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Meng M, Cao Y, Qiu J, Shan G, Wang Y, Zheng Y, Guo M, Yu J, Ma Y, Xie C, Hu C, Xu L, Mueller E, Ma X. Zinc finger protein ZNF638 regulates triglyceride metabolism via ANGPTL8 in an estrogen dependent manner. Metabolism 2024; 152:155784. [PMID: 38211696 DOI: 10.1016/j.metabol.2024.155784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND AND AIM Triglyceride (TG) levels are closely related to obesity, fatty liver and cardiovascular diseases, while the regulatory factors and mechanism for triglyceride homeostasis are still largely unknown. Zinc Finger Protein 638 (ZNF638) is a newly discovered member of zinc finger protein family for adipocyte function in vitro. The aim of the present work was to investigate the role of ZNF638 in regulating triglyceride metabolism in mice. METHODS We generated ZNF638 adipose tissue specific knockout mice (ZNF638 FKO) by cross-breeding ZNF638 flox to Adiponectin-Cre mice and achieved adipose tissue ZNF638 overexpression via adenoviral mediated ZNF638 delivery in inguinal adipose tissue (iWAT) to examined the role and mechanisms of ZNF638 in fat biology and whole-body TG homeostasis. RESULTS Although ZNF638 FKO mice showed similar body weights, body composition, glucose metabolism and serum parameters compared to wild-type mice under chow diet, serum TG levels in ZNF638 FKO mice were increased dramatically after refeeding compared to wild-type mice, accompanied with decreased endothelial lipoprotein lipase (LPL) activity and increased lipid absorption of the small intestine. Conversely, ZNF638 overexpression in iWAT reduced serum TG levels while enhanced LPL activity after refeeding in female C57BL/6J mice and obese ob/ob mice. Specifically, only female mice exhibited altered TG metabolism upon ZNF638 expression changes in fat. Mechanistically, RNA-sequencing analysis revealed that the TG regulator angiopoietin-like protein 8 (Angptl8) was highly expressed in iWAT of female ZNF638 FKO mice. Neutralizing circulating ANGPTL8 in female ZNF638 FKO mice abolished refeeding-induced TG elevation. Furthermore, we demonstrated that ZNF638 functions as a transcriptional repressor by recruiting HDAC1 for histone deacetylation and broad lipid metabolic gene suppression, including Angptl8 transcription inhibition. Moreover, we showed that the sexual dimorphism is possibly due to estrogen dependent regulation on ZNF638-ANGPTL8 axis. CONCLUSION We revealed a role of ZNF638 in the regulation of triglyceride metabolism by affecting Angptl8 transcriptional level in adipose tissue with sexual dimorphism.
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Affiliation(s)
- Meiyao Meng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Yuxiang Cao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jin Qiu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Guangyu Shan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yingwen Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ying Zheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mingwei Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China
| | - Yuandi Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cen Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China; Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Elisabetta Mueller
- Division of Endocrinology, Diabetes and Metabolism Department of Medicine New York University, Grossman School of Medicine, New York, NY, USA
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China; Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China.
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Park S. Height-Related Polygenic Variants Are Associated with Metabolic Syndrome Risk and Interact with Energy Intake and a Rice-Main Diet to Influence Height in KoGES. Nutrients 2023; 15:nu15071764. [PMID: 37049604 PMCID: PMC10096788 DOI: 10.3390/nu15071764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/01/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023] Open
Abstract
Adult height is inversely related to metabolic syndrome (MetS) risk, but its genetic impacts have not been revealed. The present study aimed to examine the hypothesis that adult height-related genetic variants interact with lifestyle to influence adult height and are associated with MetS risk in adults aged >40 in Korea during 2010–2014. Participants were divided into short stature (SS; control) and tall stature (TS; case) by the 85th percentile of adult height. The genetic variants linked to adult height were screened from a genome-wide association study in a city hospital-based cohort (n = 58,701) and confirmed in Ansan/Ansung plus rural cohorts (n = 13,783) among the Korean Genome and Epidemiology Study. Genetic variants that interacted with each other were identified using the generalized multifactor dimensionality reduction (GMDR) analysis. The interaction between the polygenic risk score (PRS) of the selected genetic variants and lifestyles was examined. Adult height was inversely associated with MetS, cardiovascular diseases, and liver function. The PRS, including zinc finger and BTB domain containing 38 (ZBTB38)_rs6762722, polyadenylate-binding protein-interacting protein-2B (PAIP2B)_rs13034890, carboxypeptidase Z (CPZ)_rs3756173, and latent-transforming growth factor beta-binding protein-1 (LTBP1)_rs4630744, was positively associated with height by 1.29 times and inversely with MetS by 0.894 times after adjusting for covariates. In expression quantitative trait loci, the gene expression of growth/differentiation factor-5 (GDF5)_rs224331, non-SMC condensin I complex subunit G (NCAPG)_rs2074974, ligand-dependent nuclear receptor corepressor like (LCORL)_rs7700107, and insulin-like growth factor-1 receptor (IGF1R)_rs2871865 was inversely linked to their risk allele in the tibial nerve and brain. The gene expression of PAIP2B_rs13034890 and a disintegrin and metalloproteinase with thrombospondin motifs-like-3 (ADAMTSL3)_rs13034890 was positively related to it. The PRS was inversely associated with MetS, hyperglycemia, HbA1c, and white blood cell counts. The wild type of GDF5_rs224331 (Ala276) lowered binding energy with rugosin A, D, and E (one of the hydrolyzable tannins) but not the mutated one (276Ser) in the in-silico analysis. The PRS interacted with energy intake and rice-main diet; PRS impact was higher in the high energy intake and the low rice-main diet. In conclusion, the PRS for adult height interacted with energy intake and diet patterns to modulate height and was linked to height and MetS by modulating their expression in the tibial nerve and brain.
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Affiliation(s)
- Sunmin Park
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, 165 Sechul-Ri, BaeBang-Yup, Asan-Si 336-795, ChungNam-Do, Republic of Korea
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3
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Bhandari S, Dolma P, Mukerji M, Prasher B, Montgomery H, Kular D, Jain V, Dadhwal V, Williams DJ, Bhattacharyaa A, Gilbert E, Cavalleri GL, Hillman SL. Population history and genome wide association studies of birth weight in a native high altitude Ladakhi population. PLoS One 2022; 17:e0269671. [PMID: 36126061 PMCID: PMC9488766 DOI: 10.1371/journal.pone.0269671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022] Open
Abstract
Pathological low birth weight due to fetal growth restriction (FGR) is an important predictor of adverse obstetric and neonatal outcomes. It is more common amongst native lowlanders when gestating in the hypoxic environment of high altitude, whilst populations who have resided at high altitude for many generations are relatively protected. Genetic study of pregnant populations at high altitude permits exploration of the role of hypoxia in FGR pathogenesis, and perhaps of FGR pathogenesis more broadly. We studied the umbilical cord blood DNA of 316 neonates born to pregnant women managed at the Sonam Norboo Memorial Hospital, Ladakh (altitude 3540m) between February 2017 and January 2019. Principal component, admixture and genome wide association studies (GWAS) were applied to dense single nucleotide polymorphism (SNP) genetic data, to explore ancestry and genetic predictors of low birth weight. Our findings support Tibetan ancestry in the Ladakhi population, with subsequent admixture with neighboring Indo-Aryan populations. Fetal growth protection was evident in Ladakhi neonates. Although no variants achieved genome wide significance, we observed nominal association of seven variants across genes (ZBTB38, ZFP36L2, HMGA2, CDKAL1, PLCG1) previously associated with birthweight.
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Affiliation(s)
| | - Padma Dolma
- Sonam Norboo Memorial Hospital, Leh, Ladakh, India
| | - Mitali Mukerji
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | - Bhavana Prasher
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | - Hugh Montgomery
- Centre for Human Health and Performance, University College London, London, United Kingdom
| | | | - Vandana Jain
- All India Institute for Medical Sciences, New Delhi, India
| | - Vatsla Dadhwal
- All India Institute for Medical Sciences, New Delhi, India
| | - David J. Williams
- University College London Institute for Women’s Health, London, United Kingdom
| | - Aniket Bhattacharyaa
- Council Scientific Industrial Research-Institute for Genomics and Integrative Biology, New Delhi, India
| | | | | | - Sara L. Hillman
- University College London Institute for Women’s Health, London, United Kingdom
- * E-mail:
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Sakaguchi C, Ichihara K, Nita A, Katayama Y, Nakayama KI. Identification and characterization of novel proteins associated with CHD4. Genes Cells 2021; 27:61-71. [PMID: 34897913 DOI: 10.1111/gtc.12909] [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: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
The CHD (chromodomain helicase DNA binding protein) family consists of nine chromatin remodeling factors that alter chromatin structure in an ATP-dependent manner. CHD4 contributes to the regulation of various cellular activities and processes including development through interaction with multiple proteins including formation of the NuRD (nucleosome remodeling and deacetylase activity) complex. Functions of CHD4 that appear not to be mediated by the NuRD complex or other known interactors have also been identified, however, suggesting the existence of unrecognized proteins that also associate with CHD4. We here generated HeLa-S3 and HEK293T cells with a knock-in allele for FLAG epitope-tagged CHD4 and used these cells to identify proteins that bind to CHD4 with the use of immunoprecipitation followed by liquid chromatography and tandem mass spectrometry. LCORL (ligand-dependent nuclear receptor corepressor like) and NOL4L (nucleolar protein 4 like) were reproducibly identified as novel CHD4 interactors. Furthermore, RNA-sequencing analysis of HEK293T cells depleted of CHD4, LCORL, or NOL4L revealed consistent up-regulation of genes related to the Notch signaling pathway. Our results thus suggest that both LCORL and NOL4L may cooperate with CHD4 to suppress the Notch pathway in mammalian cells.
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Affiliation(s)
- Chihiro Sakaguchi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akihiro Nita
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Yang M, Deng X, Wang S, Zhou B, Niu W, Zhang Z. Identification and characterization of factors associated with short stature and pre-shortness in Chinese preschool-aged children. Endocr Connect 2021; 10:607-619. [PMID: 34010149 PMCID: PMC8240712 DOI: 10.1530/ec-21-0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES We aimed to identify and characterize potential factors, both individually and jointly as a nomogram, associated with short stature and pre-shortness in Chinese preschool-aged children. METHODS Total of 9501 children aged 3-6 years were recruited from 30 kindergartens in Beijing and Tangshan from September to December 2020 using a stratified random sampling method. Effect-size estimates are expressed as odds ratio (OR) and 95% CI. RESULTS The prevalence of short stature and pre-shortness in preschool-aged children was 3.9% (n = 375) and 13.1% (n = 1616), respectively. Factors simultaneously associated with the significant risk for short stature, pre-shortness and both included BMI, paternal height, maternal height, birth weight, birth height, latter birth order (≥2) and less parental patience to children. Besides, breastfeeding duration (≥12 months) was exclusively associated with pre-shortness (OR, 95% CI, P: 1.16, 1.01 to 1.33, 0.037), and childhood obesity with both short stature (3.45, 2.62 to 4.54, <0.001) and short stature/pre-shortness (1.37, 1.15 to 1.64, <0.001). Modeling of significant factors in nomograms had descent prediction accuracies, with the C-index being 77.0, 70.1 and 71.2% for short stature, pre-shortness and both, respectively (all P < 0.001). CONCLUSIONS Our findings indicate the joint contribution of inherited characteristics, nutrition status from the uterus to childhood, and family psychological environment to short stature and pre-shortness in Chinese preschool-aged children. Further validation in other independent groups is warranted.
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Affiliation(s)
- Min Yang
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Xiangling Deng
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Shunan Wang
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Bo Zhou
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Wenquan Niu
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
- Correspondence should be addressed to W Niu or Z Zhang: or
| | - Zhixin Zhang
- International Medical Services, China-Japan Friendship Hospital, Beijing, China
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
- Correspondence should be addressed to W Niu or Z Zhang: or
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6
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Łukasik P, Załuski M, Gutowska I. Cyclin-Dependent Kinases (CDK) and Their Role in Diseases Development-Review. Int J Mol Sci 2021; 22:ijms22062935. [PMID: 33805800 PMCID: PMC7998717 DOI: 10.3390/ijms22062935] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are involved in many crucial processes, such as cell cycle and transcription, as well as communication, metabolism, and apoptosis. The kinases are organized in a pathway to ensure that, during cell division, each cell accurately replicates its DNA, and ensure its segregation equally between the two daughter cells. Deregulation of any of the stages of the cell cycle or transcription leads to apoptosis but, if uncorrected, can result in a series of diseases, such as cancer, neurodegenerative diseases (Alzheimer’s or Parkinson’s disease), and stroke. This review presents the current state of knowledge about the characteristics of cyclin-dependent kinases as potential pharmacological targets.
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Affiliation(s)
- Paweł Łukasik
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Michał Załuski
- Department of Pharmaceutical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
- Correspondence:
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Gharahkhani P, Jorgenson E, Hysi P, Khawaja AP, Pendergrass S, Han X, Ong JS, Hewitt AW, Segrè AV, Rouhana JM, Hamel AR, Igo RP, Choquet H, Qassim A, Josyula NS, Cooke Bailey JN, Bonnemaijer PWM, Iglesias A, Siggs OM, Young TL, Vitart V, Thiadens AAHJ, Karjalainen J, Uebe S, Melles RB, Nair KS, Luben R, Simcoe M, Amersinghe N, Cree AJ, Hohn R, Poplawski A, Chen LJ, Rong SS, Aung T, Vithana EN, Tamiya G, Shiga Y, Yamamoto M, Nakazawa T, Currant H, Birney E, Wang X, Auton A, Lupton MK, Martin NG, Ashaye A, Olawoye O, Williams SE, Akafo S, Ramsay M, Hashimoto K, Kamatani Y, Akiyama M, Momozawa Y, Foster PJ, Khaw PT, Morgan JE, Strouthidis NG, Kraft P, Kang JH, Pang CP, Pasutto F, Mitchell P, Lotery AJ, Palotie A, van Duijn C, Haines JL, Hammond C, Pasquale LR, Klaver CCW, Hauser M, Khor CC, Mackey DA, Kubo M, Cheng CY, Craig JE, MacGregor S, Wiggs JL. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries. Nat Commun 2021; 12:1258. [PMID: 33627673 PMCID: PMC7904932 DOI: 10.1038/s41467-020-20851-4] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022] Open
Abstract
Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross-ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates.
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Affiliation(s)
- Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | - Pirro Hysi
- Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Sarah Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, PA, USA
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jue Sheng Ong
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, VIC, Australia
| | - Ayellet V Segrè
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - John M Rouhana
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Andrew R Hamel
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Helene Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | - Ayub Qassim
- Department of Ophthalmology, Flinders University, Bedford Park, SA, Australia
| | - Navya S Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, MD, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pieter W M Bonnemaijer
- Depatment of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands
| | - Adriana Iglesias
- Depatment of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Owen M Siggs
- Department of Ophthalmology, Flinders University, Bedford Park, SA, Australia
| | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Alberta A H J Thiadens
- Depatment of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Erlangen, Germany
| | | | - K Saidas Nair
- Department of Ophthalmology, School of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Robert Luben
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Mark Simcoe
- Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Ophthalmology, Kings College London, London, United Kingdom
- Institute of Ophthalmology, University College London, London, UK
| | | | - Angela J Cree
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rene Hohn
- Department of Ophthalmology, Inselspital, University Hospital Bern, University of Bern, Bern, Germany
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, Mainz, Germany
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shi-Song Rong
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Certre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eranga Nishanthie Vithana
- Singapore Eye Research Institute, Singapore National Eye Certre, Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore, Republic of Singapore
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, Japan
| | - Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
| | - Hannah Currant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xin Wang
- 23 and Me Inc., San Francisco, CA, USA
| | | | | | | | - Adeyinka Ashaye
- Department of Ophthalmology, University of Ibadan, Ibadan, Nigeria
| | - Olusola Olawoye
- Department of Ophthalmology, University of Ibadan, Ibadan, Nigeria
| | - Susan E Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Akafo
- Unit of Ophthalmology, Department of Surgery, University of Ghana Medical School, Accra, Ghana
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, 1-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul J Foster
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital National Health Service Foundation Trust & UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Peng T Khaw
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital National Health Service Foundation Trust & UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - James E Morgan
- Cardiff Centre for Vision Sciences, College of Biomedical and Life Sciences, Maindy Road, Cardiff University, Cardiff, UK
| | - Nicholas G Strouthidis
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital National Health Service Foundation Trust & UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Francesca Pasutto
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Erlangen, Germany
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Andrew J Lotery
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Chris Hammond
- Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Caroline C W Klaver
- Depatment of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Michael Hauser
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Ophthalmology, Duke University, Durham, NC, USA
- Singapore Eye Research Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, VIC, Australia
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Nedlands, WA, Australia
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Certre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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8
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Molecular characterization of the stress network in individuals at risk for schizophrenia. Neurobiol Stress 2021; 14:100307. [PMID: 33644266 PMCID: PMC7893486 DOI: 10.1016/j.ynstr.2021.100307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 01/24/2023] Open
Abstract
The biological mechanisms underlying inter-individual differences in human stress reactivity remain poorly understood. We aimed to identify the molecular underpinning of aberrant neural stress sensitivity in individuals at risk for schizophrenia. Linking mRNA expression data from the Allen Human Brain Atlas to task-based fMRI revealed 201 differentially expressed genes in cortex-specific brain regions differentially activated by stress in individuals with low (healthy siblings of schizophrenia patients) or high (healthy controls) stress sensitivity. These genes are associated with stress-related psychiatric disorders (e.g. schizophrenia and anxiety) and include markers for specific neuronal populations (e.g. ADCYAP1, GABRB1, SSTR1, and TNFRSF12A), neurotransmitter receptors (e.g. GRIN3A, SSTR1, GABRB1, and HTR1E), and signaling factors that interact with the corticosteroid receptor and hypothalamic-pituitary-adrenal axis (e.g. ADCYAP1, IGSF11, and PKIA). Overall, the identified genes potentially underlie altered stress reactivity in individuals at risk for schizophrenia and other psychiatric disorders and play a role in mounting an adaptive stress response in at-risk individuals, making them potentially druggable targets for stress-related diseases.
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9
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Cousminer DL, Grant SFA. Insights into the Genetic Underpinnings of Endocrine Traits from Large-Scale Genome-Wide Association Studies. Endocrinol Metab Clin North Am 2020; 49:725-739. [PMID: 33153676 DOI: 10.1016/j.ecl.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Great strides have been made in genetic association studies of endocrine traits and diseases, with hundreds or thousands of variants associated with height, body mass index, bone density, pubertal timing, and diabetes in recent years. The common variants associated with these traits explain up to half of the trait variation owing to genetic factors, and when aggregated into polygenic risk scores, can also impact clinically relevant phenotypes at the tail ends of the trait distributions. However, pediatric studies tend to lag behind, and it is often unclear how adult-associated variants behave across life.
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Affiliation(s)
- Diana L Cousminer
- Center for Spatial and Functional Genomics, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building 500, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building 500, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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10
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Lin YJ, Cheng CF, Wang CH, Liang WM, Tang CH, Tsai LP, Chen CH, Wu JY, Hsieh AR, Lee MTM, Lin TH, Liao CC, Huang SM, Zhang Y, Tsai CH, Tsai FJ. Genetic Architecture Associated With Familial Short Stature. J Clin Endocrinol Metab 2020; 105:5805154. [PMID: 32170311 DOI: 10.1210/clinem/dgaa131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
CONTEXT Human height is an inheritable, polygenic trait under complex and multilocus genetic regulation. Familial short stature (FSS; also called genetic short stature) is the most common type of short stature and is insufficiently known. OBJECTIVE To investigate the FSS genetic profile and develop a polygenic risk predisposition score for FSS risk prediction. DESIGN AND SETTING The FSS participant group of Han Chinese ancestry was diagnosed by pediatric endocrinologists in Taiwan. PATIENTS AND INTERVENTIONS The genetic profiles of 1163 participants with FSS were identified by using a bootstrapping subsampling and genome-wide association studies (GWAS) method. MAIN OUTCOME MEASURES Genetic profile, polygenic risk predisposition score for risk prediction. RESULTS Ten novel genetic single nucleotide polymorphisms (SNPs) and 9 reported GWAS human height-related SNPs were identified for FSS risk. These 10 novel SNPs served as a polygenic risk predisposition score for FSS risk prediction (area under the curve: 0.940 in the testing group). This FSS polygenic risk predisposition score was also associated with the height reduction regression tendency in the general population. CONCLUSION A polygenic risk predisposition score composed of 10 genetic SNPs is useful for FSS risk prediction and the height reduction tendency. Thus, it might contribute to FSS risk in the Han Chinese population from Taiwan.
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Affiliation(s)
- Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Chi-Fung Cheng
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Department of Health Services Administration, China Medical University, Taichung, Taiwan
| | - Chung-Hsing Wang
- Children's Hospital of China Medical University, Taichung, Taiwan
| | - Wen-Miin Liang
- Department of Health Services Administration, China Medical University, Taichung, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Li-Ping Tsai
- Department of Pediatrics, Taipei Tzu Chi Hospital, New Taipei City, Taiwan
| | - Chien-Hsiun Chen
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | | | - Ting-Hsu Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chiu-Chu Liao
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Mei Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Chang-Hai Tsai
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Children's Hospital of China Medical University, Taichung, Taiwan
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
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11
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Wong HSC, Lin YJ, Lu HF, Liao WL, Chen CH, Wu JY, Chang WC, Tsai FJ. Genomic interrogation of familial short stature contributes to the discovery of the pathophysiological mechanisms and pharmaceutical drug repositioning. J Biomed Sci 2019; 26:91. [PMID: 31699087 PMCID: PMC6836357 DOI: 10.1186/s12929-019-0581-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/09/2019] [Indexed: 01/06/2023] Open
Abstract
Background Genetic factors, dysregulation in the endocrine system, cytokine and paracrine factors are implicated in the pathogenesis of familial short stature (FSS). Nowadays, the treatment choice for FSS is limited, with only recombinant human growth hormone (rhGH) being available. Methods Herein, starting from the identification of 122 genetic loci related to FSS, we adopted a genetic-driven drug discovery bioinformatics pipeline based on functional annotation to prioritize crucial biological FSS-related genes. These genes were suggested to be potential targets for therapeutics. Results We discovered five druggable subnetworks, which contained seven FSS-related genes and 17 druggable targerts. Conclusions This study provides a valuable drug repositioning accompanied by corresponding targetable gene clusters for FSS therapy.
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Affiliation(s)
- Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Hsing-Fang Lu
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan. .,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan. .,Department of Medical Research, Shuang Ho Hospital, Taipei Medical University , New Taipei City, Taiwan. .,Pain Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan. .,School of Chinese Medicine, China Medical University, Taichung, Taiwan. .,Children's Hospital of China Medical University, Taichung, Taiwan. .,Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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12
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Abstract
PURPOSE OF REVIEW The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature. RECENT FINDINGS Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
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Affiliation(s)
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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13
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Wiberg A, Ng M, Schmid AB, Smillie RW, Baskozos G, Holmes MV, Künnapuu K, Mägi R, Bennett DL, Furniss D. A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome. Nat Commun 2019; 10:1030. [PMID: 30833571 PMCID: PMC6399342 DOI: 10.1038/s41467-019-08993-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 02/13/2019] [Indexed: 01/07/2023] Open
Abstract
Carpal tunnel syndrome (CTS) is a common and disabling condition of the hand caused by entrapment of the median nerve at the level of the wrist. It is the commonest entrapment neuropathy, with estimates of prevalence ranging between 5-10%. Here, we undertake a genome-wide association study (GWAS) of an entrapment neuropathy, using 12,312 CTS cases and 389,344 controls identified in UK Biobank. We discover 16 susceptibility loci for CTS with p < 5 × 10-8. We identify likely causal genes in the pathogenesis of CTS, including ADAMTS17, ADAMTS10 and EFEMP1, and using RNA sequencing demonstrate expression of these genes in surgically resected tenosynovium from CTS patients. We perform Mendelian randomisation and demonstrate a causal relationship between short stature and higher risk of CTS. We suggest that variants within genes implicated in growth and extracellular matrix architecture contribute to the genetic predisposition to CTS by altering the environment through which the median nerve transits.
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Affiliation(s)
- Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Annina B Schmid
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Robert W Smillie
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK
| | - Georgios Baskozos
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Michael V Holmes
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, OX3 7LF, UK.,Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LF, UK
| | - K Künnapuu
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - R Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23 B, 51010, Tartu, Estonia
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, OX3 7LD, UK. .,Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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14
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Knowles EEM, Mathias SR, Mollon J, Rodrigue A, Koenis MMG, Dyer TD, Goring HHH, Curran JE, Olvera RL, Duggirala R, Almasy L, Blangero J, Glahn DC. A QTL on chromosome 3q23 influences processing speed in humans. GENES BRAIN AND BEHAVIOR 2018; 18:e12530. [PMID: 30379395 DOI: 10.1111/gbb.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/24/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Processing speed is a psychological construct that refers to the speed with which an individual can perform any cognitive operation. Processing speed correlates strongly with general cognitive ability, declines sharply with age and is impaired across a number of neurological and psychiatric disorders. Thus, identifying genes that influence processing speed will likely improve understanding of the genetics of intelligence, biological aging and the etiologies of numerous disorders. Previous genetics studies of processing speed have relied on simple phenotypes (eg, mean reaction time) derived from single tasks. This strategy assumes, erroneously, that processing speed is a unitary construct. In the present study, we aimed to characterize the genetic architecture of processing speed by using a multidimensional model applied to a battery of cognitive tasks. Linkage and QTL-specific association analyses were performed on the factors from this model. The randomly ascertained sample comprised 1291 Mexican-American individuals from extended pedigrees. We found that performance on all three distinct processing-speed factors (Psychomotor Speed; Sequencing and Shifting and Verbal Fluency) were moderately and significantly heritable. We identified a genome-wide significant quantitative trait locus (QTL) on chromosome 3q23 for Psychomotor Speed (LOD = 4.83). Within this locus, we identified a plausible and interesting candidate gene for Psychomotor Speed (Z = 2.90, P = 1.86 × 10-03 ).
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Affiliation(s)
- Emma E M Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Samuel R Mathias
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Josephine Mollon
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Amanda Rodrigue
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Marinka M G Koenis
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley School of Medicine, Brownsville, Texas
| | - Harald H H Goring
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley School of Medicine, Brownsville, Texas
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley School of Medicine, Brownsville, Texas
| | - Rene L Olvera
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Ravi Duggirala
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley School of Medicine, Brownsville, Texas
| | - Laura Almasy
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Blangero
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas of the Rio Grande Valley School of Medicine, Brownsville, Texas
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Olin Neuropsychiatric Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
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15
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Windpassinger C, Piard J, Bonnard C, Alfadhel M, Lim S, Bisteau X, Blouin S, Ali NB, Ng AYJ, Lu H, Tohari S, Talib SZA, van Hul N, Caldez MJ, Van Maldergem L, Yigit G, Kayserili H, Youssef SA, Coppola V, de Bruin A, Tessarollo L, Choi H, Rupp V, Roetzer K, Roschger P, Klaushofer K, Altmüller J, Roy S, Venkatesh B, Ganger R, Grill F, Ben Chehida F, Wollnik B, Altunoglu U, Al Kaissi A, Reversade B, Kaldis P. CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays. Am J Hum Genet 2017; 101:391-403. [PMID: 28886341 DOI: 10.1016/j.ajhg.2017.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/01/2017] [Indexed: 10/18/2022] Open
Abstract
In five separate families, we identified nine individuals affected by a previously unidentified syndrome characterized by growth retardation, spine malformation, facial dysmorphisms, and developmental delays. Using homozygosity mapping, array CGH, and exome sequencing, we uncovered bi-allelic loss-of-function CDK10 mutations segregating with this disease. CDK10 is a protein kinase that partners with cyclin M to phosphorylate substrates such as ETS2 and PKN2 in order to modulate cellular growth. To validate and model the pathogenicity of these CDK10 germline mutations, we generated conditional-knockout mice. Homozygous Cdk10-knockout mice died postnatally with severe growth retardation, skeletal defects, and kidney and lung abnormalities, symptoms that partly resemble the disease's effect in humans. Fibroblasts derived from affected individuals and Cdk10-knockout mouse embryonic fibroblasts (MEFs) proliferated normally; however, Cdk10-knockout MEFs developed longer cilia. Comparative transcriptomic analysis of mutant and wild-type mouse organs revealed lipid metabolic changes consistent with growth impairment and altered ciliogenesis in the absence of CDK10. Our results document the CDK10 loss-of-function phenotype and point to a function for CDK10 in transducing signals received at the primary cilia to sustain embryonic and postnatal development.
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