC2A1 gene were genotyped in 375 cases and 199 controls from an initial discovery cohort (the Amsterdam-Rotterdam-Netherlands study). Replication testing was performed in The Rotterdam Study (the Netherlands) and study populations from Würzburg (Germany), the Age Related Eye Disease Study (AREDS; United States), Columbia University (United States), and Iowa University (United States). Subsequently, a meta-analysis of SNP association was performed. RESULTS In the discovery cohort, significant genotypic association between three SNPs (rs3754219, rs4660687, and rs841853) and AMD was found. Replication in five large independent (Caucasian) cohorts (4,860 cases and 4,004 controls) did not yield consistent association results. The genotype frequencies for these SNPs were significantly different for the controls and/or cases among the six individual populations. Meta-analysis revealed significant heterogeneity of effect between the studies. CONCLUSIONS No overall association between SLC2A1 SNPs and AMD was demonstrated. Since the genotype frequencies for the three SLC2A1 SNPs were significantly different for the controls and/or cases between the six cohorts, this study corroborates previous evidence that population dependent genetic risk heterogeneity in AMD exists.
Collapse
Affiliation(s)
- Dominique C. Baas
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Lintje Ho
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Michael W.T. Tanck
- Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Lars G. Fritsche
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Joanna E. Merriam
- Department of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, NY
| | - Ruben van het Slot
- Department of Medical Genetics Research Section, Utrecht Medical Center (UMC), Utrecht, The Netherlands
| | - Bobby P.C. Koeleman
- Department of Medical Genetics Research Section, Utrecht Medical Center (UMC), Utrecht, The Netherlands
| | - Theo G.M.F. Gorgels
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Internal Medicine, EMC, Rotterdam, The Netherlands
| | - Paulus T.V.M. de Jong
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands,Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, AMC, Amsterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands
| | - Jacoline B. ten Brink
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands
| | - Johannes R. Vingerling
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Caroline C.W. Klaver
- Department of Epidemiology, Erasmus Medical Center (EMC), Rotterdam, The Netherlands,Department of Ophthalmology, EMC, Rotterdam, The Netherlands
| | - Michael Dean
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD
| | | | - Rando Allikmets
- Department of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, NY
| | - Gregory S. Hageman
- Department of Ophthalmology and Visual Sciences, The University of Iowa, IA,Center for the Study of Macular Degeneration, University of California, Santa Barbara, CA
| | - Arthur A.B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands,Department of Ophthalmology, AMC, Amsterdam, The Netherlands,Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| |
Collapse
|
29
|
Whitmore SS, Mullins RF. Transcriptome changes in age-related macular degeneration. BMC Med 2012; 10:21. [PMID: 22369667 PMCID: PMC3307472 DOI: 10.1186/1741-7015-10-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 02/27/2012] [Indexed: 12/03/2022] Open
Abstract
Age-related macular degeneration (AMD) is a debilitating, common cause of visual impairment. While the last decade has seen great progress in understanding the pathophysiology of AMD, the molecular changes that occur in eyes with AMD are still poorly understood. In the current issue of Genome Medicine, Newman and colleagues present the first systematic transcriptional profile analysis of AMD-affected tissues, providing a comprehensive set of expression data for different regions (macula versus periphery), tissues (retina versus retinal pigment epithelium (RPE)/choroid), and disease state (control versus early or advanced AMD). Their findings will serve as a foundation for additional systems-level research into the pathogenesis of this blinding disease.
Collapse
Affiliation(s)
- S Scott Whitmore
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, 4135E MERF, 375 Newton Rd, Iowa City, IA 52242, USA
| | | |
Collapse
|
30
|
Lamba DA, Reh TA. Microarray characterization of human embryonic stem cell--derived retinal cultures. Invest Ophthalmol Vis Sci 2011; 52:4897-906. [PMID: 21345990 DOI: 10.1167/iovs.10-6504] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PURPOSE A number of protocols have been published to induce retinal determination from human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC). Although all these studies have shown some degree of expression of markers of retinal cells, fewer than 30 markers are typically used to characterize the ESC-derived retinal cells. Hence, it is not known whether they express all the genes present in normal developing retinal cells. To assess the efficiency of their retinal determination protocol at the transcriptome level and to understand the changes in human retinal gene expression patterns during development, the authors conducted a microarray-based analysis comparing human retina to hESC-derived retinal cells. METHODS The authors extracted total RNA from 60-day, 80-day, and 96-day human fetal retina and hESC-derived retinal cells at 3 weeks and 9 weeks after induction. RNA was subjected to analysis using a commercial microarray. Data were normalized using Affymetrix Power Tools and analyzed using commercial microarray software. RESULTS On K-median clustering analysis, the authors found that overall there was a very high correlation between genes expressed in human fetal retina and those in ESC-derived retinal cultures. The cultures were at similar developmental ages to the corresponding fetal retinal ages. They found only 1% of the genes on the array to be expressed at a higher level in ESC-derived retinal cells than in fetal retina, and most of these were expressed in the retinal pigment epithelium and ciliary epithelium. CONCLUSIONS In sum, gene array profiling provides an effective method for characterization of the efficiency of directed differentiation of hESCs to retinal cells.
Collapse
Affiliation(s)
- Deepak A Lamba
- Department of Ophthalmology, University of Washington, Seattle, Washington 98195, USA
| | | |
Collapse
|
31
|
Lachke SA, Maas RL. Building the developmental oculome: systems biology in vertebrate eye development and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:305-323. [PMID: 20836031 DOI: 10.1002/wsbm.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate eye is a sophisticated multicomponent organ that has been actively studied for over a century, resulting in the identification of the major embryonic and molecular events involved in its complex developmental program. Data gathered so far provides sufficient information to construct a rudimentary network of the various signaling molecules, transcription factors, and their targets for several key stages of this process. With the advent of genomic technologies, there has been a rapid expansion in our ability to collect and process biological information, and the use of systems-level approaches to study specific aspects of vertebrate eye development has already commenced. This is beginning to result in the definition of the dynamic developmental networks that operate in ocular tissues, and the interactions of such networks between coordinately developing ocular tissues. Such an integrative understanding of the eye by a comprehensive systems-level analysis can be termed the 'oculome', and that of serial developmental stages of the eye as it transits from its initiation to a fully formed functional organ represents the 'developmental oculome'. Construction of the developmental oculome will allow novel mechanistic insights that are essential for organ regeneration-based therapeutic applications, and the generation of computational models for eye disease states to predict the effects of drugs. This review discusses our present understanding of two of the individual components of the developing vertebrate eye--the lens and retina--at both the molecular and systems levels, and outlines the directions and tools required for construction of the developmental oculome.
Collapse
Affiliation(s)
- Salil A Lachke
- Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard L Maas
- Division of Genetics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
32
|
Polisetti N, Agarwal P, Khan I, Kondaiah P, Sangwan VS, Vemuganti GK. Gene expression profile of epithelial cells and mesenchymal cells derived from limbal explant culture. Mol Vis 2010; 16:1227-40. [PMID: 20664697 PMCID: PMC2903463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 06/23/2010] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Limbal stem cell deficiency is a challenging clinical problem and the current treatment involves replenishing the depleted limbal stem cell (LSC) pool by either limbal tissue transplantation or use of cultivated limbal epithelial cells (LEC). Our experience of cultivating the LEC on denuded human amniotic membrane using a feeder cell free method, led to identification of mesenchymal cells of limbus (MC-L), which showed phenotypic resemblance to bone marrow derived mesenchymal stem cells (MSC-BM). To understand the transcriptional profile of these cells, microarray experiments were carried out. METHODS RNA was isolated from cultured LEC, MC-L and MSC-BM and microarray experiments were carried out by using Agilent chip (4x44 k). The microarray data was validated by using Realtime and semiquntitative reverse transcription polymerase chain reaction. RESULTS The microarray analysis revealed specific gene signature of LEC and MC-L, and also their complementary role related to cytokine and growth factor profile, thus supporting the nurturing roles of the MC-L. We have also observed similar and differential gene expression between MC-L and MSC-BM. CONCLUSIONS This study represents the first extensive gene expression analysis of limbal explant culture derived epithelial and mesenchymal cells and as such reveals new insight into the biology, ontogeny, and in vivo function of these cells.
Collapse
Affiliation(s)
- Naresh Polisetti
- Sudhakar and Sreekanth Ravi Stem Cell Biology Laboratory, C-TRACER, Hyderabad Eye Research Foundation, L.V. Prasad Eye Institute, Hyderabad, India
| | - Prasoon Agarwal
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Banglore, India
| | - Imran Khan
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Banglore, India
| | - Paturu Kondaiah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Banglore, India
| | - Virender S. Sangwan
- Cornea and Anterior Segment Service, L.V. Prasad Eye Institute, Hyderabad, India
| | - Geeta K. Vemuganti
- Sudhakar and Sreekanth Ravi Stem Cell Biology Laboratory, C-TRACER, Hyderabad Eye Research Foundation, L.V. Prasad Eye Institute, Hyderabad, India
| |
Collapse
|
33
|
Lahooti H, Parmar KR, Wall JR. Pathogenesis of thyroid-associated ophthalmopathy: does autoimmunity against calsequestrin and collagen XIII play a role? Clin Ophthalmol 2010; 4:417-25. [PMID: 20505833 PMCID: PMC2874268 DOI: 10.2147/opth.s6534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Indexed: 02/03/2023] Open
Abstract
Thyroid-associated ophthalmopathy (TAO), or thyroid eye disease, is a complex inflammatory disorder of the eye that, as its name implies, is associated with thyroid disease. TAO can be divided into three subtypes: ocular myopathy, congestive myopathy and mixed congestive and myopathic ophthalmopathy. Although the precise pathophysiology of TAO remains unclear it is likely to reflect an autoimmune reaction involving sensitized T-cells and autoantibodies directed against a thyroid and orbital tissue shared antigen. One well studied candidate in this immune reaction is the thyroid-stimulating hormone receptor (TSH-r), expressed in the orbital fibroblast and pre adipocyte. In our studies of TAO, we have investigated the nature and significance of antibodies targeting other eye muscle and orbital connective tissue (OCT) antigens. Our findings suggest that autoimmunity against the eye muscle antigen calsequestrin and the OCT antigen collagen XIII plays a role in the pathogenesis of TAO. We propose that ocular myopathy and chronic eyelid retraction are due to autoimmunity against skeletal muscle calsequestrin in the extraocular and eyelid muscles, respectively. This may be initiated in the thyroid where calsequestrin expression is upregulated, possibly due to a stimulatory effect of TSH-r antibodies. We also propose that congestive ophthalmopathy results from a reaction against the TSH-r or collagen XIII in orbital fibroblast cell membranes. Further insight into the role of eye muscle and OCT antigens in the pathogenesis of TAO may allow for the development of new therapies to treat the eye disorder and reduce patient morbidity.
Collapse
Affiliation(s)
- Hooshang Lahooti
- The Department of Medicine, University of Sydney, Nepean Clinical School, Penrith, NSW, Australia
| | | | | |
Collapse
|
34
|
Trimarchi JM, Cho SH, Cepko CL. Identification of genes expressed preferentially in the developing peripheral margin of the optic cup. Dev Dyn 2009; 238:2327-9. [PMID: 19449303 PMCID: PMC2916742 DOI: 10.1002/dvdy.21973] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Specification of the peripheral optic cup by Wnt signaling is critical for formation of the ciliary body/iris. Identification of marker genes for this region during development provides a starting point for functional analyses. During transcriptional profiling of single cells from the developing eye, two cells were identified that expressed genes not found in most other single cell profiles. In situ hybridizations demonstrated that many of these genes were expressed in the peripheral optic cup in both early mouse and chicken development, and in the ciliary body/iris at subsequent developmental stages. These analyses indicate that the two cells probably originated from the developing ciliary body/iris. Changes in expression of these genes were assayed in embryonic chicken retinas when canonical Wnt signaling was ectopically activated by CA-beta-catenin. Twelve ciliary body/iris genes were identified as upregulated following induction, suggesting they are excellent candidates for downstream effectors of Wnt signaling in the optic cup.
Collapse
Affiliation(s)
- Jeffrey M Trimarchi
- Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | |
Collapse
|
35
|
Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW. Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Mol Vis 2009; 15:1730-63. [PMID: 19727342 PMCID: PMC2736153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 08/25/2009] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Individual differences in patterns of gene expression account for much of the diversity of ocular phenotypes and variation in disease risk. We examined the causes of expression differences, and in their linkage to sequence variants, functional differences, and ocular pathophysiology. METHODS mRNAs from young adult eyes were hybridized to oligomer microarrays (Affymetrix M430v2). Data were embedded in GeneNetwork with millions of single nucleotide polymorphisms, custom array annotation, and information on complementary cellular, functional, and behavioral traits. The data include male and female samples from 28 common strains, 68 BXD recombinant inbred lines, as well as several mutants and knockouts. RESULTS We provide a fully integrated resource to map, graph, analyze, and test causes and correlations of differences in gene expression in the eye. Covariance in mRNA expression can be used to infer gene function, extract signatures for different cells or tissues, to define molecular networks, and to map quantitative trait loci that produce expression differences. These data can also be used to connect disease phenotypes with sequence variants. We demonstrate that variation in rhodopsin expression efficiently predicts candidate genes for eight uncloned retinal diseases, including WDR17 for the human RP29 locus. CONCLUSIONS The high level of strain variation in gene expression is a powerful tool that can be used to explore and test molecular networks underlying variation in structure, function, and disease susceptibility. The integration of these data into GeneNetwork provides users with a workbench to test linkages between sequence differences and eye structure and function.
Collapse
Affiliation(s)
- Eldon E. Geisert
- Department of Ophthalmology and Center for Vision Research, Memphis, TN
| | - Lu Lu
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, Memphis, TN
| | | | | | - Mohamed Nassr
- Department of Ophthalmology and Center for Vision Research, Memphis, TN
| | - Xusheng Wang
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, Memphis, TN
| | - Weikuan Gu
- Department of Orthopedics, University of Tennessee Health Science Center, Memphis, TN
| | - Yan Jiao
- Department of Orthopedics, University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, Memphis, TN
| |
Collapse
|
36
|
Wang X, Nookala S, Narayanan C, Giorgianni F, Beranova-Giorgianni S, McCollum G, Gerling I, Penn JS, Jablonski MM. Proteomic analysis of the retina: removal of RPE alters outer segment assembly and retinal protein expression. Glia 2009; 57:380-92. [PMID: 18803304 PMCID: PMC2653273 DOI: 10.1002/glia.20765] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mechanisms that regulate the complex physiological task of photoreceptor outer segment assembly remain an enigma. One limiting factor in revealing the mechanism(s) by which this process is modulated is that not all of the role players who participate in this process are known. The purpose of this study was to determine some of the retinal proteins that likely play a critical role in regulating photoreceptor outer segment assembly. To do so, we analyzed and compared the proteome map of tadpole Xenopus laevis retinal pigment epithelium (RPE)-supported retinas containing organized outer segments with that of RPE-deprived retinas containing disorganized outer segments. Solubilized proteins were labeled with CyDye fluors followed by multiplexed two-dimensional separation. The intensity of protein spots and comparison of proteome maps was performed using DeCyder software. Identification of differentially regulated proteins was determined using nanoLC-ESI-MS/MS analysis. We found a total of 27 protein spots, 21 of which were unique proteins, which were differentially expressed in retinas with disorganized outer segments. We predict that in the absence of the RPE, oxidative stress initiates an unfolded protein response. Subsequently, downregulation of several candidate Müller glial cell proteins may explain the inability of photoreceptors to properly fold their outer segment membranes. In this study, we have used identification and bioinformatics assessment of proteins that are differentially expressed in retinas with disorganized outer segments as a first step in determining probable key molecules involved in regulating photoreceptor outer segment assembly.
Collapse
Affiliation(s)
- XiaoFei Wang
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
| | - Suba Nookala
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
| | | | - Francesco Giorgianni
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN
| | | | - Gary McCollum
- Department of Ophthalmology, Vanderbilt University, Nashville, TN
| | - Ivan Gerling
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - John S. Penn
- Department of Ophthalmology, Vanderbilt University, Nashville, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
| |
Collapse
|
37
|
Prophylactic and therapeutic efficacy of a fully human immunoglobulin G1 monoclonal antibody to Pseudomonas aeruginosa alginate in murine keratitis infection. Infect Immun 2008; 76:4720-5. [PMID: 18644881 DOI: 10.1128/iai.00496-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of ulcerative keratitis due to Pseudomonas aeruginosa is difficult, time-consuming, and uncomfortable owing to the need for the frequent application of antibiotic drops to the infected corneal surface. We examined here whether a fully human immunoglobulin G1 monoclonal antibody (MAb) specific to the conserved alginate surface polysaccharide of P. aeruginosa could mediate protective immunity against typically nonmucoid strains isolated from human cases of keratitis. MAb F429 effectively opsonized alginate-positive, but not alginate-negative, nonmucoid strains in conjunction with phagocytes and complement. Prophylactic administration of MAb F429 18 h prior to infection with two clinical isolates significantly reduced bacterial levels in the eye and the associated corneal pathology. Along similar lines, systemic intraperitoneal injection, as well as topical application of the MAb onto the infected eye, starting 8 h postinfection in both experimental protocols resulted in significant reductions in bacteria in the eye, as well as minimizing pathological damage to the cornea. These findings indicate that MAb F429 could be useful as an additional therapeutic component for the treatment of P. aeruginosa keratitis.
Collapse
|
38
|
Kalathur RKR, Gagniere N, Berthommier G, Poidevin L, Raffelsberger W, Ripp R, Léveillard T, Poch O. RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina. BMC Genomics 2008; 9:208. [PMID: 18457592 PMCID: PMC2386825 DOI: 10.1186/1471-2164-9-208] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 05/05/2008] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including age-related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina. DESCRIPTION RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression meta-data and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed in 5 different model systems: drosophila, zebrafish, rat, mouse and human. The database is supported by a platform that is designed to easily integrate new functionalities and is also frequently updated. CONCLUSION The results obtained from various biological scenarios can be visualized, compared and downloaded. The results of a case study are presented that highlight the utility of RETINOBASE. Overall, RETINOBASE provides efficient access to the global expression profiling of retinal genes from different organisms under various conditions.
Collapse
Affiliation(s)
- Ravi Kiran Reddy Kalathur
- Laboratoire de Bioiformatique et de Genomique Integratives, Institut de Génétique et de Biologie Moléculaire et Céllulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Functionally active complement system and complement regulatory proteins are present in the normal human and rodent eye. Complement activation and its regulation by ocular complement regulatory proteins contribute to the pathology of various ocular diseases including keratitis, uveitis and age-related macular degeneration. Furthermore, a strong relationship between age-related macular degeneration and polymorphism in the genes of certain complement components/complement regulatory proteins is now well established. Recombinant forms of the naturally occurring complement regulatory proteins have been exploited in the animal models for treatment of these ocular diseases. It is hoped that in the future recombinant complement regulatory proteins will be used as novel therapeutic agents in the clinic for the treatment of keratitis, uveitis, and age-related macular degeneration.
Collapse
|
40
|
Borrás T. Chapter 11 What is Functional Genomics Teaching us about Intraocular Pressure Regulation and Glaucoma? CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00411-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Papaioannou M, Melle C, Baniahmad A. The coregulator Alien. NUCLEAR RECEPTOR SIGNALING 2007; 5:e008. [PMID: 18174916 PMCID: PMC2121318 DOI: 10.1621/nrs.05008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/27/2007] [Indexed: 11/28/2022]
Abstract
Alien has characteristics of a corepressor for selected members of the nuclear hormone receptor (NHR) superfamily and also for transcription factors involved in cell cycle regulation and DNA repair. Alien mediates gene silencing and represses the transactivation of specific NHRs and other transcription factors to modulate hormone response and cell proliferation. Alien is a highly conserved protein and is expressed in a wide variety of tissues. Knockout of the gene encoding Alien in mice is embryonic lethal at a very early stage, indicating an important evolutionary role in multicellular organisms. From a mechanistic perspective, the corepressor function of Alien is in part mediated by histone deacetylase (HDAC) activity. In addition, Alien seems to modulate nucleosome assembly activity. This suggests that Alien is acting on chromatin not only through recruitment of histone-modifying activities, but also through enhancing nucleosome assembly.
Collapse
Affiliation(s)
- Maria Papaioannou
- Molecular Genetics, Institute of Human Genetics and Anthropology, Friedrich-Schiller-University, Jena, Germany
| | | | | |
Collapse
|
42
|
Radeke MJ, Peterson KE, Johnson LV, Anderson DH. Disease susceptibility of the human macula: Differential gene transcription in the retinal pigmented epithelium/choroid. Exp Eye Res 2007; 85:366-80. [PMID: 17662275 DOI: 10.1016/j.exer.2007.05.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 05/18/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
The discoveries of gene variants associated with macular diseases have provided valuable insight into their molecular mechanisms, but they have not clarified why the macula is particularly vulnerable to degenerative disease. Its predisposition may be attributable to specialized structural features and/or functional properties of the underlying macular RPE/choroid. To examine the molecular basis for the macula's disease susceptibility, we compared the gene expression profile of the human RPE/choroid in the macula with the profile in the extramacular region using DNA microarrays. Seventy-five candidate genes with differences in macular:extramacular expression levels were identified by microarray analysis, of which 29 were selected for further analysis. Quantitative PCR confirmed that 21 showed statistically significant differences in expression. Five genes were expressed at higher levels in the macula. Two showed significant changes in the macular:extramacular expression ratio; another two exhibited changes in absolute expression level, as a function of age or AMD. Several of the differentially expressed genes have potential relevance to AMD pathobiology. One is an RPE cell growth factor (TFPI2), five are extracellular matrix components (DCN, MYOC, OGN, SMOC2, TFPI2), and six are related to inflammation (CCL19, CCL26, CXCL14, SLIT2) and/or angiogenesis (CXCL14, SLIT2, TFPI2, WFDC1). The identification of regional differences in gene expression in the RPE/choroid is a first step in clarifying the macula's propensity for degeneration. These findings lay the groundwork for further studies into the roles of the corresponding gene products in the normal, aged, and diseased macula.
Collapse
Affiliation(s)
- Monte J Radeke
- Center for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | | | | | | |
Collapse
|
43
|
DeVoss J, Hou Y, Johannes K, Lu W, Liou GI, Rinn J, Chang H, Caspi RR, Caspi R, Fong L, Anderson MS. Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J Exp Med 2006; 203:2727-35. [PMID: 17116738 PMCID: PMC2118158 DOI: 10.1084/jem.20061864] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 10/26/2006] [Indexed: 12/20/2022] Open
Abstract
The expression of self-antigen in the thymus is believed to be responsible for the deletion of autoreactive T lymphocytes, a critical process in the maintenance of unresponsiveness to self. The Autoimmune regulator (Aire) gene, which is defective in the disorder autoimmune polyglandular syndrome type 1, has been shown to promote the thymic expression of self-antigens. A clear link, however, between specific thymic self-antigens and a single autoimmune phenotype in this model has been lacking. We show that autoimmune eye disease in aire-deficient mice develops as a result of loss of thymic expression of a single eye antigen, interphotoreceptor retinoid-binding protein (IRBP). In addition, lack of IRBP expression solely in the thymus, even in the presence of aire expression, is sufficient to trigger spontaneous eye-specific autoimmunity. These results suggest that failure of thymic expression of selective single self-antigens can be sufficient to cause organ-specific autoimmune disease, even in otherwise self-tolerant individuals.
Collapse
Affiliation(s)
- Jason DeVoss
- Diabetes Center and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Yu X, Lin J, Zack DJ, Qian J. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res 2006; 34:4925-36. [PMID: 16982645 PMCID: PMC1635265 DOI: 10.1093/nar/gkl595] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex TF interaction networks, we performed a large-scale analysis of TF interactions for 30 human tissues. We first identified tissue-specific genes for 30 tissues based on gene expression databases. We then evaluated the relationships between TFs using the relative position and co-occurrence of their binding sites in the promoters of tissue-specific genes. The predicted TF–TF interactions were validated by both known protein–protein interactions and co-expression of their target genes. We found that our predictions are enriched in known protein–protein interactions (>80 times that of random expectation). In addition, we found that the target genes show the highest co-expression in the tissue of interest. Our findings demonstrate that non-tissue specific TFs play a large role in regulation of tissue-specific genes. Furthermore, they show that individual TFs can contribute to tissue specificity in different tissues by interacting with distinct TF partners. Lastly, we identified several tissue-specific TF clusters that may play important roles in tissue-specific gene regulation.
Collapse
Affiliation(s)
- Xueping Yu
- Wilmer Institute, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Jimmy Lin
- Wilmer Institute, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Donald J. Zack
- Wilmer Institute, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
- Department of Neuroscience, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Jiang Qian
- Wilmer Institute, Johns Hopkins University School of MedicineMaumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
- To whom correspondence should be addressed. Tel: +1 443 287 3882; Fax: 1+ 410 502 5382;
| |
Collapse
|
45
|
Eichler E. 2005 Curt Stern Award address. Introductory speech for Patrick O. Brown. Am J Hum Genet 2006; 79:427-8. [PMID: 16909379 PMCID: PMC1559547 DOI: 10.1086/500330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Evan Eichler
- Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington School of Medicine, Health Sciences, Seattle, WA 98195, USA.
| |
Collapse
|
46
|
Zhou M, Li XM, Lavker RM. Transcriptional profiling of enriched populations of stem cells versus transient amplifying cells. A comparison of limbal and corneal epithelial basal cells. J Biol Chem 2006; 281:19600-9. [PMID: 16675456 DOI: 10.1074/jbc.m600777200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The basal layer of limbal and central corneal epithelium is enriched in stem cells and transient amplifying cells, respectively. This physical separation of stem and transient amplifying cells makes the limbal/corneal epithelium an exceptionally suitable system for isolating basal cells enriched in these two proliferative populations. Prior attempts to isolate epithelial stem cells used methods such as proteolytic tissue dissociation and cell sorting that could potentially alter their gene expression profile. Using laser capture microdissection, we were able to isolate resting limbal and corneal basal cells from frozen sections with minimal tissue processing, thereby improving the yield and quality of RNA. Analyses of RNA isolated from 300 limbal and corneal basal cells from eight mice revealed a set of approximately 100 genes that are differentially expressed in limbal cells versus corneal epithelial basal cells. Semiquantitative reverse transcription-PCR confirmed the up-regulation of three limbal and three corneal genes. LacZ identification of epiregulin from epiregulin-null mice and immunohistochemical staining of wild type mice confirmed that epiregulin, one of the limbal epithelium-enriched genes, was associated with the limbal epithelial basal cells. Within the limbal and corneal basal cells, we detected previously unknown genes that were differentially expressed in these two regions that contribute further to our understanding of the unique heterogeneity of these two closely related basal cell populations. Our findings indicate that we can obtain accurate gene expression profiles of the stem cell-enriched limbal basal cell population in their "natural" quiescent state.
Collapse
Affiliation(s)
- Mingyuan Zhou
- Department of Dermatology, Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | |
Collapse
|