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Wang JR, Zhang JY, Ji WK. Biogenesis of Rab14-positive Endosome Buds at Golgi-endosome Contacts by the RhoBTB3-SHIP164-Vps26B Complex. Curr Med Sci 2024; 44:864-866. [PMID: 38900387 DOI: 10.1007/s11596-024-2901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Affiliation(s)
- Jing-Ru Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jun-Yao Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, 430030, China.
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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Wang J, Xiong J, Zhang S, Li D, Chu Q, Chang W, Deng L, Ji WK. Biogenesis of Rab14-positive endosome buds at Golgi-endosome contacts by the RhoBTB3-SHIP164-Vps26B complex. Cell Discov 2024; 10:38. [PMID: 38565878 PMCID: PMC10987540 DOI: 10.1038/s41421-024-00651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/25/2024] [Indexed: 04/04/2024] Open
Abstract
Early endosomes (EEs) are crucial in cargo sorting within vesicular trafficking. While cargoes destined for degradation are retained in EEs and eventually transported to lysosomes, recycled cargoes for the plasma membrane (PM) or the Golgi undergo segregation into specialized membrane structures known as EE buds during cargo sorting. Despite this significance, the molecular basis of the membrane expansion during EE bud formation has been poorly understood. In this study, we identify a protein complex comprising SHIP164, an ATPase RhoBTB3, and a retromer subunit Vps26B, which promotes the formation of EE buds at Golgi-EE contacts. Our findings reveal that Vps26B acts as a novel Rab14 effector, and Rab14 activity regulates the association of SHIP164 with EEs. Depletion of SHIP164 leads to enlarged Rab14+ EEs without buds, a phenotype rescued by wild-type SHIP164 but not the lipid transfer-defective mutants. Suppression of RhoBTB3 or Vps26B mirrors the effects of SHIP164 depletion. Together, we propose a lipid transport-dependent pathway mediated by the RhoBTB3-SHIP164-Vps26B complex at Golgi-EE contacts, which is essential for EE budding.
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Affiliation(s)
- Jingru Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Department of Ultrasound Medicine, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Juan Xiong
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuhan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Dongchen Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Qingzhu Chu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | | | - Lin Deng
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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3
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Wen K, Zhang L, Cai Y, Teng H, Liang J, Yue Y, Li Y, Huang Y, Liu M, Zhang Y, Wei R, Sun J. Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract. Epigenetics 2023; 18:2192324. [PMID: 36945837 PMCID: PMC10038054 DOI: 10.1080/15592294.2023.2192324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
To explore the presence of extrachromosomal circular DNA (eccDNA) in the anterior capsule of the lens in the eyes of patients with cataract and with high myopia. Circle-Seq was performed to identify differences in the eccDNA and gene expression between the anterior capsule of the lens of patients with simple nuclear cataract (C, n = 6 cases) and patients with nuclear cataract along with high myopia (HM, n = 6 cases). The expression of eccDNA was confirmed using routine quantitative polymerase chain reaction. The eccDNA ranked in C and HM ranged in length from 0.017 kb - 9.9 Mb with two distinctive peaks detected at 0.2 kb and 0.5 kb, while eccDNA that were differentially expressed ranged in size from 0.05 kb - 57.8 kb with two distinctive peaks observed at 0.1 kb and 0.5 kb. Only 2.5% of the eccDNA in C and 2% in HM were>25 kb in size. The gene-rich chromosomes contributed to more number of eccDNA/Mb, while several well-known high myopia candidate genes, including catenin delta 2 (CTNND2) and ubiquitin-like with PHD, exhibited significantly increased levels of eccDNA in the anterior capsule of the lens in patients with high myopia. This study highlighted the topologic analysis of the anterior capsule of eyes with high myopia, which is an emerging direction for research and clinical applications. These findings suggested that eccDNA was commonly detected in eyes with high myopia and cataracts, and the candidate genes for high myopia identified in previous studies were also observed in the eccDNA.
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Affiliation(s)
- Kai Wen
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | | | - Yang Cai
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - He Teng
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Jingli Liang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Yi Yue
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Yaoling Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Yifang Huang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Ming Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Yufeng Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Ruihua Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
| | - Jing Sun
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital
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4
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Lu Q, Du Y, Zhang Y, Chen Y, Li H, He W, Tang Y, Zhao Z, Zhang Y, Wu J, Zhu X, Lu Y. A Genome-Wide Association Study for Susceptibility to Axial Length in Highly Myopic Eyes. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:255-267. [PMID: 37325711 PMCID: PMC10260730 DOI: 10.1007/s43657-022-00082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution. To identify novel susceptibility genes for axial length (AL) in highly myopic eyes, a genome-wide association study (GWAS) was performed using the genomic dataset of 350 deep whole-genome sequencing data from highly myopic patients. Top single nucleotide polymorphisms (SNPs) were functionally annotated. Immunofluorescence staining, quantitative polymerase chain reaction, and western blot were performed using neural retina of form-deprived myopic mice. Enrichment analyses were further performed. We identified the four top SNPs and found that ADAM Metallopeptidase With Thrombospondin Type 1 Motif 16 (ADAMTS16) and Phosphatidylinositol Glycan Anchor Biosynthesis Class Z (PIGZ) had the potential of clinical significance. Animal experiments confirmed that PIGZ expression could be observed and showed higher expression level in form-deprived mice, especially in the ganglion cell layer. The messenger RNA (mRNA) levels of both ADAMTS16 and PIGZ were significantly higher in the neural retina of form-deprived eyes (p = 0.005 and 0.007 respectively), and both proteins showed significantly upregulated expression in the neural retina of deprived eyes (p = 0.004 and 0.042, respectively). Enrichment analysis revealed a significant role of cellular adhesion and signal transduction in AL, and also several AL-related pathways including circadian entrainment and inflammatory mediator regulation of transient receptor potential channels were proposed. In conclusion, the current study identified four novel SNPs associated with AL in highly myopic eyes and confirmed that the expression of ADAMTS16 and PIGZ was significantly upregulated in neural retina of deprived eyes. Enrichment analyses provided novel insight into the etiology of high myopia and opened avenues for future research interest. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00082-x.
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Affiliation(s)
- Qiang Lu
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Yu Du
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Ye Zhang
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Yuxi Chen
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Hao Li
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Wenwen He
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Yating Tang
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Zhennan Zhao
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Yinglei Zhang
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Jihong Wu
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
| | - Xiangjia Zhu
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
- State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032 China
| | - Yi Lu
- Department of Ophthalmology, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031 China
- Eye Institute, Eye and Ear, Nose, and Throat Hospital of Fudan University, Shanghai, 200031 China
- Key Laboratory of Myopia, Ministry of Health, Shanghai, 200031 China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, 200031 China
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5
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Zeitz C, Roger JE, Audo I, Michiels C, Sánchez-Farías N, Varin J, Frederiksen H, Wilmet B, Callebert J, Gimenez ML, Bouzidi N, Blond F, Guilllonneau X, Fouquet S, Léveillard T, Smirnov V, Vincent A, Héon E, Sahel JA, Kloeckener-Gruissem B, Sennlaub F, Morgans CW, Duvoisin RM, Tkatchenko AV, Picaud S. Shedding light on myopia by studying complete congenital stationary night blindness. Prog Retin Eye Res 2023; 93:101155. [PMID: 36669906 DOI: 10.1016/j.preteyeres.2022.101155] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023]
Abstract
Myopia is the most common eye disorder, caused by heterogeneous genetic and environmental factors. Rare progressive and stationary inherited retinal disorders are often associated with high myopia. Genes implicated in myopia encode proteins involved in a variety of biological processes including eye morphogenesis, extracellular matrix organization, visual perception, circadian rhythms, and retinal signaling. Differentially expressed genes (DEGs) identified in animal models mimicking myopia are helpful in suggesting candidate genes implicated in human myopia. Complete congenital stationary night blindness (cCSNB) in humans and animal models represents an ON-bipolar cell signal transmission defect and is also associated with high myopia. Thus, it represents also an interesting model to identify myopia-related genes, as well as disease mechanisms. While the origin of night blindness is molecularly well established, further research is needed to elucidate the mechanisms of myopia development in subjects with cCSNB. Using whole transcriptome analysis on three different mouse models of cCSNB (in Gpr179-/-, Lrit3-/- and Grm6-/-), we identified novel actors of the retinal signaling cascade, which are also novel candidate genes for myopia. Meta-analysis of our transcriptomic data with published transcriptomic databases and genome-wide association studies from myopia cases led us to propose new biological/cellular processes/mechanisms potentially at the origin of myopia in cCSNB subjects. The results provide a foundation to guide the development of pharmacological myopia therapies.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Jérome E Roger
- Paris-Saclay Institute of Neuroscience, CERTO-Retina France, CNRS, Université Paris-Saclay, Saclay, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France
| | | | | | - Juliette Varin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Helen Frederiksen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Baptiste Wilmet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jacques Callebert
- Service of Biochemistry and Molecular Biology, INSERM U942, Hospital Lariboisière, APHP, Paris, France
| | | | - Nassima Bouzidi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Frederic Blond
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Stéphane Fouquet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Florian Sennlaub
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Catherine W Morgans
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Robert M Duvoisin
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Andrei V Tkatchenko
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, China; Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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7
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Xu NY, Liu ZY, Yang QM, Bian PP, Li M, Zhao X. Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions. Front Genet 2022; 13:906447. [PMID: 35979430 PMCID: PMC9377314 DOI: 10.3389/fgene.2022.906447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.
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Affiliation(s)
- Nai-Yi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhen-Yu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi-Meng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Pei-Pei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, QC, Canada
- *Correspondence: Xin Zhao,
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8
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Shi H, Fu J, Liu X, Wang Y, Yong X, Jiang L, Ma S, Yin Z, Yao J, Yao X, Chen X, Wang T. Influence of the interaction between parental myopia and poor eye habits when reading and writing and poor reading posture on prevalence of myopia in school students in Urumqi, China. BMC Ophthalmol 2021; 21:299. [PMID: 34391397 PMCID: PMC8364037 DOI: 10.1186/s12886-021-02058-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/02/2021] [Indexed: 12/14/2022] Open
Abstract
Background To evaluate the prevalence of myopia in school students in Urumqi, China, and explore the influence of the interaction between parental myopia and poor reading and writing habits on myopia to identify the at-risk population and provide evidence to help school students avoid developing myopia. Methods A cross-sectional survey was conducted with 6,883 school students aged 7–20 years in Urumqi in December 2019. The Standard Eye Chart and mydriatic optometry were used to determine whether students had myopia. Falconer’s method was used to calculate the heritability of parental myopia. Multivariate unconditional logistic regression models were used to analyze the risk factors for myopia and the additive and multiplicative interaction of parental myopia and poor reading and writing habits. Results After standardizing the age of the 6,883 students, the overall prevalence rate of myopia was 47.50 %. The heritability of parental myopia was 66.57 % for boys, 67.82 % for girls, 65.02 % for the Han group, and 52.71 % for other ethnicities. There were additive interactions between parental myopia and poor reading and writing habits; among them, parental myopia and poor eye habits when reading and writing (the distance between the eyes and book is less than 30 cm when reading and writing, fingers block the sight of one eye while holding the pen, and leaning one’s body when reading and writing; habit 1) increased the risk of myopia by 10.99 times (odds ratio [OR] = 10.99, 95 % confidence interval [CI] = 8.33–14.68), parental myopia and poor reading posture (reading while lying down, walking, or in the car; habit 2) increased the risk of myopia by 5.92 times (OR = 5.92, 95 % CI = 4.84–7.27). There was no multiplicative interaction between parental myopia and habit 1 or habit 2 (OR = 0.69, 95 % CI = 0.44–1.08; OR = 0.89, 95 % CI = 0.66–1.21, respectively). Conclusion The prevalence of myopia among students in Urumqi, Xinjiang is relatively high. The risk of developing myopia is affected by parental myopia and poor reading and writing habits. In addition, parental myopia amplifies the harm caused by poor reading and writing habits, thereby increasing the risk of myopia. Students with parents who have myopia should be targeted during myopia prevention efforts. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-021-02058-3.
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Affiliation(s)
- Haonan Shi
- School of Public Health, Xinjiang Medical University, 830011, Urumqi, China
| | - Jing Fu
- Department of Ophthalmology, First Affiliated Hospital, Xinjiang Medical University, 830000, Urumqi, China
| | - Xiaojing Liu
- Health Care Guidance Centre in Primary and Secondary Schools, 830002, Urumqi, China
| | - Yingxia Wang
- School of Nursing & Health Management, Shanghai University of Medicine & Health Sciences, 201318, Shanghai, China
| | - Xianting Yong
- School of Public Health, Xinjiang Medical University, 830011, Urumqi, China
| | - Lan Jiang
- Maternal and Child Health Care Hospital of Uygur Autonomous Region, 830002, Urumqi, China
| | - Shaowei Ma
- School of Public Health, Xinjiang Medical University, 830011, Urumqi, China
| | - Zhe Yin
- School of Public Health, Xinjiang Medical University, 830011, Urumqi, China
| | - Jian Yao
- School of Public Health, Xinjiang Medical University, 830011, Urumqi, China
| | - Xuan Yao
- College of Medicine, Shanghai University, 200444, Shanghai, China.
| | - Xueyi Chen
- Department of Ophthalmology, First Affiliated Hospital, Xinjiang Medical University, 830000, Urumqi, China. .,Department of Ophthalmology, First Affiliated Hospital, Xinjiang Medical University, 830001, Urumqi, China.
| | - Tingting Wang
- School of Nursing & Health Management, Shanghai University of Medicine & Health Sciences, 201318, Shanghai, China.
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9
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Xiao H, Lin S, Jiang D, Lin Y, Liu L, Zhang Q, He J, Chen Y. Association of Extracellular Signal-Regulated Kinase Genes With Myopia: A Longitudinal Study of Chinese Children. Front Genet 2021; 12:654869. [PMID: 34122509 PMCID: PMC8191505 DOI: 10.3389/fgene.2021.654869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Objective The present study was designed to investigate whether the extracellular signal-regulated kinase (ERK) signaling pathway, a downstream component of dopamine signaling, is involved in myopia among Chinese children. Methods During a 3.5-year follow-up, 488 primary school students were enrolled in this study. Non-cycloplegic spherical equivalent refraction (SE) and other ocular parameters were assessed. Four variants of four genes in the ERK signaling pathway were selected: RASGRF1 rs6495367, PTPN5 rs1550870, PTPRR rs11178469, and PDGFRA rs6554163. SNPscan was used to genotype single-nucleotide polymorphisms (SNPs). PLINK software was used to assess the associations of the genetic variants with the occurrence or development of myopia, SE, and other ocular parameters. We created a protein-protein interaction (PPI) network and microRNA (miRNA)-gene network using String and Cytoscape and conducted enrichment analyses on the genes in these networks. Results In total, 426 children (baseline age: 7.28 ± 0.26 years; 236 (55.4%) boys and 190 girls) wereenrolled. After adjusting for confounding factors with 10,000 permutations, children with the CT or TT genotype of PTPN5 rs1550870 were more susceptible to myopia than those with the CC genotype (adjusted p = 0.011). Additionally, PTPN5 rs1550870 was correlated with significant myopic shift and increasing axial length (AL) and lens thickness (LT) but had a negative effect on central corneal thickness (CCT). RASGRF1 rs6495367 was negatively associated with myopic shift (additive: adjusted p = 0.034; dominant: adjusted p = 0.020), myopic SE and AL. PDGFRA rs6554163 TA or AA was negatively associated with increasing LT (adjusted p = 0.033). Evaluation of the effects of SNP-SNP combinations on incident myopia revealed a statistically significant one-locus model: PTPN5 rs1550870 [cross-validation consistency (CVC) = 10/10, adjusted p = 0.0107]. The genes in the PPI and miRNA-gene interaction networks were subjected to enrichment analyses, which suggested that these genes are involved mainly in eye development and dopaminergic synapse-related processes. Conclusion We identified genetic variants of crucial ERK signaling pathway genes that were significantly correlated with myopia and ocular parameter alterations in Chinese children. A combination of gene and miRNA functional analyses with enrichment analyses highlights the regulatory effects associated with ocular development and dopamine biological functions. This study offers novel clues to understand the role of dopamine in the molecular mechanisms of myopia.
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Affiliation(s)
- Haishao Xiao
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Shudan Lin
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Dandan Jiang
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaoyao Lin
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Linjie Liu
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Qiqi Zhang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Juan He
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yanyan Chen
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
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10
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Huang J, Yang M, Liu Z, Li X, Wang J, Fu N, Cao T, Yang X. PPFIA4 Promotes Colon Cancer Cell Proliferation and Migration by Enhancing Tumor Glycolysis. Front Oncol 2021; 11:653200. [PMID: 34094943 PMCID: PMC8173052 DOI: 10.3389/fonc.2021.653200] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Dysregulated glycolysis is one of the mechanisms employed by cancer cells to facilitate growth and metastasis. Here we aimed to characterize the PPFIA4 gene, as a glycolysis-related oncogene in promoting the proliferation and migration of colon cancer cells. Using bioinformatical tools including The Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA), we found that PPFIA4 expression and methylation levels were higher in colon cancer tissues of different stages than in normal tissues. Higher PPFIA4 level was also positively correlated with poorer survival of patients. PPFIA4 upregulation also correlated with poor prognosis and higher clinical stages of colon cancer patients. Colon cancer cell viability, migration and migration were enhanced after PPFIA4 overexpression. EMT markers and glycolysis were upregulated after PPFIA4 overexpression. PPFIA4 expression was found to be positively correlated with PFKFB3 and ENO2 levels, while knockdown of PFKFB3 and ENO2 reduced cell proliferation, migration, invasion and glycolysis. PPFIA4 upregulation is a potential biomarker in colon cancer which promotes proliferation, migration, invasion and glycolysis. The upregulation of PFKFB3/ENO2 signaling by PPFIA4 is a potential mechanism underlying the oncogenic effects of PPFIA4.
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Affiliation(s)
- Jia Huang
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Meiling Yang
- Department of Oncology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Zhaoxia Liu
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xiaoqian Li
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Junfeng Wang
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Nian Fu
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Ting Cao
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xuefeng Yang
- Department of Gastroenterology, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
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11
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Devani K, Plastow G, Orsel K, Valente TS. Genome-wide association study for mammary structure in Canadian Angus cows. PLoS One 2020; 15:e0237818. [PMID: 32853245 PMCID: PMC7451565 DOI: 10.1371/journal.pone.0237818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022] Open
Abstract
Functional and enduring mammary structure is pivotal for producer profitability, and animal health and welfare in beef production. Genetic evaluations for teat and udder score in Canadian Angus cattle have previously been developed. The aim of this study was to identify genomic regions associated with teat and udder structure in Canadian Angus cows thereby enhancing knowledge of the biological architecture of these traits. Thus, we performed a weighted single-step genome wide association study (WssGWAS) to identify candidate genes for teat and udder score in 1,582 Canadian Angus cows typed with the GeneSeek® Genomic Profiler Bovine 130K SNP array. Genomically enhanced estimated breeding values (GEBVs) were converted to SNP marker effects using unequal variances for markers to calculate weights for each SNP over three iterations. At the genome wide level, we detected windows of 20 consecutive SNPs that explained more than 0.5% of the variance observed in these traits. A total of 35 and 28 windows were identified for teat and udder score, respectively, with two SNP windows in common for both traits. Using Ensembl, the SNP windows were used to search for candidate genes and quantitative trait loci (QTL). A total of 94 and 71 characterized genes were identified in the regions for teat and udder score, respectively. Of these, 7 genes were common for both traits. Gene network and enrichment analysis, using Ingenuity Pathway Analysis (IPA), signified key pathways unique to each trait. Genes of interest were associated with immune response and wound healing, adipose tissue development and morphology, and epithelial and vascular development and morphology. Genetic architecture from this GWAS confirms that teat and udder score are distinct, polygenic traits involving varying and complex biological pathways, and that genetic selection for improved teat and udder score is possible.
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Affiliation(s)
- Kajal Devani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tiago S. Valente
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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12
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Musolf AM, Simpson CL, Alexander TA, Portas L, Murgia F, Ciner EB, Stambolian D, Bailey-Wilson JE. Genome-wide scans of myopia in Pennsylvania Amish families reveal significant linkage to 12q15, 8q21.3 and 5p15.33. Hum Genet 2019; 138:339-354. [PMID: 30826882 DOI: 10.1007/s00439-019-01991-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Myopia is one of the most common ocular disorders in the world, yet the genetic etiology of the disease remains poorly understood. Specialized founder populations, such as the Pennsylvania Amish, provide the opportunity to utilize exclusive genomic architecture, like unique haplotypes, to better understand the genetic causes of myopia. We perform genetic linkage analysis on Pennsylvania Amish families that have a strong familial history of myopia to map any potential causal variants and genes for the disease. 293 individuals from 25 extended families were genotyped on the Illumina ExomePlus array and merged with previous microsatellite data. We coded myopia affection as a binary phenotype; myopia was defined as having a mean spherical equivalent (MSE) of less than or equal to - 1 D (diopters). Two-point and multipoint parametric linkage analyses were performed under an autosomal dominant model. When allowing for locus heterogeneity, we identified two novel genome-wide significantly linked variants at 12q15 (heterogeneity LOD, HLOD = 3.77) in PTPRB and at 8q21.3 (HLOD = 3.35) in CNGB3. We identified further three genome-wide significant variants within a single family. These three variants were located in exons of SLC6A18 at 5p15.33 (LODs ranged from 3.51 to 3.37). Multipoint analysis confirmed the significant signal at 5p15.33 with six genome-wide significant variants (LODs ranged from 3.6 to 3.3). Further suggestive evidence of linkage was observed in several other regions of the genome. All three novel linked regions contain strong candidate genes, especially CNGB3 on 8q21.3, which has been shown to affect photoreceptors and cause complete color blindness. Whole genome sequencing on these regions is planned to conclusively elucidate the causal variants.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.,Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Theresa A Alexander
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Elise B Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, PA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.
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13
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Zhou H, Cao T, Li WP, Wu G. Combined expression and prognostic significance of PPFIA1 and ALG3 in head and neck squamous cell carcinoma. Mol Biol Rep 2019; 46:2693-2701. [PMID: 30805892 DOI: 10.1007/s11033-019-04712-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/20/2019] [Indexed: 01/19/2023]
Abstract
PPFIA family members and ALG3 play important roles in tumorigenesis and tumor progression. However, the exact roles of distinct PPFIA family members and ALG3 in head and neck squamous cell carcinoma (HNSCC) remain unclear. We studied the mRNA expressions of PPFIA family members and ALG3 in a variety of tumor types compared with the normal controls using the Oncomine database along with meta-analyses of their expressions in HNSCC cancer cell line. The mRNA expressions of PPFIA family members and ALG3 in laryngeal squamous cell carcinoma cell line and normal laryngeal cell line were detected by quantitative real-time polymerase chain reaction. Based on the cBioportal database, we further studied mRNA expression alterations and co-occurrence relationships of the PPFIA family members and ALG3 in HNSCC. The relationship between PPFIA1 and ALG3 mRNA expression alterations and prognoses in patients with HNSCC was explored. We found that PPFIA1 and ALG3 were distinctively overexpressed at the mRNA level in HNSCC tissues compared with normal tissues, they had a significant co-occurrence relationship, their mRNA expressions were significantly higher than other PPFIA family members in laryngeal squamous cell carcinoma cell line, and their mRNA expressions were also significantly higher in laryngeal carcinoma cell line than in normal laryngeal cell line. Patients without both PPFIA1 and ALG3 mRNA expression alterations had better overall survival and disease/progression-free survival compared with patients with both PPFIA1 and ALG3 alterations. Based on these findings, PPFIA1 and ALG3 may play roles in oncogene expression in HNSCC. Their combined overexpression is significantly associated with poor survival outcomes. The relationship between them and the mechanism of action in head and neck cancers deserve further investigation.
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Affiliation(s)
- Hong Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Ting Cao
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Wen Ping Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Gang Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China.
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14
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Tedja MS, Wojciechowski R, Hysi PG, Eriksson N, Furlotte NA, Verhoeven VJ, Iglesias AI, Meester-Smoor MA, Tompson SW, Fan Q, Khawaja AP, Cheng CY, Höhn R, Yamashiro K, Wenocur A, Grazal C, Haller T, Metspalu A, Wedenoja J, Jonas JB, Wang YX, Xie J, Mitchell P, Foster PJ, Klein BE, Klein R, Paterson AD, Hosseini SM, Shah RL, Williams C, Teo YY, Tham YC, Gupta P, Zhao W, Shi Y, Saw WY, Tai ES, Sim XL, Huffman JE, Polašek O, Hayward C, Bencic G, Rudan I, Wilson JF, Joshi PK, Tsujikawa A, Matsuda F, Whisenhunt KN, Zeller T, van der Spek PJ, Haak R, Meijers-Heijboer H, van Leeuwen EM, Iyengar SK, Lass JH, Hofman A, Rivadeneira F, Uitterlinden AG, Vingerling JR, Lehtimäki T, Raitakari OT, Biino G, Concas MP, Schwantes-An TH, Igo RP, Cuellar-Partida G, Martin NG, Craig JE, Gharahkhani P, Williams KM, Nag A, Rahi JS, Cumberland PM, Delcourt C, Bellenguez C, Ried JS, Bergen AA, Meitinger T, Gieger C, Wong TY, Hewitt AW, Mackey DA, Simpson CL, Pfeiffer N, Pärssinen O, Baird PN, Vitart V, Amin N, van Duijn CM, Bailey-Wilson JE, Young TL, Saw SM, Stambolian D, MacGregor S, Guggenheim JA, Tung JY, Hammond CJ, Klaver CC. Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error. Nat Genet 2018; 50:834-848. [PMID: 29808027 PMCID: PMC5980758 DOI: 10.1038/s41588-018-0127-7] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 03/26/2018] [Indexed: 12/18/2022]
Abstract
Refractive errors, including myopia, are the most frequent eye disorders worldwide and an increasingly common cause of blindness. This genome-wide association meta-analysis in 160,420 participants and replication in 95,505 participants increased the number of established independent signals from 37 to 161 and showed high genetic correlation between Europeans and Asians (>0.78). Expression experiments and comprehensive in silico analyses identified retinal cell physiology and light processing as prominent mechanisms, and also identified functional contributions to refractive-error development in all cell types of the neurosensory retina, retinal pigment epithelium, vascular endothelium and extracellular matrix. Newly identified genes implicate novel mechanisms such as rod-and-cone bipolar synaptic neurotransmission, anterior-segment morphology and angiogenesis. Thirty-one loci resided in or near regions transcribing small RNAs, thus suggesting a role for post-transcriptional regulation. Our results support the notion that refractive errors are caused by a light-dependent retina-to-sclera signaling cascade and delineate potential pathobiological molecular drivers.
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Affiliation(s)
- Milly S. Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert Wojciechowski
- Department of Epidemiology and Medicine, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Pirro G. Hysi
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | | | | | - Virginie J.M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adriana I. Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Magda A. Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Stuart W. Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Qiao Fan
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
| | - Anthony P. Khawaja
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Ching-Yu Cheng
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - René Höhn
- Department of Ophthalmology, University Hospital Bern, Inselspital, University of Bern, Bern, Switzerland
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Adam Wenocur
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Clare Grazal
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Juho Wedenoja
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jost B. Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jing Xie
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Paul J. Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Barbara E.K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - S. Mohsen Hosseini
- Program in Genetics and Genome Biology, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Rupal L. Shah
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, UK
| | - Cathy Williams
- Department of Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Yik Ying Teo
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Yih Chung Tham
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Preeti Gupta
- Department of Health Service Research, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Wanting Zhao
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
- Statistics Support Platform, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Yuan Shi
- Statistics Support Platform, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Woei-Yuh Saw
- Life Sciences Institute, National University of Singapore, Singapore
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Xue Ling Sim
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - James F. Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kristina N. Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | | | - Roxanna Haak
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Elisabeth M. van Leeuwen
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio, USA
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jonathan H. Lass
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.HChan School of Public Health, Boston, Massachusetts, USA
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, 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
| | - André G. 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
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere, Tampere, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Sassari, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Tae-Hwi Schwantes-An
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, Indiana, USA
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Katie M. Williams
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Jugnoo S. Rahi
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Ulverscroft Vision Research Group, University College London, London, UK
| | | | - Cécile Delcourt
- Université de Bordeaux, Inserm, Bordeaux Population Health Research Center, team LEHA, UMR 1219, F-33000 Bordeaux, France
| | - Céline Bellenguez
- Institut Pasteur de Lille, Lille, France
- Inserm, U1167, RID-AGE - Risk factors and molecular determinants of aging-related diseases, Lille, France
- Université de Lille, U1167 - Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Tien Yin Wong
- Academic Medicine Research Institute, Singapore
- Retino Center, Singapore National Eye Centre, Singapore, Singapore
| | - Alex W. Hewitt
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, Memphis, Tenessee
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Olavi Pärssinen
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Paul N. Baird
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
- Myopia Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Christopher J. Hammond
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | - Caroline C.W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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Singh M, Tyagi SC. Genes and genetics in eye diseases: a genomic medicine approach for investigating hereditary and inflammatory ocular disorders. Int J Ophthalmol 2018; 11:117-134. [PMID: 29376001 DOI: 10.18240/ijo.2018.01.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Past 25y have witnessed an exponential increase in knowledge and understanding of ocular diseases and their respective genetic underpinnings. As a result, scientists have mapped many genes and their variants that can influence vision and health of our eyes. Based on these findings, it is becoming clear that an early diagnosis employing genetic testing can help evaluate patients' conditions for instituting treatment plan(s) and follow-up care to avoid vision complications later. For example, knowing family history becomes crucial for inherited eye diseases as it can benefit members in family who may have similar eye diseases or predispositions. Therefore, gathering information from an elaborate examination along with complete assessment of past medical illness by ophthalmologists followed by consultation with geneticists can help create a roadmap for making diagnosis and treatment precise and beneficial. In this review, we present an update on ocular genomic medicine that we believe has tremendous potential towards unraveling genetic implications in ocular diseases and patients' susceptibilities. We also discuss translational aspects of genetic ophthalmology and genome engineering that may help advance molecular diagnostics and therapeutics.
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Affiliation(s)
- Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Suresh C Tyagi
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
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16
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Tolleson MW, Gill CA, Herring AD, Riggs PK, Sawyer JE, Sanders JO, Riley DG. Association of udder traits with single nucleotide polymorphisms in crossbred Bos indicus- Bos taurus cows. J Anim Sci 2018; 95:2399-2407. [PMID: 28727049 DOI: 10.2527/jas.2017.1475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The size, support, and health of udders limit the productive life of beef cows, especially those with background, because, in general, such cows have a reputation for problems with udders. Genomic association studies of bovine udder traits have been conducted in dairy cattle and recently in Continental European beef breeds but not in cows with background. The objective of this study was to determine associations of SNP and udder support scores, teat length, and teat diameter in half (Nellore), half (Angus) cows. Udders of cows ( = 295) born from 2003 to 2007 were evaluated for udder support and teat length and diameter ( = 1,746 records) from 2005 through 2014. These included a subjective score representing udder support (values of 1 indicated poorly supported, pendulous udders and values of 9 indicated very well-supported udders) and lengths and diameters of individual teats in the 4 udder quarters as well as the average. Cows were in full-sibling or half-sibling families. Residuals for each trait were produced from repeated records models with cow age category nested within birth year of cows. Those residuals were averaged to become the dependent variables for genomewide association analyses. Regression analyses of those dependent variables included genotypic values as explanatory variables for 34,980 SNP from a commercially available array and included the genomic relationship matrix. Fifteen SNP loci on BTA 5 were associated (false discovery rate controlled at 0.05) with udder support score. One of those was also detected as associated with average teat diameter. Three of those 15 SNP were located within genes, including one each in (), (), and (). These are notable for their functional role in some aspect of mammary gland formation or health. Other candidate genes for these traits in the vicinity of the SNP loci include () and (). Because these were detected in Nellore-Angus crossbred cows, which typically have very well-formed udders with excellent support across their productive lives, similar efforts in other breeds should be completed, because that may facilitate further refinement of genomic regions responsible for variation in udder traits important in multiple breeds.
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17
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Li J, Zhang Q. Insight into the molecular genetics of myopia. Mol Vis 2017; 23:1048-1080. [PMID: 29386878 PMCID: PMC5757860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Myopia is the most common cause of visual impairment worldwide. Genetic and environmental factors contribute to the development of myopia. Studies on the molecular genetics of myopia are well established and have implicated the important role of genetic factors. With linkage analysis, association studies, sequencing analysis, and experimental myopia studies, many of the loci and genes associated with myopia have been identified. Thus far, there has been no systemic review of the loci and genes related to non-syndromic and syndromic myopia based on the different approaches. Such a systemic review of the molecular genetics of myopia will provide clues to identify additional plausible genes for myopia and help us to understand the molecular mechanisms underlying myopia. This paper reviews recent genetic studies on myopia, summarizes all possible reported genes and loci related to myopia, and suggests implications for future studies on the molecular genetics of myopia.
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Affiliation(s)
- Jiali Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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18
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Musolf AM, Simpson CL, Moiz BA, Long KA, Portas L, Murgia F, Ciner EB, Stambolian D, Bailey-Wilson JE. Caucasian Families Exhibit Significant Linkage of Myopia to Chromosome 11p. Invest Ophthalmol Vis Sci 2017; 58:3547-3554. [PMID: 28715588 PMCID: PMC5510992 DOI: 10.1167/iovs.16-21271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/29/2017] [Indexed: 11/24/2022] Open
Abstract
Purpose Myopia is a common visual disorder caused by eye overgrowth, resulting in blurry vision. It affects one in four Americans, and its prevalence is increasing. The genetic mechanisms that underpin myopia are not completely understood. Here, we use genotype data and linkage analyses to identify high-risk genetic loci that are significantly linked to myopia. Methods Individuals from 56 Caucasian families with a history of myopia were genotyped on an exome-based array, and the single nucleotide polymorphism (SNP) data were merged with microsatellite genotype data. Refractive error measures on the samples were converted into binary phenotypes consisting of affected, unaffected, or unknown myopia status. Parametric linkage analyses assuming an autosomal dominant model with 90% penetrance and 10% phenocopy rate were performed. Results Single variant two-point analyses yielded three significantly linked SNPs at 11p14.1 and 11p11.2; a further 45 SNPs at 11p were found to be suggestive. No other chromosome had any significant SNPs or more than seven suggestive linkages. Two of the significant SNPs were located in BBOX1-AS1 and one in the intergenic region between ORA47 and TRIM49B. Collapsed haplotype pattern two-point analysis and multipoint analyses also yielded multiple suggestively linked genes at 11p. Multipoint analysis also identified suggestive evidence of linkage on 20q13. Conclusions We identified three genome-wide significant linked variants on 11p for myopia in Caucasians. Although the novel specific signals still need to be replicated, 11p is a promising region that has been identified by other linkage studies with a number of potentially interesting candidate genes. We hope that the identification of these regions on 11p as potential causal regions for myopia will lead to more focus on these regions and maybe possible replication of our specific linkage peaks in other studies. We further plan targeted sequencing on 11p for our most highly linked families to more clearly understand the source of the linkage in this region.
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Affiliation(s)
- Anthony M. Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Bilal A. Moiz
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Kyle A. Long
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Laura Portas
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Federico Murgia
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Elise B. Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
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19
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Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, Trinca CS, Rodrigues MR, Linderoth T, Bi K, Silveira L, Azevedo FCC, Kantek D, Ramalho E, Brassaloti RA, Villela PMS, Nunes ALV, Teixeira RHF, Morato RG, Loska D, Saragüeta P, Gabaldón T, Teeling EC, O’Brien SJ, Nielsen R, Coutinho LL, Oliveira G, Murphy WJ, Eizirik E. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. SCIENCE ADVANCES 2017; 3:e1700299. [PMID: 28776029 PMCID: PMC5517113 DOI: 10.1126/sciadv.1700299] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/19/2017] [Indexed: 05/05/2023]
Abstract
The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.
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Affiliation(s)
- Henrique V. Figueiró
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Fernanda J. Trindade
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Juliana Assis
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Fabiano Pais
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Fernandes
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Sarah H. D. Santos
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Agostinho Antunes
- Departamento de Biologia, Faculdade de Ciências and CIIMAR/CIMAR, Universidade do Porto, Porto, Portugal
| | - Cristine S. Trinca
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Maíra R. Rodrigues
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Fernando C. C. Azevedo
- Universidade Federal de São João Del Rey, São João Del Rey, Minas Gerais, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
| | - Daniel Kantek
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Emiliano Ramalho
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Ricardo A. Brassaloti
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | | | - Rodrigo H. F. Teixeira
- Zoológico Municipal de Sorocaba, Sorocaba, São Paulo, Brazil
- Programa de Pós-Graduação em Animais Selvagens, Universidade Estadual Paulista–Botucatu, São Paulo, Brazil
| | - Ronaldo G. Morato
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Distrito Federal, Brazil
| | - Damian Loska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720–3140, USA
| | - Luiz L. Coutinho
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | - Guilherme Oliveira
- Centro de Pesquisa René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
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20
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Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues. Sci Rep 2016; 6:39655. [PMID: 28000796 PMCID: PMC5175133 DOI: 10.1038/srep39655] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/24/2016] [Indexed: 12/23/2022] Open
Abstract
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a computational method to segregate DEPDCs and non-DEPDCs. First, we examined the Pfam numbers of the known DEPDCs and used the longest sequences for each Pfam to construct a phylogenetic tree. Subsequently, we extracted 188-dimensional (188D) and 20D features of DEPDCs and non-DEPDCs and classified them with random forest classifier. We also mined the motifs of human DEPDCs to find the related domains. Finally, we designed experimental verification methods of human DEPDC expression at the mRNA level in hepatocellular carcinoma (HCC) and adjacent normal tissues. The phylogenetic analysis showed that the DEPDCs superfamily can be divided into three clusters. Moreover, the 188D and 20D features can both be used to effectively distinguish the two protein types. Motif analysis revealed that the DEP and RhoGAP domain was common in human DEPDCs, human HCC and the adjacent tissues that widely expressed DEPDCs. However, their regulation was not identical. In conclusion, we successfully constructed a binary classifier for DEPDCs and experimentally verified their expression in human HCC tissues.
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21
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Uehara DT, Hayashi S, Okamoto N, Mizuno S, Chinen Y, Kosaki R, Kosho T, Kurosawa K, Matsumoto H, Mitsubuchi H, Numabe H, Saitoh S, Makita Y, Hata A, Imoto I, Inazawa J. SNP array screening of cryptic genomic imbalances in 450 Japanese subjects with intellectual disability and multiple congenital anomalies previously negative for large rearrangements. J Hum Genet 2016; 61:335-43. [PMID: 26740234 DOI: 10.1038/jhg.2015.154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/30/2015] [Accepted: 11/20/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a heterogeneous condition affecting 2-3% of the population, often associated with multiple congenital anomalies (MCA). The genetic cause remains largely unexplained for most cases. To investigate the causes of ID/MCA of unknown etiology in the Japanese population, 645 subjects have been recruited for the screening of pathogenic copy-number variants (CNVs). Two screenings using bacterial artificial chromosome (BAC) arrays were previously performed, which identified pathogenic CNVs in 133 cases (20.6%; Hayashi et al., J. Hum. Genet., 2011). Here, we present the findings of the third screening using a single-nucleotide polymorphism (SNP) array, performed in 450 negative cases from our previous report. Pathogenic CNVs were found in 22 subjects (4.9%), in which 19 CNVs were located in regions where clinical significance had been previously established. Among the 22 cases, we identified PPFIA2 as a novel candidate gene for ID. Analysis of copy-neutral loss of heterozygosity (CNLOH) detected one case in which the CNLOH regions seem to be significant. The SNP array detected a modest fraction of small causative CNVs, which is explained by the fact that the majority of causative CNVs have larger sizes, and those had been mostly identified in the two previous screenings.
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Affiliation(s)
- Daniela Tiaki Uehara
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Yasutsugu Chinen
- Department of Pediatrics, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Hiroshi Mitsubuchi
- Department of Pediatrics, Kumamoto University Graduate School of Medical Science, Kumamoto, Japan
| | - Hironao Numabe
- Department of Genetic Counseling, Faculty of Core Research, Ochanomizu University, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa, Japan
| | - Akira Hata
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Issei Imoto
- Department of Human Genetics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Hard Tissue Genome Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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22
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Li YT, Xie MK, Wu J. Association between Ocular Axial Length-Related Genes and High Myopia in a Han Chinese Population. Ophthalmologica 2015; 235:57-60. [PMID: 26485405 DOI: 10.1159/000439446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/10/2015] [Indexed: 11/19/2022]
Abstract
AIMS A previous genome-wide association study of high myopia identified five genome-wide loci for ocular axial length (C3orf26, ZC3H11B, RSPO1, GJD2, and ZNRF3). The aim of our study was to investigate the association between high myopia and genetic variants in the five loci in Han Chinese subjects. METHODS Five single nucleotide polymorphisms were genotyped in 296 unrelated high-myopia subjects and 300 matched emmetropic controls by the SNaPshot method. The distribution of genotypes in the cases and controls was compared in codominant, dominant, and recessive genetic models by using SNPStats online software. RESULTS Significant associations between rs994767 near ZC3H11B (p = 0.001), rs4074961 in RSPO1 (p < 0.001), and rs11073058 in GJD2 (p = 0.029) and high myopia were observed. Odds ratios (95% confidence intervals) were 1.532 (1.200-1.955), 1.603 (1.267-2.029), and 1.290 (1.027-1.621) for the rs994767 T allele, rs4074961 T allele, and rs11073058 T allele, respectively. But rs9811920 in C3orf26 and rs12321 in ZNRF3 were not associated with high myopia. CONCLUSION Our findings suggested that genetic variants in ZC3H11B, RSPO1, and GJD2 are associated with susceptibility to the development of high myopia in a Han Chinese population. Functional roles of ZC3H11B, RSPO1, and GJD2 in the pathology of high myopia need to be further investigated.
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Affiliation(s)
- Ya-Ting Li
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, PR China
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23
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Zhang X, Zhou X, Qu X. Association between COL1A1 polymorphisms and high myopia: a meta-analysis. Int J Clin Exp Med 2015; 8:5862-5868. [PMID: 26131177 PMCID: PMC4483928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Previous studies of the association between COL1A1 polymorphisms and high myopia risk have yielded conflicting results. To help resolve the discrepancies, we performed a meta-analysis to estimate the relationship between COL1A1 polymorphisms and high myopia risk. METHODS We searched for case-control and cohort studies in MEDLINE, EMBASE, and OVID. Odds ratios (OR) with 95% confidence intervals (CI) were derived for single-nucleotide polymorphisms (SNPs). We also analyzed heterogeneity and publication bias. RESULTS This meta-analysis was based on five studies of rs2075555 (1,944 high myopia cases and 3,060 controls), and three studies of rs2269336 (1,454 high myopia cases and 1,512 controls). The combined results showed an association between rs2075555 and high myopia in the dominant (OR = 0.86, 95% CI = 0.71-0.99) and homozygote models (OR = 0.79, 95% CI = 0.64-0.97). In the recessive model for rs2269336, OR was 1.26 (95% CI = 1.05-1.50); in the heterozygote model, OR was 0.81 (95% CI = 0.69-0.96). Begg's and Egger's tests for rs2075555 showed no evidence of publication bias. CONCLUSIONS This meta-analysis suggests COL1A1 rs2075555 is a potential low risk factor for high myopia.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Myopia Key Laboratory of The Health MinistryShanghai, China
| | - Xingtao Zhou
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Myopia Key Laboratory of The Health MinistryShanghai, China
| | - Xinhua Qu
- Translational Medicine Center, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of MedicineShanghai, China
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Abstract
PURPOSE The PAX6 gene is among the most studied genes in high myopia, but reported findings of association studies on PAX6 and high myopia are inconsistent. We conducted a systematic review and meta-analysis to evaluate the association of PAX6 polymorphisms and high myopia. METHODS All case-control association studies on PAX6 and high myopia reported in EMBASE and MEDLINE were retrieved. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for single-nucleotide polymorphisms (SNPs) that have been involved in at least two studies. Heterogeneity and publication bias analyses were also conducted. RESULTS There were totally 63 publications on PAX6 and myopia. Among them, six articles met all the inclusion criteria, involving 3626 patients and 3262 controls of Asian ancestry. Five PAX6 SNPs, rs3026354, rs667773, rs2071754, rs644242, and rs3026393, were meta-analyzed in high myopia and two, rs667773 and rs644242, in extreme myopia. Single-nucleotide polymorphism rs644242 was associated with high myopia in the dominant model (OR = 0.87; 95% CI, 0.76 to 0.99; p = 0.035) and heterozygous model (OR = 0.85; 95% CI, 0.74 to 0.97; p = 0.019) and with extreme myopia in the dominant model (OR = 0.79; 95% CI, 0.65 to 0.95; p = 0.015), allelic model (OR = 0.81; 95% CI, 0.68 to 0.96; p = 0.014), and heterozygous model (OR = 0.80; 95% CI, 0.65 to 0.97; p = 0.024). However, the associations cannot withstand Bonferroni correction (p > 0.005). The other four SNPs did not show significant association with high myopia. CONCLUSIONS Meta-analysis of existing data revealed a suggestive association of PAX6 rs644242 with extreme and high myopia, which awaits validation in further studies. Nevertheless, PAX6 may only confer a small effect to myopia development.
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Young TL, Hawthorne F, Feng S, Luo X, St Germain E, Wang M, Metlapally R. Whole genome expression profiling of normal human fetal and adult ocular tissues. Exp Eye Res 2013; 116:265-78. [PMID: 24016867 PMCID: PMC3875233 DOI: 10.1016/j.exer.2013.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 07/21/2013] [Accepted: 08/13/2013] [Indexed: 11/21/2022]
Abstract
To study growth and development of ocular tissues, gene expression patterns in normal human fetal versus adult eyes were compared. Human retina/retinal pigment epithelium, choroid, sclera, optic nerve* and cornea* tissues were dissected from fetal (24 week gestational age) (N = 9; *N = 6), and adult (N = 6) normal donor eyes. The Illumina(®) whole genome expression microarray platform was used to assess differential expression. Statistical significance for all comparisons was determined using the Benjamin and Hochberg False Discovery Rate (FDR, 5%). Significant gene expression fold changes > 1.5 were found in adult versus fetal retina/RPE (N = 1185), choroid (N = 6446), sclera (N = 1349), and cornea (N = 3872), but not optic nerve. Genes showing differential expression were assessed using Ingenuity Pathway Analysis (IPA) for enriched functions and canonical pathways. In all tissues, development, cell death/growth, cancer functions, and signaling canonical pathways were enriched. There was also a general trend of down-regulation of collagen genes in adult tissues.
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Affiliation(s)
- Terri L Young
- Center for Human Genetics, Duke University, Durham, NC 27710, USA.
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