1
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Huang Z, Haile K, Gedefaw L, Lau BWM, Jin L, Yip SP, Huang CL. Blood Biomarkers as Prognostic Indicators for Neurological Injury in COVID-19 Patients: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:15738. [PMID: 37958721 PMCID: PMC10649265 DOI: 10.3390/ijms242115738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been linked to various neurological complications. This meta-analysis assessed the relationship between glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL) levels in the blood and neurological injury in COVID-19 patients. A comprehensive search of various databases was conducted until 18 August 2023, to find studies reporting GFAP and NfL blood levels in COVID-19 patients with neurological complications. GFAP and NfL levels were estimated between COVID-19 patients and healthy controls, and meta-analyses were performed using RevMan 5.4 software for analysis. In the 21 collected studies, it was found that COVID-19 patients had significantly higher levels of pooled GFAP (SMD = 0.52; 95% CI: 0.31, 0.73; p ≤ 0.001) and NfL (SMD = 0.60; 95% CI: 0.37, 0.82; p ≤ 0.001) when compared to the healthy controls. The pooled GFAP (SMD = 0.86; 95% CI: 0.26, 1.45; p ≤ 0.01) and NfL (SMD = 0.87; 95% CI: 0.48, 1.26; p ≤ 0.001) were significantly higher in non-survivors. These findings indicate a significant association between COVID-19 severity and elevated levels of GFAP and NfL, suggesting that GFAP and NfL could serve as potential diagnostic and prognostic markers for the early detection and monitoring of COVID-19-related neurological injuries.
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Affiliation(s)
- Zhiwei Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (Z.H.); (L.G.); (L.J.)
| | - Kassahun Haile
- Department of Medical Laboratory Science, Wolkite University, Wolkite P.O. Box 07, Ethiopia;
| | - Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (Z.H.); (L.G.); (L.J.)
| | - Benson Wui-Man Lau
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, China;
| | - Ling Jin
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (Z.H.); (L.G.); (L.J.)
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (Z.H.); (L.G.); (L.J.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (Z.H.); (L.G.); (L.J.)
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2
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Wong NK, Yip SP, Huang CL. Establishing Functional Retina in a Dish: Progress and Promises of Induced Pluripotent Stem Cell-Based Retinal Neuron Differentiation. Int J Mol Sci 2023; 24:13652. [PMID: 37686457 PMCID: PMC10487913 DOI: 10.3390/ijms241713652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
The human eye plays a critical role in vision perception, but various retinal degenerative diseases such as retinitis pigmentosa (RP), glaucoma, and age-related macular degeneration (AMD) can lead to vision loss or blindness. Although progress has been made in understanding retinal development and in clinical research, current treatments remain inadequate for curing or reversing these degenerative conditions. Animal models have limited relevance to humans, and obtaining human eye tissue samples is challenging due to ethical and legal considerations. Consequently, researchers have turned to stem cell-based approaches, specifically induced pluripotent stem cells (iPSCs), to generate distinct retinal cell populations and develop cell replacement therapies. iPSCs offer a novel platform for studying the key stages of human retinogenesis and disease-specific mechanisms. Stem cell technology has facilitated the production of diverse retinal cell types, including retinal ganglion cells (RGCs) and photoreceptors, and the development of retinal organoids has emerged as a valuable in vitro tool for investigating retinal neuron differentiation and modeling retinal diseases. This review focuses on the protocols, culture conditions, and techniques employed in differentiating retinal neurons from iPSCs. Furthermore, it emphasizes the significance of molecular and functional validation of the differentiated cells.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
- Centre for Eye and Vision Research (CEVR), Hong Kong Science Park, Hong Kong, China
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3
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Gedefaw L, Liu CF, Ip RKL, Tse HF, Yeung MHY, Yip SP, Huang CL. Artificial Intelligence-Assisted Diagnostic Cytology and Genomic Testing for Hematologic Disorders. Cells 2023; 12:1755. [PMID: 37443789 PMCID: PMC10340428 DOI: 10.3390/cells12131755] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Artificial intelligence (AI) is a rapidly evolving field of computer science that involves the development of computational programs that can mimic human intelligence. In particular, machine learning and deep learning models have enabled the identification and grouping of patterns within data, leading to the development of AI systems that have been applied in various areas of hematology, including digital pathology, alpha thalassemia patient screening, cytogenetics, immunophenotyping, and sequencing. These AI-assisted methods have shown promise in improving diagnostic accuracy and efficiency, identifying novel biomarkers, and predicting treatment outcomes. However, limitations such as limited databases, lack of validation and standardization, systematic errors, and bias prevent AI from completely replacing manual diagnosis in hematology. In addition, the processing of large amounts of patient data and personal information by AI poses potential data privacy issues, necessitating the development of regulations to evaluate AI systems and address ethical concerns in clinical AI systems. Nonetheless, with continued research and development, AI has the potential to revolutionize the field of hematology and improve patient outcomes. To fully realize this potential, however, the challenges facing AI in hematology must be addressed and overcome.
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Affiliation(s)
- Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Chia-Fei Liu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Rosalina Ka Ling Ip
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China; (R.K.L.I.); (H.-F.T.)
| | - Hing-Fung Tse
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China; (R.K.L.I.); (H.-F.T.)
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (C.-F.L.); (M.H.Y.Y.)
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4
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Wang S, Qin A, Chau LY, Fok EWT, Choy MY, Brackman CJ, Siu GKH, Huang CL, Yip SP, Lee TMH. Amine-Functionalized Quantum Dots as a Universal Fluorescent Nanoprobe for a One-Step Loop-Mediated Isothermal Amplification Assay with Single-Copy Sensitivity. ACS Appl Mater Interfaces 2022; 14:35299-35308. [PMID: 35895859 DOI: 10.1021/acsami.2c02508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) has received considerable attention for decentralized (point-of-care and on-site) nucleic acid testing in view of its simple temperature control (60-65 °C) and short assay time (15-60 min). There remains a challenge in its wide adoption and acceptance due to the limitations of the existing amplification result reporter probes, e.g., photobleaching of organic fluorophore and reduced sensitivity of the pH-sensitive colorimetric dye. Herein, we demonstrate CdSeS/ZnS quantum dots (semiconductor fluorescent nanocrystals with superior photostability than organic fluorophore) with surface modification of cysteamine (amine-QDs) as a new reporter probe for LAMP that enabled single-copy sensitivity (limit of detection of 83 zM; 20 μL reaction volume). For a negative LAMP sample (absence of target sequence), positively charged amine-QDs remained dispersed due to interparticle electrostatic repulsion. While for a positive LAMP sample (presence of target sequence), amine-QDs became precipitated. The characterization data showed that amine-QDs were embedded in magnesium pyrophosphate crystals (generated during positive LAMP), thus leading to their coprecipitation. This amine-QD-based one-step LAMP assay advances the field of QD-based nucleic acid amplification assays in two aspects: (1) compatibility─one-step amplification and detection (versus separation of amplification and detection steps); and (2) universality─the same amine-QDs for different target sequences (versus different oligonucleotide-modified QDs for different target sequences).
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Affiliation(s)
- Shiyao Wang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Ailin Qin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Li Yin Chau
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Eunice W T Fok
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Mei Yue Choy
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Christopher J Brackman
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Thomas M H Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
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5
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Shan SSW, Wang PF, Cheung JKW, Yu F, Zheng H, Luo S, Yip SP, To CH, LAM C. Transcriptional profiling of the chick retina identifies down-regulation of VIP and UTS2B genes during early lens-induced myopia. Mol Omics 2022; 18:449-459. [DOI: 10.1039/d1mo00407g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gene expression of the chick retina was examined during the early development of lens-induced myopia (LIM) using whole transcriptome sequencing. Monocular treatment of the right eyes with −10 diopter (D)...
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Gedefaw L, Ullah S, Lee TMH, Yip SP, Huang CL. Targeting Inflammasome Activation in COVID-19: Delivery of RNA Interference-Based Therapeutic Molecules. Biomedicines 2021; 9:1823. [PMID: 34944639 PMCID: PMC8698532 DOI: 10.3390/biomedicines9121823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Mortality and morbidity associated with COVID-19 continue to be significantly high worldwide, owing to the absence of effective treatment strategies. The emergence of different variants of SARS-CoV-2 is also a considerable source of concern and has led to challenges in the development of better prevention and treatment strategies, including vaccines. Immune dysregulation due to pro-inflammatory mediators has worsened the situation in COVID-19 patients. Inflammasomes play a critical role in modulating pro-inflammatory cytokines in the pathogenesis of COVID-19 and their activation is associated with poor clinical outcomes. Numerous preclinical and clinical trials for COVID-19 treatment using different approaches are currently underway. Targeting different inflammasomes to reduce the cytokine storm, and its associated complications, in COVID-19 patients is a new area of research. Non-coding RNAs, targeting inflammasome activation, may serve as an effective treatment strategy. However, the efficacy of these therapeutic agents is highly dependent on the delivery system. MicroRNAs and long non-coding RNAs, in conjunction with an efficient delivery vehicle, present a potential strategy for regulating NLRP3 activity through various RNA interference (RNAi) mechanisms. In this regard, the use of nanomaterials and other vehicle types for the delivery of RNAi-based therapeutic molecules for COVID-19 may serve as a novel approach for enhancing drug efficacy. The present review briefly summarizes immune dysregulation and its consequences, the roles of different non-coding RNAs in regulating the NLRP3 inflammasome, distinct types of vectors for their delivery, and potential therapeutic targets of microRNA for treatment of COVID-19.
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Affiliation(s)
- Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (S.U.)
| | - Sami Ullah
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (S.U.)
| | - Thomas M. H. Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, China;
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (S.U.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China; (L.G.); (S.U.)
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China
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7
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Wong NK, Luo S, Chow EYD, Meng F, Adesanya A, Sun J, Ma HMH, Jin W, Li WC, Yip SP, Huang CL. The Tyrosine Kinase-Driven Networks of Novel Long Non-coding RNAs and Their Molecular Targets in Myeloproliferative Neoplasms. Front Cell Dev Biol 2021; 9:643043. [PMID: 34414175 PMCID: PMC8369571 DOI: 10.3389/fcell.2021.643043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/09/2021] [Indexed: 01/16/2023] Open
Abstract
Recent research has focused on the mechanisms by which long non-coding RNAs (lncRNAs) modulate diverse cellular processes such as tumorigenesis. However, the functional characteristics of these non-coding elements in the genome are poorly understood at present. In this study, we have explored several mechanisms that involve the novel lncRNA and microRNA (miRNA) axis participating in modulation of drug response and the tumor microenvironment of myeloproliferative neoplasms (MPNs). We identified novel lncRNAs via mRNA sequencing that was applied to leukemic cell lines derived from BCR-ABL1-positive and JAK2-mutant MPNs under treatment with therapeutic tyrosine kinase inhibitors (TKI). The expression and sequence of novel LNC000093 were further validated in both leukemic cells and normal primary and pluripotent cells isolated from human blood, including samples from patients with chronic myelogenous leukemia (CML). Downregulation of LNC000093 was validated in TKI-resistant CML while a converse expression pattern was observed in blood cells isolated from TKI-sensitive CML cases. In addition to BCR-ABL1-positive CML cells, the driver mutation JAK2-V617F-regulated lncRNA BANCR axis was further identified in BCR-ABL1-negative MPNs. Further genome-wide validation using MPN patient specimens identified 23 unique copy number variants including the 7 differentially expressed lncRNAs from our database. The newly identified LNC000093 served as a competitive endogenous RNA for miR-675-5p and reversed the imatinib resistance in CML cells through regulating RUNX1 expression. The extrinsic function of LNC000093 in exosomal H19/miR-675-induced modulation for the microenvironment was also determined with significant effect on VEGF expression.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Eudora Y D Chow
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - Fei Meng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Adenike Adesanya
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Jiahong Sun
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong.,Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Herman M H Ma
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong.,Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wan-Chun Li
- Institute of Oral Biology, College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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8
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Meng F, Siu GKH, Mok BWY, Sun J, Fung KSC, Lam JYW, Wong NK, Gedefaw L, Luo S, Lee TMH, Yip SP, Huang CL. Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells. Cells 2021; 10:1762. [PMID: 34359932 PMCID: PMC8307234 DOI: 10.3390/cells10071762] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression that may be used to identify the pathological pathways influenced by disease and cellular interactions. Viral miRNAs (v-miRNAs) encoded by both DNA and RNA viruses induce immune dysregulation, virus production, and disease pathogenesis. Given the absence of effective treatment and the prevalence of highly infective SARS-CoV-2 strains, improved understanding of viral-associated miRNAs could provide novel mechanistic insights into the pathogenesis of COVID-19. In this study, SARS-CoV-2 v-miRNAs were identified by deep sequencing in infected Calu-3 and Vero E6 cell lines. Among the ~0.1% small RNA sequences mapped to the SARS-CoV-2 genome, the top ten SARS-CoV-2 v-miRNAs (including three encoded by the N gene; v-miRNA-N) were selected. After initial screening of conserved v-miRNA-N-28612, which was identified in both SARS-CoV and SARS-CoV-2, its expression was shown to be positively associated with viral load in COVID-19 patients. Further in silico analysis and synthetic-mimic transfection of validated SARS-CoV-2 v-miRNAs revealed novel functional targets and associations with mechanisms of cellular metabolism and biosynthesis. Our findings support the development of v-miRNA-based biomarkers and therapeutic strategies based on improved understanding of the pathophysiology of COVID-19.
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Affiliation(s)
- Fei Meng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Bobo Wing-Yee Mok
- Department of Microbiology, The University of Hong Kong, Hong Kong, China;
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Jiahong Sun
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong, China;
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China;
| | - Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Thomas M. H. Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China;
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
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9
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Lam STS, To CH, Leung KW, Yip SP, Lo IFM, Tsang KP. Lessons learnt from a genetic disease registry in Hong Kong. Hong Kong Med J 2021; 27:226-228. [PMID: 34168092 DOI: 10.12809/hkmj208659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- S T S Lam
- Department of Clinical Genetics Service, Hong Kong Sanatorium & Hospital, Hong Kong
| | - C H To
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong
| | - K W Leung
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong
| | - S P Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - I F M Lo
- Clinical Genetic Service, Department of Health, Hong Kong
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Wong N, Meng F, Adesanya A, Yip SP, Huang C. The Novel H19/miR‐675‐5p/LNC000093‐Mediated Non‐Coding RNA Pathway Regulates Treatment Response in BCR‐ABL1‐Positive CML Cells. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.01630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nonthaphat Wong
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong
| | - Fei Meng
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong
| | - Adenike Adesanya
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong
| | - Shea Ping Yip
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong
| | - Chien‐Ling Huang
- Department of Health Technology and InformaticsThe Hong Kong Polytechnic UniversityHong Kong
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Affiliation(s)
| | - Shea Ping Yip
- Centre for Myopia Research, School of Optometry and
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, PR China
E‐mail:
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Chen SG, Ugwu F, Li WC, Caplice NM, Petcu E, Yip SP, Huang CL. Vascular Tissue Engineering: Advanced Techniques and Gene Editing in Stem Cells for Graft Generation. Tissue Engineering Part B: Reviews 2021; 27:14-28. [DOI: 10.1089/ten.teb.2019.0264] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sin-Guang Chen
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Felix Ugwu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Wan-Chun Li
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan, China
| | - Noel M. Caplice
- Centre for Research in Vascular Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Eugen Petcu
- Griffith University School of Medicine, Menzies Health Institute Queensland, Griffith University, Nathan, Australia
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, SAR, China
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13
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Leung KSS, Ng TTL, Wu AKL, Yau MCY, Lao HY, Choi MP, Tam KKG, Lee LK, Wong BKC, Man Ho AY, Yip KT, Lung KC, Liu RWT, Tso EYK, Leung WS, Chan MC, Ng YY, Sin KM, Fung KSC, Chau SKY, To WK, Que TL, Shum DHK, Yip SP, Yam WC, Siu GKH. Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. Emerg Infect Dis 2021; 27:196-204. [PMID: 33350913 PMCID: PMC7774584 DOI: 10.3201/eid2701.201543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10−3 substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.
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Siu GKH, Lee LK, Leung KSS, Leung JSL, Ng TTL, Chan CTM, Tam KKG, Lao HY, Wu AKL, Yau MCY, Lai YWM, Fung KSC, Chau SKY, Wong BKC, To WK, Luk K, Ho AYM, Que TL, Yip KT, Yam WC, Shum DHK, Yip SP. Will a new clade of SARS-CoV-2 imported into the community spark a fourth wave of the COVID-19 outbreak in Hong Kong? Emerg Microbes Infect 2020; 9:2497-2500. [PMID: 33206025 PMCID: PMC7717696 DOI: 10.1080/22221751.2020.1851146] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Alan Ka-Lun Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong Special Administrative Region, People's Republic of China
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong Special Administrative Region, People's Republic of China
| | - Yvette Wai-Man Lai
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong Special Administrative Region, People's Republic of China
| | - Kitty Sau-Chun Fung
- Department of Clinical Pathology, United Christian Hospital, Kwun Tong, Hong Kong Special Administrative Region, People's Republic of China
| | - Sandy Ka-Yee Chau
- Department of Clinical Pathology, United Christian Hospital, Kwun Tong, Hong Kong Special Administrative Region, People's Republic of China
| | - Barry Kin-Chung Wong
- Department of Clinical Pathology, United Christian Hospital, Kwun Tong, Hong Kong Special Administrative Region, People's Republic of China
| | - Wing-Kin To
- Department of Pathology, Princess Margaret Hospital, Kwai Chung, Hong Kong Special Administrative Region, People's Republic of China
| | - Kristine Luk
- Department of Pathology, Princess Margaret Hospital, Kwai Chung, Hong Kong Special Administrative Region, People's Republic of China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Kwai Chung, Hong Kong Special Administrative Region, People's Republic of China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong Special Administrative Region, People's Republic of China
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong Special Administrative Region, People's Republic of China
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - David Ho-Keung Shum
- Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong Special Administrative Region, People's Republic of China
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15
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Leung KH, Luo S, Kwarteng R, Chen SG, Yap MKH, Huang CL, Yip SP. The myopia susceptibility locus vasoactive intestinal peptide receptor 2 (VIPR2) contains variants with opposite effects. Sci Rep 2019; 9:18165. [PMID: 31796800 PMCID: PMC6890636 DOI: 10.1038/s41598-019-54619-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
Myopia is the commonest eye disorder in the world. High myopes are predisposed to ocular pathologies. The vasoactive intestinal peptide receptor 2 (VIPR2) gene was identified as a myopia susceptibility locus by our group and another group. We continued to fine-map this locus. A case-control study was performed in 4 sequential stages with a total of 941 highly myopic subjects and 846 control subjects, all unrelated Chinese. Stage 1 experimentally genotyped 64.4% of the entire cohort for 152 single-nucleotide polymorphisms (SNPs) and Stage 2 the remaining subjects for 21 SNPs. Stage 3 combined the genotypes for 21 SNPs for the entire cohort, and identified one group of high-risk haplotypes and one group of protective haplotypes significantly associated with high myopia. Stage 4 imputed genotypes for variants in the VIPR2 region and identified two independent groups of variants: one group with high-risk minor alleles and another with protective minor alleles. Variants within each group were generally in strong linkage disequilibrium among themselves while high-risk variants were in linkage equilibrium with protective variants. Therefore, the VIPR2 locus seems to contain variants with opposite effects. This is the first study that has examined the genetic architecture of a myopia susceptibility locus in detail.
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Affiliation(s)
- Kim Hung Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Regina Kwarteng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Sin-Guang Chen
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Maurice K H Yap
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
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16
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Song YQ, Sham PS, Yip SP, Fan YH, Bao SY. DNA sequence patterns in human major histocompatibility complex region in southern Chinese. Hong Kong Med J 2019; 25 Suppl 7:13-16. [PMID: 31761764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Affiliation(s)
- Y Q Song
- School of Biomedical Sciences, The University of Hong Kong
| | - P S Sham
- Department of Psychiatry, The University of Hong Kong
| | - S P Yip
- Department of Health Technology & Informatics, The Hong Kong Polytechnic University
| | - Y H Fan
- School of Biomedical Sciences, The University of Hong Kong
| | - S Y Bao
- School of Biomedical Sciences, The University of Hong Kong
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17
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Huang Y, Kee CS, Hocking PM, Williams C, Yip SP, Guggenheim JA. A Genome-Wide Association Study for Susceptibility to Visual Experience-Induced Myopia. Invest Ophthalmol Vis Sci 2019; 60:559-569. [PMID: 30721303 PMCID: PMC6363377 DOI: 10.1167/iovs.18-25597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/18/2018] [Indexed: 01/18/2023] Open
Abstract
Purpose The rapid rise in prevalence over recent decades and high heritability of myopia suggest a role for gene-environment (G × E) interactions in myopia susceptibility. Few such G × E interactions have been discovered to date. We aimed to test the hypothesis that genetic analysis of susceptibility to visual experience-induced myopia in an animal model would identify novel G × E interaction loci. Methods Chicks aged 7 days (n = 987) were monocularly deprived of form vision for 4 days. A genome-wide association study (GWAS) was carried out in the 20% of chicks most susceptible and least susceptible to form deprivation (n = 380). There were 304,963 genetic markers tested for association with the degree of induced axial elongation in treated versus control eyes (A-scan ultrasonography). A GWAS candidate region was examined in the following three human cohorts: CREAM consortium (n = 44,192), UK Biobank (n = 95,505), and Avon Longitudinal Study of Parents and Children (ALSPAC; n = 4989). Results A locus encompassing the genes PIK3CG and PRKAR2B was genome-wide significantly associated with myopia susceptibility in chicks (lead variant rs317386235, P = 9.54e-08). In CREAM and UK Biobank GWAS datasets, PIK3CG and PRKAR2B were enriched for strongly-associated markers (meta-analysis lead variant rs117909394, P = 1.7e-07). In ALSPAC participants, rs117909394 had an age-dependent association with refractive error (-0.22 diopters [D] change over 8 years, P = 5.2e-04) and nearby variant rs17153745 showed evidence of a G × E interaction with time spent reading (effect size -0.23 D, P = 0.022). Conclusions This work identified the PIK3CG-PRKAR2B locus as a mediator of susceptibility to visually induced myopia in chicks and suggests a role for this locus in conferring susceptibility to myopia in human cohorts.
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Affiliation(s)
- Yu Huang
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
- School of Optometry, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, United Kingdom
| | - Chea-Su Kee
- School of Optometry, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Paul M Hocking
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Cathy Williams
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Shea Ping Yip
- Department of Health Technology & Informatics, Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Jeremy A Guggenheim
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
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18
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Wong NK, Huang CL, Islam R, Yip SP. Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies. J Hematol Oncol 2018; 11:131. [PMID: 30466456 PMCID: PMC6251105 DOI: 10.1186/s13045-018-0673-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/23/2018] [Indexed: 12/26/2022] Open
Abstract
Recent studies have revealed that non-coding regions comprise the vast majority of the human genome and long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs that has been implicated in a variety of biological processes. Abnormal expression of lncRNAs has also been linked to different human diseases including cancers, yet the regulatory mechanisms and functional effects of lncRNAs are still ambiguous, and the molecular details also need to be confirmed. Unlike protein-coding gene, it is much more challenging to unravel the roles of lncRNAs owing to their unique and complex features such as functional diversity and low conservation among species, which greatly hamper their experimental characterization. In this review, we summarize and discuss both conventional and advanced approaches for the identification and functional characterization of lncRNAs related to hematological malignancies. In particular, the utility and advancement of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system as gene-editing tools are envisioned to facilitate the molecular dissection of lncRNAs via different knock-in/out strategies. Besides experimental considerations specific to lncRNAs, the roles of lncRNAs in the pathogenesis and progression of leukemia are also highlighted in the review. We expect that these insights may ultimately lead to clinical applications including development of biomarkers and novel therapeutic approaches targeting lncRNAs.
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Affiliation(s)
- Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
| | - Rashidul Islam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Y9/F, Lee Shau Kee Building, Hung Hom, Hong Kong SAR, China.
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19
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Baig FN, Liu SYW, Yip SP, Law HKW, Ying MTC. Update on Ultrasound Diagnosis for Thyroid Cancer. Hong Kong J Radiol 2018. [DOI: 10.12809/hkjr1816960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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20
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Xi LYY, Yip SP, Shan SW, Summers-Rada J, Kee CS. Region-specific differential corneal and scleral mRNA expressions of MMP2, TIMP2, and TGFB2 in highly myopic-astigmatic chicks. Sci Rep 2017; 7:11423. [PMID: 28900109 PMCID: PMC5595952 DOI: 10.1038/s41598-017-08765-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/12/2017] [Indexed: 12/11/2022] Open
Abstract
Myopia and astigmatism, two common refractive errors frequently co-exist, are affecting vision at all working distances in the affected populations worldwide. Eyeballs having these refractive errors are known to exhibit abnormal eye shape at the anterior and posterior eye segments, but whether the outer coats of these abnormal eyeballs, cornea anteriorly and sclera posteriorly, are regulated by region-specific molecular mechanism remains unclear. Here we presented the changes in mRNA expression levels of three genes (MMP2, TIMP2, and TGFB2), all known to participate in extracellular matrix organization, at five regions of the cornea and sclera in chickens developing high myopia and astigmatism induced by form deprivation. We found that, compared to normal chicks, the highly myopic-astigmatic chicks had significantly higher expression of all three genes in the superior sclera (Mann-Whitney tests, all p ≤ 0.05), as well as higher TIMP2 expression in the central cornea and nasal sclera (Mann-Whitney tests, both p ≤ 0.05). Strikingly, the superior scleral region stood out as showing the strongest and most widespread correlations between mRNA expression and biometry parameters including axial and astigmatic components (r = + 0.52~ + 0.85, all p < 0.05). These results imply that local molecular mechanism may manipulate the eye shape remodeling across the globe during refractive-error development.
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Affiliation(s)
- Lisa Yan-Yan Xi
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Sze Wan Shan
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Jody Summers-Rada
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Chea-Su Kee
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR.
- Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR.
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21
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Yuan C, Wu VW, Yip SP, Kwong DL, Ying M. Ultrasound Evaluation of Carotid Atherosclerosis in Post-Radiotherapy Nasopharyngeal Carcinoma Patients, Type 2 Diabetics, and Healthy Controls. Ultraschall Med 2017; 38:190-197. [PMID: 25830344 DOI: 10.1055/s-0034-1399293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Purpose To comprehensively evaluate and compare the degree of carotid atherosclerosis in patients treated with radiotherapy (RT) for nasopharyngeal carcinoma (NPC) and in patients with type 2 diabetes mellitus (DM), and using healthy subjects as controls. Materials and Methods The present study recruited 69 post-RT NPC patients without conventional cardiovascular risk factors, 70 type 2 diabetic patients without previous RT, and 76 healthy controls without conventional cardiovascular risk factors and previous RT. For each participant, 5 carotid atherosclerotic parameters, namely carotid intima-media thickness (CIMT), carotid arterial stiffness (CAS), presence of carotid plaque, carotid plaque score, and presence of ≥ 50 % carotid stenosis, were assessed using ultrasonography. The differences in these carotid atherosclerotic parameters between study groups were compared using ANCOVA or logistic regression after the adjustment for age and gender. Multiple comparisons were corrected using the Benjamini-Hochberg false discovery rate. Results Post-RT NPC patients and type 2 diabetics had a significantly higher CIMT, CAS and carotid plaque burden compared to the healthy subjects (corrected P-value, Pcor < 0.05). In addition, carotid atherosclerosis in post-RT NPC patients tended to be more severe with significantly higher CAS and carotid plaque burden than that in type 2 diabetics (Pcor < 0.05). Conclusion Neck RT for NPC is an independent risk factor of carotid atherosclerosis, and radiation induces more severe carotid atherosclerosis in post-RT NPC patients. Thus, assessment of carotid atherosclerosis using ultrasonography may be necessary for these patients and should be indicated in the routine follow-up of NPC.
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Affiliation(s)
- Chuang Yuan
- Medical Research Center, Changsha Central Hospital, Changsha, China
| | - Vincent Wc Wu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Dora Lw Kwong
- Department of Clinical Oncology, The University of Hong Kong
| | - Michael Ying
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
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22
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Qin A, Fu LT, Wong JKF, Chau LY, Yip SP, Lee TMH. Precipitation of PEG/Carboxyl-Modified Gold Nanoparticles with Magnesium Pyrophosphate: A New Platform for Real-Time Monitoring of Loop-Mediated Isothermal Amplification. ACS Appl Mater Interfaces 2017; 9:10472-10480. [PMID: 28276674 DOI: 10.1021/acsami.7b00046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Gold nanoparticles have proven to be promising for decentralized nucleic acid testing by virtue of their simple visual readout and absorbance-based quantification. A major challenge toward their practical application is to achieve ultrasensitive detection without compromising simplicity. The conventional strategy of thermocycling amplification is unfavorable (because of both instrumentation and preparation of thermostable oligonucleotide-modified gold nanoparticle probes). Herein, on the basis of a previously unreported co-precipitation phenomenon between thiolated poly(ethylene glycol)/11-mercaptoundecanoic acid co-modified gold nanoparticles and magnesium pyrophosphate crystals (an isothermal DNA amplification reaction byproduct), a new ultrasensitive and simple DNA assay platform is developed. The binding mechanism underlying the co-precipitation phenomenon is found to be caused by the complexation of carboxyl and pyrophosphate with free magnesium ions. Remarkably, poly(ethylene glycol) does not hinder the binding and effectively stabilizes gold nanoparticles against magnesium ion-induced aggregation (without pyrophosphate). In fact, a similar phenomenon is observed in other poly(ethylene glycol)- and carboxyl-containing nanomaterials. When the gold nanoparticle probe is incorporated into a loop-mediated isothermal amplification reaction, it remains as a red dispersion for a negative sample (in the absence of a target DNA sequence) but appears as a red precipitate for a positive sample (in the presence of a target). This results in a first-of-its-kind gold nanoparticle-based DNA assay platform with isothermal amplification and real-time monitoring capabilities.
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Affiliation(s)
- Ailin Qin
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
| | - Lok Tin Fu
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
| | - Jacky K F Wong
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
| | - Li Yin Chau
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
| | - Shea Ping Yip
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
| | - Thomas M H Lee
- Interdisciplinary Division of Biomedical Engineering, ‡Department of Health Technology and Informatics, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, China
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23
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Kao PYP, Leung KH, Chan LWC, Yip SP, Yap MKH. Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions. Biochim Biophys Acta Gen Subj 2016; 1861:335-353. [PMID: 27888147 DOI: 10.1016/j.bbagen.2016.11.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/17/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) is a major method for studying the genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of a disease is difficult because of their small effect sizes. To better explain disease mechanisms, pathway analysis is used to consolidate the effects of multiple variants, and hence increase the power of the study. While pathway analysis has previously been performed within GWAS only, it can now be extended to examining rare variants, other "-omics" and interaction data. SCOPE OF REVIEW 1. Factors to consider in the choice of software for GWAS pathway analysis. 2. Examples of how pathway analysis is used to analyse rare variants, other "-omics" and interaction data. MAJOR CONCLUSIONS To choose appropriate software tools, factors for consideration include covariate compatibility, null hypothesis, one- or two-step analysis required, curation method of gene sets, size of pathways, and size of flanking regions to define gene boundaries. For rare variants, analysis performance depends on consistency between assumed and actual effect distribution of variants. Integration of other "-omics" data and interaction can better explain gene functions. GENERAL SIGNIFICANCE Pathway analysis methods will be more readily used for integration of multiple sources of data, and enable more accurate prediction of phenotypes.
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Affiliation(s)
- Patrick Y P Kao
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Kim Hung Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Lawrence W C Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
| | - Maurice K H Yap
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Fan Q, Verhoeven VJM, Wojciechowski R, Barathi VA, Hysi PG, Guggenheim JA, Höhn R, Vitart V, Khawaja AP, Yamashiro K, Hosseini SM, Lehtimäki T, Lu Y, Haller T, Xie J, Delcourt C, Pirastu M, Wedenoja J, Gharahkhani P, Venturini C, Miyake M, Hewitt AW, Guo X, Mazur J, Huffman JE, Williams KM, Polasek O, Campbell H, Rudan I, Vatavuk Z, Wilson JF, Joshi PK, McMahon G, St Pourcain B, Evans DM, Simpson CL, Schwantes-An TH, Igo RP, Mirshahi A, Cougnard-Gregoire A, Bellenguez C, Blettner M, Raitakari O, Kähönen M, Seppala I, Zeller T, Meitinger T, Ried JS, Gieger C, Portas L, van Leeuwen EM, Amin N, Uitterlinden AG, Rivadeneira F, Hofman A, Vingerling JR, Wang YX, Wang X, Tai-Hui Boh E, Ikram MK, Sabanayagam C, Gupta P, Tan V, Zhou L, Ho CEH, Lim W, Beuerman RW, Siantar R, Tai ES, Vithana E, Mihailov E, Khor CC, Hayward C, Luben RN, Foster PJ, Klein BEK, Klein R, Wong HS, Mitchell P, Metspalu A, Aung T, Young TL, He M, Pärssinen O, van Duijn CM, Jin Wang J, Williams C, Jonas JB, Teo YY, Mackey DA, Oexle K, Yoshimura N, Paterson AD, Pfeiffer N, Wong TY, Baird PN, Stambolian D, Wilson JEB, Cheng CY, Hammond CJ, Klaver CCW, Saw SM, Rahi JS, Korobelnik JF, Kemp JP, Timpson NJ, Smith GD, Craig JE, Burdon KP, Fogarty RD, Iyengar SK, Chew E, Janmahasatian S, Martin NG, MacGregor S, Xu L, Schache M, Nangia V, Panda-Jonas S, Wright AF, Fondran JR, Lass JH, Feng S, Zhao JH, Khaw KT, Wareham NJ, Rantanen T, Kaprio J, Pang CP, Chen LJ, Tam PO, Jhanji V, Young AL, Döring A, Raffel LJ, Cotch MF, Li X, Yip SP, Yap MK, Biino G, Vaccargiu S, Fossarello M, Fleck B, Yazar S, Tideman JWL, Tedja M, Deangelis MM, Morrison M, Farrer L, Zhou X, Chen W, Mizuki N, Meguro A, Mäkelä KM. Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error. Nat Commun 2016; 7:11008. [PMID: 27020472 PMCID: PMC4820539 DOI: 10.1038/ncomms11008] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 02/10/2016] [Indexed: 02/07/2023] Open
Abstract
Myopia is the most common human eye disorder and it results from complex genetic and environmental causes. The rapidly increasing prevalence of myopia poses a major public health challenge. Here, the CREAM consortium performs a joint meta-analysis to test single-nucleotide polymorphism (SNP) main effects and SNP × education interaction effects on refractive error in 40,036 adults from 25 studies of European ancestry and 10,315 adults from 9 studies of Asian ancestry. In European ancestry individuals, we identify six novel loci (FAM150B-ACP1, LINC00340, FBN1, DIS3L-MAP2K1, ARID2-SNAT1 and SLC14A2) associated with refractive error. In Asian populations, three genome-wide significant loci AREG, GABRR1 and PDE10A also exhibit strong interactions with education (P<8.5 × 10(-5)), whereas the interactions are less evident in Europeans. The discovery of these loci represents an important advance in understanding how gene and environment interactions contribute to the heterogeneity of myopia.
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Affiliation(s)
- Qiao Fan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Robert Wojciechowski
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 20205, USA
| | - Veluchamy A. Barathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London SE1 7EH, UK
| | - Jeremy A. Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, 55131 Mainz, Germany
- Department of Ophthalmology, Inselspital, University Hospital Bern, CH-3010 Bern, Switzerland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Anthony P. Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge CB2 0SR, UK
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto 6068507, Japan
| | - S Mohsen Hosseini
- Program in Genetics and Genome Biology, The Hospital for Sick Children and Institute for Medical Sciences, University of Toronto, Toronto Ontario, Canada M5G 1X8
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Yi Lu
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4029, Australia
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Jing Xie
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria 3002, Australia
| | - Cécile Delcourt
- Université de Bordeaux, ISPED (Institut de Santé Publique d'Épidémiologie et de Développement), Bordeaux 33000, France
- INSERM, U1219-Bordeaux Population Health Research Center, Bordeaux 33000, France
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council, Sassari 07100, Italy
| | - Juho Wedenoja
- Department of Public Health, University of Helsinki, Helsinki 00014, Finland
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Puya Gharahkhani
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4029, Australia
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London SE1 7EH, UK
- UCL Institute of Ophthalmology, London SE1 7EH, UK
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto 6068507, Japan
| | - Alex W. Hewitt
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria 3002, Australia
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Xiaobo Guo
- Department of Statistical Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Johanna Mazur
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Jenifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Katie M. Williams
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London SE1 7EH, UK
- Department of Ophthalmology, King's College London, London SE1 7EH, UK
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Igor Rudan
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Zoran Vatavuk
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb 10000, Croatia
| | - James F. Wilson
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - Peter K. Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland
| | - George McMahon
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD Nijmegen, The Netherlands
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Tae-Hwi Schwantes-An
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, 55131 Mainz, Germany
- Dardenne Eye Hospital, Bonn-Bad Godesberg, 53177 Bonn, Germany
| | - Audrey Cougnard-Gregoire
- Université de Bordeaux, ISPED (Institut de Santé Publique d'Épidémiologie et de Développement), Bordeaux 33000, France
- INSERM, U1219-Bordeaux Population Health Research Center, Bordeaux 33000, France
| | - Céline Bellenguez
- Inserm, U1167, Lille 59000, France
- Univ. Lille, U1167, Lille 59000, France
- Université Lille 2, Lille 59000, France
| | - Maria Blettner
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Olli Raitakari
- Research Centre of Applied and Preventive Medicine, University of Turku, Turku 20520, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Ilkka Seppala
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, 20246 Hamburg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | | | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Laura Portas
- Institute of Population Genetics, National Research Council, Sassari 07100, Italy
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, 2518 AD Hague, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, 2518 AD Hague, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, 2518 AD Hague, The Netherlands
| | | | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing 100044, China
| | - Xu Wang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
| | - Eileen Tai-Hui Boh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
| | - M. Kamran Ikram
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Preeti Gupta
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
| | - Vincent Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
| | - Lei Zhou
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
| | - Candice E. H. Ho
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
| | - Wan'e Lim
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Roger W. Beuerman
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Rosalynn Siantar
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - E-Shyong Tai
- Duke-NUS Medical School, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
- Department of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Robert N. Luben
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge CB2 0SR, UK
| | - Paul J. Foster
- Division of Genetics and Epidemiology, UCL Institute of Ophthalmology, London EC1V 9EL, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London EC1V 2PD, UK
| | - Barbara E. K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
| | - Hoi-Suen Wong
- Program in Genetics and Genome Biology, The Hospital for Sick Children and Institute for Medical Sciences, University of Toronto, Toronto Ontario, Canada M5G 1X8
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales 2145, Australia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Mingguang He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Olavi Pärssinen
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä 40620, Finland
- Gerontology Research Center and Department of Health Sciences, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Jie Jin Wang
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales 2145, Australia
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing 100044, China
- Medical Faculty Mannheim, Department of Ophthalmology, Ruprecht-Karls-University Heidelberg, 69115 Mannheim, Germany
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore
| | - David A. Mackey
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Konrad Oexle
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto 6068507, Japan
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, The Hospital for Sick Children and Institute for Medical Sciences, University of Toronto, Toronto Ontario, Canada M5G 1X8
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
| | - Paul N. Baird
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria 3002, Australia
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joan E. Bailey Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London School of Medicine, London SE1 7EH, UK
- Department of Ophthalmology, King's College London, London SE1 7EH, UK
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 169856, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, National University Health Systems, National University of Singapore Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health Systems, Singapore 117549, Singapore
| | - Jugnoo S. Rahi
- Medical Research Council Centre of Epidemiology for Child Health, Institute of Child Health, University College London, London WC1E 6BT, UK
- Institute of Ophthalmology, Moorfields Eye Hospital, London EC1V 2PD, UK
- Ulverscroft Vision Research Group, University College London, London WC1E 6BT, UK
| | - Jean-François Korobelnik
- Université de Bordeaux, 33400 Talence, France
- INSERM (Institut National de la Santé Et de la Recherche Médicale), ISPED (Institut de Santé Publique d'épidémiologie et de Développement), Centre INSERM U897-Epidemiologie-Biostatistique, 33076 Bordeaux, France
| | - John P. Kemp
- MRC Integrative Epidemiology Unit (IEU), The University of Bristol, Bristol BS8 2BN, UK
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit (IEU), The University of Bristol, Bristol BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), The University of Bristol, Bristol BS8 2BN, UK
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5001, Australia
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5001, Australia
| | - Rhys D. Fogarty
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5001, Australia
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, CaseWestern Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Emily Chew
- National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sarayut Janmahasatian
- Department of Epidemiology and Biostatistics, CaseWestern Reserve University, Cleveland, Ohio 44106, USA
| | - Nicholas G. Martin
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4029, Australia
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4029, Australia
| | - Liang Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing 100044, China
| | - Maria Schache
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria 3002, Australia
| | - Vinay Nangia
- Suraj Eye Institute, Nagpur, Maharashtra 440001, India
| | | | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland
| | - Jeremy R. Fondran
- Department of Epidemiology and Biostatistics, CaseWestern Reserve University, Cleveland, Ohio 44106, USA
| | - Jonathan H. Lass
- Department of Epidemiology and Biostatistics, CaseWestern Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
| | - Sheng Feng
- Department of Pediatric Ophthalmology, Duke Eye Center For Human Genetics, Durham, North Carolina 27710, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Sciences, University of Cambridge, Cambridge CB2 1TN, UK
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge CB2 0SR, UK
| | - Nick J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Taina Rantanen
- Gerontology Research Center, University of Jyväskylä, Jyväskylä Finland
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki 00014, Finland
- Institute for Molecular Medicine, University of Helsinki, Helsinki 00014, Finland
- Department of Mental Health and Alcohol Abuse Services, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Hong Kong Eye Hospital, The Chinese University of Hong Kong, Kowloon, Hong Kong
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pancy O. Tam
- Department of Ophthalmology and Visual Sciences, Hong Kong Eye Hospital, The Chinese University of Hong Kong, Kowloon, Hong Kong
| | - Vishal Jhanji
- Department of Ophthalmology and Visual Sciences, Hong Kong Eye Hospital, The Chinese University of Hong Kong, Kowloon, Hong Kong
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Alvin L. Young
- Department of Ophthalmology and Visual Sciences, Hong Kong Eye Hospital, The Chinese University of Hong Kong, Kowloon, Hong Kong
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Angela Döring
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Leslie J. Raffel
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Mary-Frances Cotch
- Division of Epidemiology and Clinical Applications, National Eye Institute, Bethesda, Maryland 20892, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, California 90502, USA
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Maurice K.H. Yap
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council, Sassari 07100, Italy
| | - Maurizio Fossarello
- Institute of Population Genetics, National Research Council, Sassari 07100, Italy
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh EH3 9HA, UK
| | - Seyhan Yazar
- Centre for Eye Research Australia (CERA), Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Victoria 3002, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Jan Willem L. Tideman
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Milly Tedja
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Margaret M. Deangelis
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, Utah 84132, USA
| | - Margaux Morrison
- Department of Ophthalmology and Visual Sciences, John Moran Eye Center, University of Utah, Salt Lake City, Utah 84132, USA
| | - Lindsay Farrer
- Departments of Medicine (Biomedical Genetics), Ophthalmology, Neurology, Epidemiology and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts 02118, USA
| | - Xiangtian Zhou
- School of ophthalmology and optometry, Wenzhou Medical University, Wenzhou 325035, China
| | - Wei Chen
- School of ophthalmology and optometry, Wenzhou Medical University, Wenzhou 325035, China
| | - Nobuhisa Mizuki
- Department of Ophthalmology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0027, Japan
| | - Akira Meguro
- Department of Ophthalmology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0027, Japan
| | - Kari Matti Mäkelä
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine, University of Tampere, Tampere 33014, Finland
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25
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Chau LY, He Q, Qin A, Yip SP, Lee TMH. Platinum nanoparticles on reduced graphene oxide as peroxidase mimetics for the colorimetric detection of specific DNA sequence. J Mater Chem B 2016; 4:4076-4083. [DOI: 10.1039/c6tb00741d] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the first demonstration of platinum nanoparticles–reduced graphene oxide nanocomposites as peroxidase mimetics for colorimetric DNA detection.
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Affiliation(s)
- Li Yin Chau
- Interdisciplinary Division of Biomedical Engineering
- The Hong Kong Polytechnic University
- Kowloon
- China
| | - Qijin He
- Interdisciplinary Division of Biomedical Engineering
- The Hong Kong Polytechnic University
- Kowloon
- China
| | - Ailin Qin
- Interdisciplinary Division of Biomedical Engineering
- The Hong Kong Polytechnic University
- Kowloon
- China
| | - Shea Ping Yip
- Department of Health Technology and Informatics
- The Hong Kong Polytechnic University
- Hung Hom
- Kowloon
- China
| | - Thomas M. H. Lee
- Interdisciplinary Division of Biomedical Engineering
- The Hong Kong Polytechnic University
- Kowloon
- China
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26
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Chan LWC, Lin X, Yung G, Lui T, Chiu YM, Wang F, Tsui NBY, Cho WCS, Yip SP, Siu PM, Wong SCC, Yung BYM. Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia. Sci Rep 2015. [PMID: 26205693 PMCID: PMC4513283 DOI: 10.1038/srep10973] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Co-expression analysis reveals useful dysregulation patterns of gene cooperativeness for understanding cancer biology and identifying new targets for treatment. We developed a structural strategy to identify co-expressed gene networks that are important for chronic myelogenous leukemia (CML). This strategy compared the distributions of expressional correlations between CML and normal states, and it identified a data-driven threshold to classify strongly co-expressed networks that had the best coherence with CML. Using this strategy, we found a transcriptome-wide reduction of co-expression connectivity in CML, reflecting potentially loosened molecular regulation. Conversely, when we focused on nucleophosmin 1 (NPM1) associated networks, NPM1 established more co-expression linkages with BCR-ABL pathways and ribosomal protein networks in CML than normal. This finding implicates a new role of NPM1 in conveying tumorigenic signals from the BCR-ABL oncoprotein to ribosome biogenesis, affecting cellular growth. Transcription factors may be regulators of the differential co-expression patterns between CML and normal.
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Affiliation(s)
- Lawrence W C Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Xihong Lin
- Department of Biostatistics, School of Public Health, Harvard University, Massachusetts, USA
| | - Godwin Yung
- Department of Biostatistics, School of Public Health, Harvard University, Massachusetts, USA
| | - Thomas Lui
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Ya Ming Chiu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Fengfeng Wang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Nancy B Y Tsui
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong
| | - S P Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Parco M Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - S C Cesar Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Benjamin Y M Yung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
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27
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Yuan C, Yip SP, Wu VWC, Kwong DLW, Cheuk IWY, Ying M. Association between genetic polymorphisms and carotid atherosclerosis in patients treated with radiotherapy for nasopharyngeal carcinoma. Radiat Oncol 2015; 10:39. [PMID: 25880731 PMCID: PMC4332433 DOI: 10.1186/s13014-015-0341-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 01/28/2015] [Indexed: 02/08/2023] Open
Abstract
Background Radiotherapy (RT) of the neck is commonly given to nasopharyngeal carcinoma (NPC) patients for preventing cervical lymph node metastasis. However, neck RT may induce the development of carotid atherosclerosis. The mechanisms of radiation-induced carotid atherosclerosis are still unclear and no previous study has investigated the genetic involvement of radiation-induced carotid atherosclerosis. The present study aims to determine the association between genetic polymorphisms and carotid atherosclerosis in patients treated with RT for nasopharyngeal carcinoma. Methods The present study recruited 128 post-RT NPC patients. Carotid plaque score was assessed using ultrasonography. Thirteen single nucleotide polymorphisms (SNPs) that affect the function of anti-atherosclerotic genes, including SOD2, SOD3, CAT, PON1, PPARG, ADIPOQ, IL10, TGFB1 and NOS3, were genotyped. Association between the 13 SNPs and carotid atherosclerosis was evaluated using multiple regression after adjustment for covariates (PLINK). Multiple testing was corrected using Benjamini-Hochberg step-up false discovery rate controlling procedure. Results rs662 and rs705379 of PON1 were close to be significantly associated with carotid plaque score (Corrected P value, Pcor = 0.0528 and Pcor = 0.0842). When the two SNPs were combined together, TC haplotype in rs662-rs705379 of PON1 was significantly associated with higher carotid plaque score (Pcor < 0.05). None of the other SNPs showed significant association with carotid plaque score. Conclusions TC haplotype in rs662-rs705379 of PON1 is likely to be a genetic risk factor of carotid plaque score. Post-RT NPC patients with the TC haplotype may need earlier and more frequent carotid ultrasound examinations for early detection of carotid atherosclerosis.
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Affiliation(s)
- Chuang Yuan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China. .,Current address: Medical Research Center, Changsha Central Hospital, Changsha, Hunan, China.
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China.
| | - Vincent W C Wu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China.
| | - Dora L W Kwong
- Department of Clinical Oncology, The University of Hong Kong, Pokfulam, Hong Kong, SAR, China.
| | - Isabella W Y Cheuk
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China.
| | - Michael Ying
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China.
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28
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Li Q, Wojciechowski R, Simpson CL, Hysi PG, Verhoeven VJM, Ikram MK, Höhn R, Vitart V, Hewitt AW, Oexle K, Mäkelä KM, MacGregor S, Pirastu M, Fan Q, Cheng CY, St Pourcain B, McMahon G, Kemp JP, Northstone K, Rahi JS, Cumberland PM, Martin NG, Sanfilippo PG, Lu Y, Wang YX, Hayward C, Polašek O, Campbell H, Bencic G, Wright AF, Wedenoja J, Zeller T, Schillert A, Mirshahi A, Lackner K, Yip SP, Yap MKH, Ried JS, Gieger C, Murgia F, Wilson JF, Fleck B, Yazar S, Vingerling JR, Hofman A, Uitterlinden A, Rivadeneira F, Amin N, Karssen L, Oostra BA, Zhou X, Teo YY, Tai ES, Vithana E, Barathi V, Zheng Y, Siantar RG, Neelam K, Shin Y, Lam J, Yonova-Doing E, Venturini C, Hosseini SM, Wong HS, Lehtimäki T, Kähönen M, Raitakari O, Timpson NJ, Evans DM, Khor CC, Aung T, Young TL, Mitchell P, Klein B, van Duijn CM, Meitinger T, Jonas JB, Baird PN, Mackey DA, Wong TY, Saw SM, Pärssinen O, Stambolian D, Hammond CJ, Klaver CCW, Williams C, Paterson AD, Bailey-Wilson JE, Guggenheim JA. Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. Hum Genet 2015; 134:131-46. [PMID: 25367360 PMCID: PMC4291519 DOI: 10.1007/s00439-014-1500-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/30/2014] [Indexed: 11/24/2022]
Abstract
To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E-8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E-07), TOX (rs7823467, P = 3.47E-07) and LINC00340 (rs12212674, P = 1.49E-06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = -0.59, P = 2.10E-04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors.
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Affiliation(s)
- Qing Li
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Robert Wojciechowski
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
| | - Claire L. Simpson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mohammad Kamran Ikram
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alex W. Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Konrad Oexle
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Kari-Matti Mäkelä
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Mario Pirastu
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - Qiao Fan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Beaté St Pourcain
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - George McMahon
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - John P. Kemp
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Kate Northstone
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Jugnoo S. Rahi
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Phillippa M. Cumberland
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Paul G. Sanfilippo
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Yi Lu
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Juho Wedenoja
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tanja Zeller
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
| | - Arne Schillert
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Dardenne Eye Hospital, Bonn, Germany
| | - Karl Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Shea Ping Yip
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Maurice K. H. Yap
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Federico Murgia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | | | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
| | - André Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lennart Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Xin Zhou
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Veluchamy Barathi
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | | | | | - Kumari Neelam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Youchan Shin
- Singapore Eye Research Institute, Singapore, Singapore
| | - Janice Lam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Ekaterina Yonova-Doing
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - S. Mohsen Hosseini
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Hoi-Suen Wong
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
| | - Chiea-Chuen Khor
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore, Singapore
| | - Terri L. Young
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
| | - Paul Mitchell
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
| | - Barbara Klein
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
| | | | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Olavi Pärssinen
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
| | - Dwight Stambolian
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
| | - Joan E. Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Jeremy A. Guggenheim
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - The CREAM Consortium
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
- Faculty of Medicine, University of Split, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
- Dardenne Eye Hospital, Bonn, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
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Koh SP, Yip SP, Lee KK, Chan CC, Lau SM, Kho CS, Lau CK, Lin SY, Lau YM, Wong LG, Au KL, Wong KF, Chu RW, Yu PH, Chow EYD, Leung KFS, Tsoi WC, Yung BYM. Genetic association between germline JAK2 polymorphisms and myeloproliferative neoplasms in Hong Kong Chinese population: a case-control study. BMC Genet 2014; 15:147. [PMID: 25526816 PMCID: PMC4293821 DOI: 10.1186/s12863-014-0147-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Myeloproliferative neoplasms (MPNs) are a group of haematological malignancies that can be characterised by a somatic mutation (JAK2V617F). This mutation causes the bone marrow to produce excessive blood cells and is found in polycythaemia vera (~95%), essential thrombocythaemia and primary myelofibrosis (both ~50%). It is considered as a major genetic factor contributing to the development of these MPNs. No genetic association study of MPN in the Hong Kong population has so far been reported. Here, we investigated the relationship between germline JAK2 polymorphisms and MPNs in Hong Kong Chinese to find causal variants that contribute to MPN development. We analysed 19 tag single nucleotide polymorphisms (SNPs) within the JAK2 locus in 172 MPN patients and 470 healthy controls. Three of these 19 SNPs defined the reported JAK2 46/1 haplotype: rs10974944, rs12343867 and rs12340895. Allele and haplotype frequencies were compared between patients and controls by logistic regression adjusted for sex and age. Permutation test was used to correct for multiple comparisons. With significant findings from the 19 SNPs, we then examined 76 additional SNPs across the 148.7-kb region of JAK2 via imputation with the SNP data from the 1000 Genomes Project. RESULTS In single-marker analysis, 15 SNPs showed association with JAK2V617F-positive MPNs (n = 128), and 8 of these were novel MPN-associated SNPs not previously reported. Exhaustive variable-sized sliding-window haplotype analysis identified 184 haplotypes showing significant differences (P < 0.05) in frequencies between patients and controls even after multiple-testing correction. However, single-marker alleles exhibited the strongest association with V617F-positive MPNs. In local Hong Kong Chinese, rs12342421 showed the strongest association signal: asymptotic P = 3.76 × 10-15, empirical P = 2.00 × 10-5 for 50,000 permutations, OR = 3.55 for the minor allele C, and 95% CI, 2.59-4.87. Conditional logistic regression also signified an independent effect of rs12342421 in significant haplotype windows, and this independent effect remained unchanged even with the imputation of additional 76 SNPs. No significant association was found between V617F-negative MPNs and JAK2 SNPs. CONCLUSION With a large sample size, we reported the association between JAK2V617F-positive MPNs and 15 tag JAK2 SNPs and the association of rs12342421 being independent of the JAK2 46/1 haplotype in Hong Kong Chinese population.
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30
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Wong JKF, Yip SP, Lee TMH. Ultrasensitive and closed-tube colorimetric loop-mediated isothermal amplification assay using carboxyl-modified gold nanoparticles. Small 2014; 10:1495-9. [PMID: 24623485 DOI: 10.1002/smll.201302348] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/06/2013] [Indexed: 05/07/2023]
Affiliation(s)
- Jacky K F Wong
- Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University Hung Hom, Kowloon, Hong Kong, China
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31
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Cheuk IWY, Yip SP, Kwong DLW, Wu VWC. Association of XRCC1 and XRCC3 gene haplotypes with the development of radiation-induced fibrosis in patients with nasopharyngeal carcinoma. Mol Clin Oncol 2014; 2:553-558. [PMID: 24940494 DOI: 10.3892/mco.2014.276] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/07/2014] [Indexed: 01/18/2023] Open
Abstract
Radiation-induced fibrosis is one of the late complications of radiotherapy (RT) for nasopharyngeal carcinoma (NPC). The aim of this study was to investigate the association between X-ray repair cross-complementing protein 1 and 3 (XRCC1 and XRCC3, respectively) gene haplotypes and radiation-induced fibrosis in NPC patients. Genomic DNA was extracted from blood samples of 120 NPC patients previously treated with RT. In total, 12 tag single-nucleotide polymorphisms (SNPs) were selected from the XRCC1 and XRCC3 genes and were genotyped using restriction fragment length polymorphism analysis or unlabeled probe melting analysis. Single-marker and haplotype analyses were performed using multivariate logistic regression analysis. The functional variant rs861539 of XRCC3 may be associated with radiation-induced fibrosis [asymptotic P-value (Pasym)<0.05]. No significant association was observed between radiation-induced fibrosis and any of the tag SNPs of XRCC1 and XRCC3 in either single-marker or haplotype analysis after 10,000 permutations [empirical P-value (Pemp)>0.05]. Our preliminary results indicated that the rs861539 variant of XRCC3 may be associated with an increased risk of radiation-induced fibrosis; however, a large-scale study is required to confirm this result.
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Affiliation(s)
- Isabella Wai Yin Cheuk
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Dora Lai Wan Kwong
- Department of Clinical Oncology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong, SAR, P.R. China
| | - Vincent Wing Cheung Wu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
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32
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Sin TK, Yu AP, Yung BY, Yip SP, Chan LW, Wong CS, Ying M, Rudd JA, Siu PM. Modulating effect of SIRT1 activation induced by resveratrol on Foxo1-associated apoptotic signalling in senescent heart. J Physiol 2014; 592:2535-48. [PMID: 24639483 DOI: 10.1113/jphysiol.2014.271387] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Elevations of cardiomyocyte apoptosis and fibrotic deposition are major characteristics of the ageing heart. Resveratrol, a polyphenol in grapes and red wine, is known to improve insulin resistance and increase mitochondrial biogenesis through the SIRT1-PGC-1α signalling axis. Recent studies attempted to relate SIRT1 activation by resveratrol to the regulation of apoptosis in various disease models of cardiac muscle. In the present study, we tested the hypothesis that long-term (8-month) treatment of resveratrol would activate SIRT1 and improve the cardiac function of senescent mice through suppression of Foxo1-associated pro-apoptotic signalling. Our echocardiographic measurements indicated that the cardiac systolic function measured as fractional shortening and ejection fraction was significantly reduced in aged mice when compared with the young mice. These reductions, however, were not observed in resveratrol-treated hearts. Ageing significantly reduced the deacetylase activity, but not the protein abundance of SIRT1 in the heart. This reduction was accompanied by increased acetylation of the Foxo1 transcription factor and transactivation of its target, pro-apoptotic Bim. Subsequent analyses indicated that pro-apoptotic signalling measured as p53, Bax and apoptotic DNA fragmentation was up-regulated in the heart of aged mice. In contrast, resveratrol restored SIRT1 activity and suppressed elevations of Foxo1 acetylation, Bim and pro-apoptotic signalling in the aged heart. In parallel, resveratrol also attenuated the ageing-induced elevations of fibrotic collagen deposition and markers of oxidative damage including 4HNE and nitrotyrosine. In conclusion, these novel data demonstrate that resveratrol mitigates pro-apoptotic signalling in senescent heart through a deacetylation mechanism of SIRT1 that represses the Foxo1-Bim-associated pro-apoptotic signalling axis.
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Affiliation(s)
- Thomas K Sin
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Angus P Yu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Benjamin Y Yung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Lawrence W Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Cesar S Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Michael Ying
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - John A Rudd
- School of Biomedical Science, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Parco M Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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33
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Pei XM, Yung BY, Yip SP, Ying M, Benzie IF, Siu PM. Desacyl ghrelin prevents doxorubicin-induced myocardial fibrosis and apoptosis via the GHSR-independent pathway. Am J Physiol Endocrinol Metab 2014; 306:E311-23. [PMID: 24326424 DOI: 10.1152/ajpendo.00123.2013] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Doxorubicin is an effective chemotherapeutic agent used to treat malignancies, but it causes cardiomyopathy. Preliminary evidence suggests that desacyl ghrelin might have protective effects on doxorubicin cardiotoxicity. This study examined the cellular effects of desacyl ghrelin on myocardial fibrosis and apoptosis in a doxorubicin cardiomyopathy experimental model. Adult C57BL/6 mice received an intraperitoneal injection of doxorubicin to induce cardiomyopathy, followed by 4-day treatment of saline (control) or desacyl ghrelin with or without [d-Lys3]-GHRP-6 (a growth hormone secretagogue receptor or GHSR1a antagonist). Ventricular structural and functional parameters were evaluated by transthoracic echocardiography. Molecular and cellular measurements were performed in ventricular muscle to examine myocardial fibrosis and apoptosis. Cardiac dysfunction was induced by doxorubicin, as indicated by significant decreases in ventricular fractional shortening and ejection fraction. This doxorubicin-induced cardiac dysfunction was prevented by the treatment of desacyl ghrelin no matter with or without the presence of [d-Lys3]-GHRP-6. Doxorubicin induced fibrosis (accumulated collagen deposition and increased CTGF), activated apoptosis (increased TUNEL index, apoptotic DNA fragmentation, and caspase-3 activity and decreased Bcl-2/Bax ratio), and suppressed phosphorylation status of prosurvival signals (ERK1/2 and Akt) in ventricular muscles. All these molecular and cellular alterations induced by doxorubicin were not found in the animals treated with desacyl ghrelin. Notably, the changes in the major markers of apoptosis, fibrosis, and Akt phosphorylation were found to be similar in the animals following the treatment of desacyl ghrelin with and without GHSR antagonist [d-Lys3]-GHRP-6. These findings demonstrate clearly that desacyl ghrelin protects the cardiomyocytes against the doxorubicin-induced cardiomyopathy by preventing the activation of cardiac fibrosis and apoptosis, and the effects are probably mediated through GHSR-independent mechanism.
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Affiliation(s)
- Xiao M Pei
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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34
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Cheng CY, Schache M, Ikram M, Young T, Guggenheim J, Vitart V, MacGregor S, Verhoeven V, Barathi V, Liao J, Hysi P, Bailey-Wilson J, St. Pourcain B, Kemp J, McMahon G, Timpson N, Evans D, Montgomery G, Mishra A, Wang Y, Wang J, Rochtchina E, Polasek O, Wright A, Amin N, van Leeuwen E, Wilson J, Pennell C, van Duijn C, de Jong P, Vingerling J, Zhou X, Chen P, Li R, Tay WT, Zheng Y, Chew M, Burdon KP, Craig JE, Iyengar SK, Igo RP, Lass JH, Chew EY, Haller T, Mihailov E, Metspalu A, Wedenoja J, Simpson CL, Wojciechowski R, Höhn R, Mirshahi A, Zeller T, Pfeiffer N, Lackner KJ, Bettecken T, Meitinger T, Oexle K, Pirastu M, Portas L, Nag A, Williams KM, Yonova-Doing E, Klein R, Klein BE, Hosseini SM, Paterson AD, Makela KM, Lehtimaki T, Kahonen M, Raitakari O, Yoshimura N, Matsuda F, Chen LJ, Pang CP, Yip SP, Yap MK, Meguro A, Mizuki N, Inoko H, Foster PJ, Zhao JH, Vithana E, Tai ES, Fan Q, Xu L, Campbell H, Fleck B, Rudan I, Aung T, Hofman A, Uitterlinden AG, Bencic G, Khor CC, Forward H, Pärssinen O, Mitchell P, Rivadeneira F, Hewitt AW, Williams C, Oostra BA, Teo YY, Hammond CJ, Stambolian D, Mackey DA, Klaver CC, Wong TY, Saw SM, Baird PN. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. Am J Hum Genet 2013; 93:264-77. [PMID: 24144296 PMCID: PMC3772747 DOI: 10.1016/j.ajhg.2013.06.016] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/17/2013] [Accepted: 06/12/2013] [Indexed: 01/15/2023] Open
Abstract
Refractive errors are common eye disorders of public health importance worldwide. Ocular axial length (AL) is the major determinant of refraction and thus of myopia and hyperopia. We conducted a meta-analysis of genome-wide association studies for AL, combining 12,531 Europeans and 8,216 Asians. We identified eight genome-wide significant loci for AL (RSPO1, C3orf26, LAMA2, GJD2, ZNRF3, CD55, MIP, and ALPPL2) and confirmed one previously reported AL locus (ZC3H11B). Of the nine loci, five (LAMA2, GJD2, CD55, ALPPL2, and ZC3H11B) were associated with refraction in 18 independent cohorts (n = 23,591). Differential gene expression was observed for these loci in minus-lens-induced myopia mouse experiments and human ocular tissues. Two of the AL genes, RSPO1 and ZNRF3, are involved in Wnt signaling, a pathway playing a major role in the regulation of eyeball size. This study provides evidence of shared genes between AL and refraction, but importantly also suggests that these traits may have unique pathways.
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Affiliation(s)
- Ching-Yu Cheng
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Centre for Quantitative Medicine, Office of Clinical Sciences, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Maria Schache
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia
| | - M. Kamran Ikram
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Centre for Quantitative Medicine, Office of Clinical Sciences, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Terri L. Young
- Department of Ophthalmology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Neuroscience and Behavioural Disorders, Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
| | - Jeremy A. Guggenheim
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stuart MacGregor
- Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
| | - Virginie J.M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Veluchamy A. Barathi
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Jiemin Liao
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London SE1 7EH, UK
| | - Joan E. Bailey-Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - Beate St. Pourcain
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - John P. Kemp
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - George McMahon
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Nicholas J. Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | | | - Aniket Mishra
- Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing 100730, China
| | - Jie Jin Wang
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Sydney, NSW 2145, Australia
| | - Elena Rochtchina
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Sydney, NSW 2145, Australia
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Croatia, Split 21000, Croatia
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | | | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Craig E. Pennell
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Paulus T.V.M. de Jong
- Netherlands Institute of Neuroscience (NIN), An Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
- Department of Ophthalmology, Academisch Medisch Centrum, Amsterdam 1105 AZ, the Netherlands and Leids Universitair Medisch Centrum, Leiden 2300 RC, the Netherlands
| | - Johannes R. Vingerling
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Xin Zhou
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Peng Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Ruoying Li
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Wan-Ting Tay
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Yingfeng Zheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Merwyn Chew
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders University, Adelaide, SA 5001, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, SA 5001, Australia
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, OH 44106, USA
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
- Center for Clinical Investigation, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jonathan H. Lass
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, OH 44106, USA
| | - Emily Y. Chew
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Juho Wedenoja
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki 00014, Finland
| | - Claire L. Simpson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert Wojciechowski
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg 20246, Germany
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Karl J. Lackner
- Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz 55131, Germany
| | - Thomas Bettecken
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Institute of Human Genetics, Technical University Munich, Munich 81675, Germany
| | - Konrad Oexle
- Institute of Human Genetics, Technical University Munich, Munich 81675, Germany
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council of Italy, Sassari 07100, Italy
| | - Laura Portas
- Institute of Population Genetics, National Research Council of Italy, Sassari 07100, Italy
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London SE1 7EH, UK
| | - Katie M. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London SE1 7EH, UK
| | - Ekaterina Yonova-Doing
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London SE1 7EH, UK
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Barbara E. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - S. Mohsen Hosseini
- Program in Genetics and Genome Biology, The Hospital for Sick Children and Institute for Medical Sciences, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, The Hospital for Sick Children and Institute for Medical Sciences, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kari-Matti Makela
- Department of Clinical Chemistry, Filmlab Laboratories, Tampere University Hospital and School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Terho Lehtimaki
- Department of Clinical Chemistry, Filmlab Laboratories, Tampere University Hospital and School of Medicine, University of Tampere, Tampere 33520, Finland
| | - Mika Kahonen
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, Tampere 33521, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, and Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20041, Finland
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Fumihiko Matsuda
- Department of Human Disease Genomics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, Kowloon, Hong Kong
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
| | - Maurice K.H. Yap
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Akira Meguro
- Department of Ophthalmology and Visual Sciences, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Sciences, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hidetoshi Inoko
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Paul J. Foster
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London EC1V 2PD, UK
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Sciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore 119228, Singapore
| | - Qiao Fan
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Liang Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing 100730, China
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh EH3 9HA, UK
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Tin Aung
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb 10000, Croatia
| | - Chiea-Chuen Khor
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Hannah Forward
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Olavi Pärssinen
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä 40014, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä 40620, Finland
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Sydney, NSW 2145, Australia
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Alex W. Hewitt
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London SE1 7EH, UK
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David A. Mackey
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Caroline C.W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Tien-Yin Wong
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Seang-Mei Saw
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Centre for Quantitative Medicine, Office of Clinical Sciences, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Paul N. Baird
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, VIC 3002, Australia
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Lechner J, Bae HA, Guduric-Fuchs J, Rice A, Govindarajan G, Siddiqui S, Abi Farraj L, Yip SP, Yap M, Das M, Souzeau E, Coster D, Mills RA, Lindsay R, Phillips T, Mitchell P, Ali M, Inglehearn CF, Sundaresan P, Craig JE, Simpson DA, Burdon KP, Willoughby CE. Mutational analysis of MIR184 in sporadic keratoconus and myopia. Invest Ophthalmol Vis Sci 2013; 54:5266-72. [PMID: 23833072 DOI: 10.1167/iovs.13-12035] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE A mutation miR-184(+57C>T) in the seed region of miR-184 (encoded by MIR184 [MIM*613146]) results in familial severe keratoconus combined with early-onset anterior polar cataract and endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning (EDICT) syndrome (MIM#614303). In order to investigate the phenotypic spectrum resulting from MIR184 mutation, MIR184 was sequenced in a keratoconus cohort of mixed ethnicity and a Chinese axial myopia cohort. METHODS Sequencing of MIR184 was performed in 780 unrelated keratoconus patients and 96 unrelated Han southern Chinese subjects with axial myopia. Effects of identified mutations on RNA secondary structure were predicted computationally using mFold and RNAFold algorithms. MIR184 amplicons from patients harboring mutations were cloned and transfected into human embryonic kidney 293T (HEK293T) cells, and mature mutant miR-184 expression was analyzed by stem-loop real-time quantitative PCR (RT-qPCR). RESULTS Two novel heterozygous substitution mutations in MIR184 were identified in the two patients with isolated keratoconus: miR-184(+8C>A) and miR-184(+3A>G). Computational modeling predicted that these mutations would alter the miR-184 stem-loop stability and secondary structure. Ex vivo miR-184 expression analysis demonstrated that miR-184(+8C>A) almost completely repressed the expression of miR-184 (P = 0.022), and miR-184(+3A>G) reduced the expression of miR-184 by approximately 40% (P = 0.002). There was no significant association of rs41280052, which lies within the stem-loop of miR-184, with keratoconus. No MIR184 mutations were detected in the axial myopia cohort. CONCLUSIONS Two novel heterozygous substitution mutations in MIR184 were identified in two patients with isolated keratoconus: miR-184(+8C>A) and miR-184(+3A>G). Mutations in MIR184 are a rare cause of keratoconus and were found in 2 of 780 (0.25%) cases.
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Affiliation(s)
- Judith Lechner
- Centre for Vision and Vascular Science, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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Pang MYC, Lau RWK, Yip SP. The effects of whole-body vibration therapy on bone turnover, muscle strength, motor function, and spasticity in chronic stroke: a randomized controlled trial. Eur J Phys Rehabil Med 2013; 49:439-450. [PMID: 23486302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Whole-body vibration (WBV) has been used in older adults to improve bone health and neuromuscular function, and may have potential applications for stroke patients. AIM To investigate the effects of WBV on bone turnover, leg muscle strength, motor function, and spasticity among chronic stroke patients. DESIGN Randomized controlled trial (RCT). SETTING Community. POPULATION Eighty-two chronic stroke patients. METHODS The experimental group underwent exercise training with WBV stimulation for a maximum of 15 minutes, 3 days per week for 8 weeks. The controls received the same exercises without WBV. Participants were evaluated for isokinetic knee muscle strength, serum levels of bone formation and resorption markers, spasticity and motor function of the paretic leg at baseline, immediately after the 8-week training period, and 1-month follow-up. RESULTS Intention-to-treat analysis revealed no significant changes in levels of bone turnover markers and motor function of the paretic leg over time in both groups. Muscle strength outcomes showed no significant group×time interaction, with similar significant improvements found in both groups. Spasticity of the paretic knee was significantly reduced in the experimental group (P=0.005), but not in controls (P=0.465). No serious adverse events were reported. CONCLUSION The WBV protocol used in this study did not induce additional effects on bone turnover, knee muscle strength and paretic leg motor function among chronic stroke patients. WBV may have potential to modulate spasticity, but this requires further investigation. CLINICAL REHABILITATION IMPACT More study on WBV is required before it can be recommended as an adjunct treatment in rehabilitation of chronic stroke patients.
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Affiliation(s)
- M Y C Pang
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong -
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Tian F, Yip SP, Kwong DLW, Lin Z, Yang Z, Wu VWC. Promoter hypermethylation of tumor suppressor genes in serum as potential biomarker for the diagnosis of nasopharyngeal carcinoma. Cancer Epidemiol 2013; 37:708-13. [PMID: 23790641 DOI: 10.1016/j.canep.2013.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 11/26/2022]
Abstract
PURPOSE Promoter hypermethylation of tumor suppressor genes may serve as a promising biomarker for the diagnosis of cancer. Cell-free circulating DNA (cf-DNA) shares hypermethylation status with primary tumors. This study investigated promoter hypermethylation of five tumor suppressor genes as markers in the detection of nasopharyngeal carcinoma (NPC) in serum samples. METHODS cf-DNA was extracted from serum collected from 40 NPC patients and 41 age- and sex-matched healthy subjects. The promoter hypermethylation status of the five genes (RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1) was assessed by methylation-specific PCR after sodium bisulfite conversion. Differences in the methylation status of these five genes between NPC patients and healthy subjects were compared. RESULTS The concentration of cf-DNA in the serum of NPC patients was significantly higher than that in normal controls. The five tumor suppressor genes - RASSF1, CDKN2A, DLEC1, DAPK1 and UCHL1 - were found to be methylated in 17.5%, 22.5%, 25.0%, 51.4% and 64.9% of patients, respectively. The combination of four-gene marker - CDKN2A, DLEC1, DAPK1 and UCHL1 - had the highest sensitivity and specificity in predicting NPC. CONCLUSION Screening DNA hypermethylation of tumor suppressor genes in serum was a promising approach for the diagnosis of NPC.
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Affiliation(s)
- Fangyun Tian
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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Abstract
OBJECTIVES To assess the extent of dengue virus exposure in the population. METHODS In this seroepidemiological study, 685 blood samples were collected (from April 2007 to July 2009) from two subject groups: (i) 344 samples from anonymous blood donors of the Hong Kong Red Cross and (ii) 341 samples from healthy volunteers recruited from a university, a community centre and a hospital. Demographic information and travel history were collected for the second subject group. All blood samples were subjected to the PanBio Dengue IgG Indirect ELISA. RESULTS Anti-dengue virus IgG was detected in 1.6% of the blood samples. Individuals who visited countries in Southeast Asia in the past year were significantly associated with seropositivity (P = 0.03, OR 5.38, CI 1.13-25.54). CONCLUSIONS The overall dengue seroprevalence was 1.6%, and visit to Southeast Asia was the only independent predictor for seropositivity. Although the current situation is not alarming, frequent travel, presence of mosquito vector and emergence of local cases suggest that the risk of dengue virus infection within the local community cannot be overlooked, and continuous vigilance is warranted.
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Affiliation(s)
- Constance Lh Lo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Polly Hm Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
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39
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Verhoeven VJM, Hysi PG, Wojciechowski R, Fan Q, Guggenheim JA, Höhn R, MacGregor S, Hewitt AW, Nag A, Cheng CY, Yonova-Doing E, Zhou X, Ikram MK, Buitendijk GHS, McMahon G, Kemp JP, Pourcain BS, Simpson CL, Mäkelä KM, Lehtimäki T, Kähönen M, Paterson AD, Hosseini SM, Wong HS, Xu L, Jonas JB, Pärssinen O, Wedenoja J, Yip SP, Ho DWH, Pang CP, Chen LJ, Burdon KP, Craig JE, Klein BEK, Klein R, Haller T, Metspalu A, Khor CC, Tai ES, Aung T, Vithana E, Tay WT, Barathi VA, Chen P, Li R, Liao J, Zheng Y, Ong RT, Döring A, Evans DM, Timpson NJ, Verkerk AJMH, Meitinger T, Raitakari O, Hawthorne F, Spector TD, Karssen LC, Pirastu M, Murgia F, Ang W, Mishra A, Montgomery GW, Pennell CE, Cumberland PM, Cotlarciuc I, Mitchell P, Wang JJ, Schache M, Janmahasatian S, Jr RPI, Lass JH, Chew E, Iyengar SK, Gorgels TGMF, Rudan I, Hayward C, Wright AF, Polasek O, Vatavuk Z, Wilson JF, Fleck B, Zeller T, Mirshahi A, Müller C, Uitterlinden AG, Rivadeneira F, Vingerling JR, Hofman A, Oostra BA, Amin N, Bergen AAB, Teo YY, Rahi JS, Vitart V, Williams C, Baird PN, Wong TY, Oexle K, Pfeiffer N, Mackey DA, Young TL, van Duijn CM, Saw SM, Bailey-Wilson JE, Stambolian D, Klaver CC, Hammond CJ. Erratum: Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet 2013. [DOI: 10.1038/ng0613-712b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
PURPOSE Whole-body vibration therapy has gained increasing popularity in enhancing neuromotor function in various patient populations. It remains uncertain, however, whether whole-body vibration is beneficial when used in stroke patients. The aim of this randomized controlled trial was to examine the efficacy of whole-body vibration in optimizing neuromotor performance and reducing falls in chronic stroke patients. METHODS Eighty-two chronic stroke patients were randomly assigned to either the experimental group or control group. The experimental group received 9-15 min of whole-body vibration (vertical vibration; frequency = 20-30 Hz. amplitude = 0.44-0.60 mm, peak acceleration = 9.5-15.8 m·s or 0.97-1.61 U of Earth gravitational acceleration (g) while performing a variety of dynamic leg exercises on the vibration platform. The control group performed the same exercises without vibration. The subjects underwent their respective training three times a week for 8 wk. Balance (Berg balance scale), mobility (10-m walk test and 6-min walk test), knee muscle strength (isokinetic dynamometry), and fall-related self-efficacy (activities-specific balance confidence scale) were assessed at baseline, immediately after the 8-wk training and at a 1-month follow-up. The incidence of falls was recorded until 6 months after the termination of training. RESULTS Intention-to-treat analysis revealed similar significant improvement in all balance, mobility, muscle strength, and fall-related self-efficacy measures in both groups after the 8-wk treatment period (P < 0.001), and these were maintained at the 1-month follow-up. The incidence of falls did not differ significantly between the two groups (P > 0.05). CONCLUSIONS The addition of the presently used whole-body vibration paradigm to a leg exercise protocol was no more effective in improving neuromotor performance and reducing the incidence of falls than leg exercises alone in chronic stroke patients who have mild to moderate motor impairments.
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Affiliation(s)
- Ricky W K Lau
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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Yiu WC, Yap MKH, Fung WY, Ng PW, Yip SP. Genetic susceptibility to refractive error: association of vasoactive intestinal peptide receptor 2 (VIPR2) with high myopia in Chinese. PLoS One 2013; 8:e61805. [PMID: 23637909 PMCID: PMC3630195 DOI: 10.1371/journal.pone.0061805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/14/2013] [Indexed: 11/26/2022] Open
Abstract
Myopia is the most common ocular disease worldwide. We investigated the association of high myopia with the common single nucleotide polymorphisms (SNPs) of five candidate genes – early growth response 1 (EGR1), v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS), jun oncogene (JUN), vasoactive intestinal peptide (VIP), and vasoactive intestinal peptide receptor 2 (VIPR2). We recruited 1200 unrelated Chinese subjects with 600 cases (spherical equivalent ≤−8.00 diopters) and 600 controls (spherical equivalent within ±1.00 diopter). A discovery sample set was formed from 300 cases and 300 controls, and a replication sample set from the remaining samples. Tag SNPs were genotyped for the discovery sample set, and the most significant haplotypes and their constituent SNPs were followed up with the replication sample set. The allele and haplotype frequencies in cases and controls were compared by logistic regression adjusted for sex and age to give Pa values, and multiple comparisons were corrected by permutation test to give Paemp values. Odd ratios (OR) were calculated accordingly. In the discovery phase, EGR1, JUN and VIP did not show any significant association while FOS and VIPR2 demonstrated significant haplotype association with high myopia. In the replication phase, the haplotype association for VIPR2 was successfully replicated, but not FOS. In analysis combining both sample sets, the most significant association signals of VIPR2 were the single marker rs2071625 (Pa = 0.0008, Paemp = 0.0046 and OR = 0.75) and the 4-SNP haplotype window rs2071623-rs2071625-rs2730220-rs885863 (omnibus test, Pa = 9.10e-10 and Paemp = 0.0001) with one protective haplotype (GGGG: Paemp = 0.0002 and OR = 0.52) and one high-risk haplotype (GAGA: Paemp = 0.0027 and OR = 4.68). This 4-SNP haplotype window was the most significant in all sample sets examined. This is the first study to suggest a role of VIPR2 in the genetic susceptibility to high myopia. EGR1, JUN, FOS and VIP are unlikely to be important in predisposing humans to high myopia.
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Affiliation(s)
- Wai Chi Yiu
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Lee N, Wong CK, Hui DSC, Lee SKW, Wong RYK, Ngai KLK, Chan MCW, Chu YJ, Ho AWY, Lui GCY, Wong BCK, Wong SH, Yip SP, Chan PKS. Role of human Toll-like receptors in naturally occurring influenza A infections. Influenza Other Respir Viruses 2013; 7:666-75. [PMID: 23552014 PMCID: PMC5781199 DOI: 10.1111/irv.12109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND We investigated the roles of Toll-like receptors (TLRs) in naturally occurring influenza. METHODS A prospective, case - control study was conducted. Adults hospitalized with virologically confirmed influenza A infections (onset <48 hours, before treatment) were compared with age-/gender-matched controls. TLRs (2, 3, 4, 7, 8, 9) expression in monocytes and dendritic cells (DCs - total, myeloid, plasmacytoid) was quantitated using flow cytometry. Gene expression of RLRs (RIG-1, MDA-5) was evaluated using real-time PCR. Concomitant signaling molecules expression, plasma cytokine/chemokine concentrations, and respiratory tract viral loads were measured. PBMCs were cultured and stimulated ex vivo with TLR-specific ligands for cytokine responses. RESULTS Forty two patients with influenza (24 A/H3N2, 18 A/H1N1pdm09) and 20 controls were studied. Patients' mean age was 68 ± 16 years; 81% had respiratory/cardiovascular complications. There were increased cellular expressions of TLR9, TLR8, TLR3, and TLR7 during influenza; TLR2 and TLR4 were suppressed. Results were similar for both virus strains. Higher TLR expression levels at presentation significantly correlated with lower viral loads (Spearman's rho: -0.46 to -0.69 for TLR9, TLR8, and TLR3; P-values <0.05). Multivariate regression models (adjusted for age, comorbidity, disease severity, time from onset) confirmed their independent associations. Increased signaling molecules (phospho-MAPKs, IκB) and inflammatory cytokines (IL-6, sTNFR-1, CCL2/MCP-1; CXCL10/IP-10, IFN-γ) correlated with increased TLR expression. RLRs were upregulated simultaneously. PBMCs of patients with influenza showed significant, dynamic changes in their cytokine responses upon TLR stimulation, compared with controls. CONCLUSIONS Our results suggest that TLRs play an important role in early, innate viral inhibition in naturally occurring influenza. Inflammatory cytokine responses are concomitantly induced. These findings support investigation of TLR targeting as a novel intervention approach for prophylaxis against influenza.
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Affiliation(s)
- Nelson Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
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Yip SP, Li CC, Yiu WC, Hung WH, Lam WW, Lai MC, Ng PW, Fung WY, Chu PHW, Jiang B, Chan HHL, Yap MKH. A novel missense mutation in the NYX gene associated with high myopia. Ophthalmic Physiol Opt 2013; 33:346-53. [PMID: 23406521 DOI: 10.1111/opo.12036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 01/15/2013] [Indexed: 11/28/2022]
Abstract
PURPOSE Myopia is a complex eye disorder. The X-linked form of complete congenital stationary night blindness (CSNB1A) is usually associated with moderate to high myopia, and is caused by mutations in the NYX gene. We explored if NYX mutations could be associated with high myopia, but not CSNB1A. METHODS The coding regions of the NYX gene were sequenced for 204 Chinese males with high myopia (-8.00 dioptres or worse for both eyes). The frequencies of any sequence variations identified were determined in 200 Chinese males without myopia. Electro-oculography, electroretinography and standard cone function tests were performed on a male high myope carrying a mutation. RESULTS A missense mutation (c.529_530GC>AT or p.Ala177Met) was identified in one male subject with high myopia, but not in 200 male emmetropes. Neither was this variant found in any of the 529 male and 567 female subjects of various ethnic backgrounds whose genome sequences are documented in the 1000 Genomes Project database. The mutation was predicted to affect the protein function. From ocular electrophysiological tests, the proband was found to have normal rod function, but mildly abnormal cone function and inner retina function. He did not seem to suffer from CSNB1A. CONCLUSIONS One novel missense NYX mutation was identified in an adult male presented with high myopia, but without the major electrophysiological features normally associated with CSNB1A. NYX gene mutations may be considered as one of the rare genetic risk factors for high myopia without key features of CSNB1A.
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Affiliation(s)
- Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
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Verhoeven VJM, Hysi PG, Wojciechowski R, Fan Q, Guggenheim JA, Höhn R, MacGregor S, Hewitt AW, Nag A, Cheng CY, Yonova-Doing E, Zhou X, Ikram MK, Buitendijk GHS, McMahon G, Kemp JP, Pourcain BS, Simpson CL, Mäkelä KM, Lehtimäki T, Kähönen M, Paterson AD, Hosseini SM, Wong HS, Xu L, Jonas JB, Pärssinen O, Wedenoja J, Yip SP, Ho DWH, Pang CP, Chen LJ, Burdon KP, Craig JE, Klein BEK, Klein R, Haller T, Metspalu A, Khor CC, Tai ES, Aung T, Vithana E, Tay WT, Barathi VA, Chen P, Li R, Liao J, Zheng Y, Ong RT, Döring A, Evans DM, Timpson NJ, Verkerk AJMH, Meitinger T, Raitakari O, Hawthorne F, Spector TD, Karssen LC, Pirastu M, Murgia F, Ang W, Mishra A, Montgomery GW, Pennell CE, Cumberland PM, Cotlarciuc I, Mitchell P, Wang JJ, Schache M, Janmahasatian S, Janmahasathian S, Igo RP, Lass JH, Chew E, Iyengar SK, Gorgels TGMF, Rudan I, Hayward C, Wright AF, Polasek O, Vatavuk Z, Wilson JF, Fleck B, Zeller T, Mirshahi A, Müller C, Uitterlinden AG, Rivadeneira F, Vingerling JR, Hofman A, Oostra BA, Amin N, Bergen AAB, Teo YY, Rahi JS, Vitart V, Williams C, Baird PN, Wong TY, Oexle K, Pfeiffer N, Mackey DA, Young TL, van Duijn CM, Saw SM, Bailey-Wilson JE, Stambolian D, Klaver CC, Hammond CJ. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet 2013; 45:314-8. [PMID: 23396134 DOI: 10.1038/ng.2554] [Citation(s) in RCA: 330] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/16/2013] [Indexed: 02/06/2023]
Abstract
Refractive error is the most common eye disorder worldwide and is a prominent cause of blindness. Myopia affects over 30% of Western populations and up to 80% of Asians. The CREAM consortium conducted genome-wide meta-analyses, including 37,382 individuals from 27 studies of European ancestry and 8,376 from 5 Asian cohorts. We identified 16 new loci for refractive error in individuals of European ancestry, of which 8 were shared with Asians. Combined analysis identified 8 additional associated loci. The new loci include candidate genes with functions in neurotransmission (GRIA4), ion transport (KCNQ5), retinoic acid metabolism (RDH5), extracellular matrix remodeling (LAMA2 and BMP2) and eye development (SIX6 and PRSS56). We also confirmed previously reported associations with GJD2 and RASGRF1. Risk score analysis using associated SNPs showed a tenfold increased risk of myopia for individuals carrying the highest genetic load. Our results, based on a large meta-analysis across independent multiancestry studies, considerably advance understanding of the mechanisms involved in refractive error and myopia.
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Zhu MM, Yap MKH, Ho DWH, Fung WY, Ng PW, Gu YS, Yip SP. Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case-control study in Chinese. BMC Med Genet 2012; 13:64. [PMID: 22857148 PMCID: PMC3489600 DOI: 10.1186/1471-2350-13-64] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 07/27/2012] [Indexed: 12/23/2022]
Abstract
Background The UMODL1 gene was found to be associated with high myopia in Japanese. This study aimed to investigate this gene for association with high myopia in Chinese. Methods Two groups of unrelated Han Chinese from Hong Kong were recruited using the same criteria: Sample Set 1 comprising 356 controls (spherical equivalent, SE, within ±1 diopter or D) and 356 cases (SE ≤ −8D), and Sample Set 2 comprising 394 controls and 526 cases. Fifty-nine tag single nucleotide polymorphisms (SNPs) were selected and genotyped for Sample Set 1. Four SNPs were followed up with Sample Set 2. Both single-marker and haplotype analyses were performed with cases defined by different SE thresholds. Secondary phenotypes were also analyzed for association with genotypes. Results Data filtering left 57 SNPs for analysis. Single-marker analysis did not reveal any significant differences between cases and controls in the initial study. However, haplotype GCT for markers rs220168-rs220170-rs11911271 showed marginal significance (empirical P = 0.076; SE ≤ −12D for cases), but could not be replicated in the follow-up study. In contrast, non-synonymous SNP rs3819142 was associated with high myopia (SE ≤ −10D) in the follow-up study, but could not be confirmed using Sample Set 1. The SNP rs2839471, positive in the original Japanese study, gave negative results in all our analyses. Exploratory analysis of secondary phenotypes indicated that allele C of rs220120 was associated with anterior chamber depth (adjusted P = 0.0460). Conclusions Common UMODL1 polymorphisms were unlikely to be important in the genetic susceptibility to high myopia in Han Chinese.
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Affiliation(s)
- Miao-miao Zhu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Ho DWH, Yap MKH, Ng PW, Fung WY, Yip SP. Association of high myopia with crystallin beta A4 (CRYBA4) gene polymorphisms in the linkage-identified MYP6 locus. PLoS One 2012; 7:e40238. [PMID: 22792142 PMCID: PMC3389832 DOI: 10.1371/journal.pone.0040238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 06/03/2012] [Indexed: 12/03/2022] Open
Abstract
Background Myopia is the most common ocular disorder worldwide and imposes tremendous burden on the society. It is a complex disease. The MYP6 locus at 22 q12 is of particular interest because many studies have detected linkage signals at this interval. The MYP6 locus is likely to contain susceptibility gene(s) for myopia, but none has yet been identified. Methodology/Principal Findings Two independent subject groups of southern Chinese in Hong Kong participated in the study an initial study using a discovery sample set of 342 cases and 342 controls, and a follow-up study using a replication sample set of 316 cases and 313 controls. Cases with high myopia were defined by spherical equivalent ≤ -8 dioptres and emmetropic controls by spherical equivalent within ±1.00 dioptre for both eyes. Manual candidate gene selection from the MYP6 locus was supported by objective in silico prioritization. DNA samples of discovery sample set were genotyped for 178 tagging single nucleotide polymorphisms (SNPs) from 26 genes. For replication, 25 SNPs (tagging or located at predicted transcription factor or microRNA binding sites) from 4 genes were subsequently examined using the replication sample set. Fisher P value was calculated for all SNPs and overall association results were summarized by meta-analysis. Based on initial and replication studies, rs2009066 located in the crystallin beta A4 (CRYBA4) gene was identified to be the most significantly associated with high myopia (initial study: P = 0.02; replication study: P = 1.88e-4; meta-analysis: P = 1.54e-5) among all the SNPs tested. The association result survived correction for multiple comparisons. Under the allelic genetic model for the combined sample set, the odds ratio of the minor allele G was 1.41 (95% confidence intervals, 1.21-1.64). Conclusions/Significance A novel susceptibility gene (CRYBA4) was discovered for high myopia. Our study also signified the potential importance of appropriate gene prioritization in candidate selection.
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Affiliation(s)
- Daniel W. H. Ho
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Maurice K. H. Yap
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Po Wah Ng
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Wai Yan Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
- * E-mail:
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Zaki HY, Leung KH, Yiu WC, Gasmelseed N, Elwali NEM, Yip SP. Common polymorphisms in TLR4 gene associated with susceptibility to pulmonary tuberculosis in the Sudanese. Int J Tuberc Lung Dis 2012; 16:934-40. [PMID: 22525209 DOI: 10.5588/ijtld.11.0517] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Host genetic risk factors influence susceptibility to tuberculosis (TB). There is ample evidence supporting the involvement of toll-like receptor 4 (TLR4) in mycobacterial infection. OBJECTIVE To study the relationship between the TLR4 gene and TB susceptibility in the Sudanese population. DESIGN A case-control study was conducted among 207 patients with pulmonary TB and 395 healthy controls. Ten tag single nucleotide polymorphisms (SNPs) of the TLR4 gene were genotyped using restriction digestion or hybridisation assays, and analysed. RESULTS The genotypes were in Hardy-Weinberg equilibrium. After controlling for sex using the Mantel-Haenszel test, four SNPs showed significant differences between cases and controls, even after correction of multiple comparisons by Bonferroni procedure. The Mantel-Haenszel estimates of allelic odds ratios for the high-risk alleles were 1.67 for rs1927911 (P = 0.0001), 1.85 for rs5030725 (P = 0.0008), 2.14 for rs7869402 (P = 1.87e-07) and 2.31 for rs1927906 (P = 1.23e-10). Haplotype analysis showed that rs1927911 and rs5030725 were in one haplotype block, and rs7869402 and rs1927906 were in another haplotype block. Conditional haplotype analysis suggested the presence of one causal variant downstream of a recombination hot spot at the 3' region of the TLR4 gene. CONCLUSION This is the first study to show that common TLR4 polymorphisms are associated with TB susceptibility in the Sudanese population.
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Affiliation(s)
- H Y Zaki
- Department of Molecular Biology, National Cancer Institute, University of Gezira, Wad Medani, Sudan
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Wong JKF, Yip SP, Lee TMH. Silica-modified oligonucleotide-gold nanoparticle conjugate enables closed-tube colorimetric polymerase chain reaction. Small 2012; 8:214-9. [PMID: 22095584 DOI: 10.1002/smll.201101925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Indexed: 05/11/2023]
Abstract
A facile silica coating significantly enhances the thermal stability and polymerase chain reaction (PCR) compatibility of oligonucleotide-gold nanoparticle conjugates, thus enabling colorimetric detection of PCR results in a closed-tube format. This method is specific, sensitive, and generally applicable. Its simplicity, visual readout, and carryover contamination-free features hold promise for point-of-care or on-site DNA testing.
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Affiliation(s)
- Jacky K F Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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Abstract
Background Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS). Results UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background. Conclusions UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.
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Affiliation(s)
- Daniel W H Ho
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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