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Wang Y, Li H, Huang J, Jiang M, Tian S, Liu S, Zhang L, Wu S, Kan H, Gao X. Short-Term PM 2.5 Exposure and DNA Methylation Changes of Circadian Rhythm Genes: Evidence from Two Experimental Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9991-10000. [PMID: 38814053 DOI: 10.1021/acs.est.4c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The circadian rhythm regulates many crucial physiological processes, impacting human aging and aging-related outcomes. Observational evidence links circadian rhythm disturbance to PM2.5 exposure, yet the underlying DNA methylation mechanisms remain unclear due to limited PM2.5-dominated experimental settings. Therefore, we investigated the associations between short-term PM2.5 exposure and DNA methylation changes of 1188 CpG candidates across circadian genes among 32 young adults in the FDU study, with the validation in 26 individuals from the PKU study. Further mediation analyses tested whether DNA methylation of circadian genes could mediate the influence of PM2.5 on aging measured by three epigenetic ages: DNAmGrimAge, DunedinPoAm, and the mortality risk score. We identified three CpG sites associated with personal PM2.5 exposure: cg01248361 (CSNK2A2), cg17728065 (RORA), and cg22513396 (PRKAG2). Acute effects of PM2.5 on the three loci could be mediated by several circulating biomarkers, including MDA and EGF, with up to ∼30% of mediated proportions. Three loci further showed varying potentials in mediating the aging acceleration effect of PM2.5. Locus cg17728065 is the key site exhibiting a robust mediating effect (7.54-12.52%) on PM2.5-induced aging acceleration. Our findings demonstrated that PM2.5, even short-term peaks, could leave imprints on human aging via inducing aberrant temporal fluctuation in circadian homeostasis captured by DNA methylation profiles.
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Affiliation(s)
- Yuting Wang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Huichu Li
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai 200032, China
| | - Jing Huang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Meijie Jiang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Sifan Tian
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Shuzhen Liu
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
| | - Ling Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University and Beijing Municipal Key Laboratory of Clinical Epidemiology, Beijing 100069, China
| | - Shaowei Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi 710049, China
- Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi 710049, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi 710049, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai 200032, China
- IRDR ICoE on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China
- National Center for Children's Health, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xu Gao
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100871, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100871, China
- Peking University Institute of Environmental Medicine, Beijing 100191, China
- Center for Healthy Aging, Peking University Health Science Center, Beijing 100083, China
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Zhu Y, Liu Y, Escames G, Yang Z, Zhao H, Qian L, Xue C, Xu D, Acuña-Castroviejo D, Yang Y. Deciphering clock genes as emerging targets against aging. Ageing Res Rev 2022; 81:101725. [PMID: 36029999 DOI: 10.1016/j.arr.2022.101725] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
The old people often suffer from circadian rhythm disturbances, which in turn accelerate aging. Many aging-related degenerative diseases such as Alzheimer's disease, Parkinson's disease, and osteoarthritis have an inextricable connection with circadian rhythm. In light of the predominant effects of clock genes on regulating circadian rhythm, we systematically present the elaborate network of roles that clock genes play in aging in this review. First, we briefly introduce the basic background regarding clock genes. Second, we systemically summarize the roles of clock genes in aging and aging-related degenerative diseases. Third, we discuss the relationship between clock genes polymorphisms and aging. In summary, this review is intended to clarify the indispensable roles of clock genes in aging and sheds light on developing clock genes as anti-aging targets.
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Affiliation(s)
- Yanli Zhu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yanqing Liu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Germaine Escames
- Biomedical Research Center, Health Sciences Technology Park, University of Granada, Avda. del Conocimiento s/n, Granada, Spain; Ibs. Granada and CIBERfes, Granada, Spain; UGC of Clinical Laboratories, Universitu San Cecilio's Hospital, Granada, Spain
| | - Zhi Yang
- Department of General Surgery, Tangdu Hospital, The Airforce Medical University, 1 Xinsi Road, Xi'an, China
| | - Huadong Zhao
- Department of General Surgery, Tangdu Hospital, The Airforce Medical University, 1 Xinsi Road, Xi'an, China
| | - Lu Qian
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Chengxu Xue
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Danni Xu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Darío Acuña-Castroviejo
- Biomedical Research Center, Health Sciences Technology Park, University of Granada, Avda. del Conocimiento s/n, Granada, Spain; Ibs. Granada and CIBERfes, Granada, Spain; UGC of Clinical Laboratories, Universitu San Cecilio's Hospital, Granada, Spain.
| | - Yang Yang
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi'an, China.
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3
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Barth E, Srivastava A, Wengerodt D, Stojiljkovic M, Axer H, Witte OW, Kretz A, Marz M. Age-dependent expression changes of circadian system-related genes reveal a potentially conserved link to aging. Aging (Albany NY) 2021; 13:25694-25716. [PMID: 34923482 PMCID: PMC8751596 DOI: 10.18632/aging.203788] [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: 03/16/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022]
Abstract
The circadian clock system influences the biology of life by establishing circadian rhythms in organisms, tissues, and cells, thus regulating essential biological processes based on the day/night cycle. Circadian rhythms change over a lifetime due to maturation and aging, and disturbances in the control of the circadian system are associated with several age-related pathologies. However, the impact of chronobiology and the circadian system on healthy organ and tissue aging remains largely unknown. Whether aging-related changes of the circadian system’s regulation follow a conserved pattern across different species and tissues, hence representing a common driving force of aging, is unclear. Based on a cross-sectional transcriptome analysis covering 329 RNA-Seq libraries, we provide indications that the circadian system is subjected to aging-related gene alterations shared between evolutionarily distinct species, such as Homo sapiens, Mus musculus, Danio rerio, and Nothobranchius furzeri. We discovered differentially expressed genes by comparing tissue-specific transcriptional profiles of mature, aged, and old-age individuals and report on six genes (per2, dec2, cirp, klf10, nfil3, and dbp) of the circadian system, which show conserved aging-related expression patterns in four organs of the species examined. Our results illustrate how the circadian system and aging might influence each other in various tissues over a long lifespan and conceptually complement previous studies tracking short-term diurnal and nocturnal gene expression oscillations.
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Affiliation(s)
- Emanuel Barth
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Diane Wengerodt
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Milan Stojiljkovic
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Hubertus Axer
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Alexandra Kretz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Manja Marz
- Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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Hou SJ, Tsai SJ, Kuo PH, Lin WY, Liu YL, Yang AC, Lin E, Lan TH. An association study in the Taiwan Biobank elicits the GABAA receptor genes GABRB3, GABRA5, and GABRG3 as candidate loci for sleep duration in the Taiwanese population. BMC Med Genomics 2021; 14:223. [PMID: 34530807 PMCID: PMC8447520 DOI: 10.1186/s12920-021-01083-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Gamma-aminobutyric acid type A (GABAA) receptors mainly mediate the effects of gamma-aminobutyric acid, which is the primary inhibitory neurotransmitter in the central nervous system. Abundant evidence suggests that GABAA receptors play a key role in sleep-regulating processes. No genetic association study has explored the relationships between GABAA receptor genes and sleep duration, sleep quality, and sleep timing in humans. Methods We determined the association between single-nucleotide polymorphisms (SNPs) in the GABAA receptor genes GABRA1, GABRA2, GABRB3, GABRA5, and GABRG3 and sleep duration, sleep quality, and sleep timing in the Taiwan Biobank with a sample of 10,127 Taiwanese subjects. There were 10,142 subjects in the original study cohort. We excluded 15 subjects with a medication history of sedative-hypnotics. Results Our data revealed an association of the GABRB3-GABRA5-GABRG3 gene cluster with sleep duration, which has not been previously identified: rs79333046 (beta = − 0.07; P = 1.21 × 10–3) in GABRB3, rs189790076 (beta = 0.92; P = 1.04 × 10–3) in GABRA5, and rs147619342 (beta = − 0.72; P = 3.97 × 10–3) in GABRG3. The association between rs189790076 in GABRA5 and sleep duration remained significant after Bonferroni correction. A variant (rs12438141) in GABRB3 was also found to act as a potential expression quantitative trait locus. Additionally, we discovered interactions between variants in the GABRB3-GABRA5-GABRG3 gene cluster and lifestyle factors, such as tea and coffee consumption, smoking, and physical activity, that influenced sleep duration, although some interactions became nonsignificant after Bonferroni correction. We also found interactions among GABRB3, GABRA5, and GABRG3 that affected sleep duration. Furthermore, we identified an association of rs7165524 (beta = − 0.06; P = 2.20 × 10–3) in GABRA5 with sleep quality and an association of rs79465949 (beta = − 0.12; P = 3.95 × 10–3) in GABRB3 with sleep timing, although these associations became nonsignificant after Bonferroni correction. However, we detected no evidence of an association of individual SNPs in GABRA1 and GABRA2. Conclusions Our results indicate that rs189790076 in GABRA5 and gene–gene interactions among GABRB3, GABRA5, and GABRG3 may contribute to sleep duration in the Taiwanese population. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01083-x.
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Affiliation(s)
- Sheue-Jane Hou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Psychiatry, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan.,Department of Psychiatry, National Taiwan University Hospital, Taipei, Taiwan
| | - Wan-Yu Lin
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.,Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Eugene Lin
- Department of Biostatistics, University of Washington, 3980 15th Avenue NE, Box 351617, Seattle, WA, 98195, USA. .,Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
| | - Tsuo-Hung Lan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Tsaotun Psychiatric Center, Ministry of Health and Welfare, Nantou, Taiwan.
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5
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Akbor MM, Kim J, Nomura M, Sugioka J, Kurosawa N, Isobe M. A candidate gene of Alzheimer diseases was mutated in senescence-accelerated mouse prone (SAMP) 8 mice. Biochem Biophys Res Commun 2021; 572:112-117. [PMID: 34364289 DOI: 10.1016/j.bbrc.2021.07.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
The senescence-accelerated mouse prone (SAMP) 8 strain exhibits age-related learning and memory deficits (LMD) at 2 months of age. We have found strong association of chromosome 12 locus with learning memory deficit (LMD) phenotype in SAMP8 strain. In the course of searching candidate gene, here we identified solute carrier family 24 sodium/potassium/calcium exchanger member 4 (Slc24a4) in SAMP8 chromosome 12 LMD possessing one single nucleotide polymorphism causing amino acid replacement of Threonine at 413 position with Methionine. Since SLC24A4 has been postulated as a candidate of late onset Alzheimer's diseases (LOAD), we further analyze the functional importance of this polymorphism. By expressing Slc24a4 protein in HEK293 cells, here we showed polymorphic SAMP8 type Slc24a4-T413 M causing significant loss of calcium ion (Ca2+) transporter activity in cells compared with that of wild type mouse (Slc24a4-WT). However, no study yet shows any functional association of human SLC24A4 polymorphism with the onset of LOAD pathogenesis. Thus, our present finding may further help to clarify the importance of this ion exchanger with age related cognitive dysfunction.
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Affiliation(s)
- Maruf Mohammad Akbor
- Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, Faculty of Engineering, University of Toyama, Toyama, Japan
| | - Juhyon Kim
- Division of Bio-Information Engineering, Faculty of Engineering, University of Toyama, Toyama, Japan
| | - Mai Nomura
- Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, Faculty of Engineering, University of Toyama, Toyama, Japan
| | - Juno Sugioka
- Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, Faculty of Engineering, University of Toyama, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, Faculty of Engineering, University of Toyama, Toyama, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Department of Life Sciences and Bioengineering, Faculty of Engineering, University of Toyama, Toyama, Japan.
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An association study in the Taiwan Biobank elicits three novel candidates for cognitive aging in old adults: NCAM1, TTC12 and ZBTB20. Aging (Albany NY) 2021; 13:18769-18788. [PMID: 34285142 PMCID: PMC8351692 DOI: 10.18632/aging.203321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/08/2021] [Indexed: 01/11/2023]
Abstract
The dopamine receptor-related loci have been suggested to be associated with cognitive functions and neurodegenerative diseases. It is unknown whether genetic variants such as single nucleotide polymorphisms (SNPs) in the dopamine receptor-related loci could contribute to cognitive aging independently as well as by virtue of complicated interplays in the elder population. To assess whether SNPs in the dopamine receptor-related loci are associated with cognitive aging in the elder population, we evaluated SNPs in the DRD1, NCAM1-TTC12-ANKK1-DRD2, DRD3-LOC107986115-ZNF80-TIGIT-MIR568-ZBTB20, DRD4, and DRD5-SLC2A9 loci from 25,195 older Taiwanese individuals from the Taiwan Biobank. Mini-Mental State Examination (MMSE) was scrutinized for all participants, where MMSE scores were employed to evaluate cognitive functions. From our analysis, we identified three novel genes for cognitive aging that have not previously been reported: ZBTB20 on chromosome 3 and NCAM1 and TTC12 on chromosome 11. NCAM1 and ZBTB20 are strong candidates for having a role in cognitive aging with mutations in ZBTB20 resulting in intellectual disability, and NCAM1 previously found to be associated with associative memory in humans. Additionally, we found the effects of interplays between physical activity and these three novel genes. Our study suggests that genetic variants in the dopamine receptor-related loci may influence cognitive aging individually and by means of gene-physical activity interactions.
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Yi Lee PM, Ling Kwok BH, Ting Ma JY, Tse LA. A population-based prospective study on rest-activity rhythm and mild cognitive impairment among Hong Kong healthy community-dwelling older adults. Neurobiol Sleep Circadian Rhythms 2021; 10:100065. [PMID: 33997474 PMCID: PMC8091051 DOI: 10.1016/j.nbscr.2021.100065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 02/28/2021] [Accepted: 04/06/2021] [Indexed: 01/13/2023] Open
Abstract
Background Relatively few studies investigated the association between rest-activity circadian rhythm and cognitive impairment in population-based study, and the evidence from Asian populations is sparse. We aimed to examine the relationship of actigraphy measured rest-activity circadian rhythm with mild cognitive impairment (MCI) or cognitive impairment in Hong Kong healthy community-dwelling older adults. Methods We recruited 174 Hong Kong healthy adults aged ≥65 years (36 male vs. 138 female) during April-September 2018, and followed up them for 12 months. Participants were invited to wear wrist actigraphy for 7 days in both baseline and follow-up study. We used the actigraph data to calculate their midline statistic of rhythm (MESOR), amplitude, acrophase and percent rhythm. Montreal Cognitive Assessment (MoCA) was used to assess their cognitive scores at baseline and follow-up. Multivariate logistic regression model was performed to estimate the association of rest-activity circadian rhythm parameters with MCI; whilst multinomial logistic regression model was used to examine the association between rhythm parameters and changes of cognitive scores (i.e., worsen: <-1, stable: -1 to 1, better cognition: ≥2) after 12-months follow-up respectively. Results There was no association between rest-activity circadian rhythm parameters and MCI or cognitive impairment at baseline. Compared to those with an averaged value of acrophase (1:24pm-3:00pm), results of multinominal logistic regression showed that participants with a delayed acrophase (after 3:00pm) were less likely to have better cognition (adjusted odds ratio (AOR) = 0.32, 95% confidence interval (CI) = 0.11-0.88). Upon one year of follow-up, participants who delayed their acrophase for 24 min than their baseline measurements were also less likely to have better cognitive functions (AOR = 0.26, 95%CI = 0.08-0.79). Conclusions Results from both the baseline survey and follow-up study consistently confirmed that older adults, especially in light of the majority of participants being the females, with delayed acrophase were less likely to have better cognition in the Asian population.
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Affiliation(s)
- Priscilla Ming Yi Lee
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Bonnie Ho Ling Kwok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Julie Yuen Ting Ma
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Lap Ah Tse
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
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CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption. Sci Rep 2020; 10:18118. [PMID: 33093602 PMCID: PMC7583246 DOI: 10.1038/s41598-020-75199-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 10/12/2020] [Indexed: 12/21/2022] Open
Abstract
Molecular mechanisms that prompt or mitigate excessive alcohol consumption could be partly explained by metabolic shifts. This genome-wide association study aims to identify the susceptibility gene loci for excessive alcohol consumption by jointly measuring weekly alcohol consumption and γ-GT levels. We analysed the Taiwan Biobank data of 18,363 Taiwanese people, including 1945 with excessive alcohol use. We found that one or two copies of the G allele in rs671 (ALDH2) increased the risk of excessive alcohol consumption, while one or two copies of the C allele in rs3782886 (BRAP) reduced the risk of excessive alcohol consumption. To minimize the influence of extensive regional linkage disequilibrium, we used the ridge regression. The ridge coefficients of rs7398833, rs671 and rs3782886 were unchanged across different values of the shrinkage parameter. The three variants corresponded to posttranscriptional activity, including cut-like homeobox 2 (a protein coded by CUX2), Glu504Lys of acetaldehyde dehydrogenase 2 (a protein encoded by ALDH2) and Glu4Gly of BRCA1-associated protein (a protein encoded by BRAP). We found that Glu504Lys of ALDH2 and Glu4Gly of BRAP are involved in the negative regulation of excessive alcohol consumption. The mechanism underlying the γ-GT-catalytic metabolic reaction in excessive alcohol consumption is associated with ALDH2, BRAP and CUX2. Further study is needed to clarify the roles of ALDH2, BRAP and CUX2 in the liver–brain endocrine axis connecting metabolic shifts with excessive alcohol consumption.
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9
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Hou SJ, Tsai SJ, Kuo PH, Liu YL, Yang AC, Lin E, Lan TH. An association study in the Taiwan Biobank reveals RORA as a novel locus for sleep duration in the Taiwanese Population. Sleep Med 2020; 73:70-75. [PMID: 32791442 DOI: 10.1016/j.sleep.2020.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/26/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Sleep is a key factor for health-related quality of life since sleep disturbances are a significant and common problem for patients with various human diseases such as psychiatric disorders. While single nucleotide polymorphisms (SNPs) in circadian clock genes have been indicated to be associated with sleep duration, most of the association studies have been investigated in populations with European ancestry. It is believed that no studies have been conducted to investigate a link between sleep duration and the circadian clock genes RORA and RORB, which play a key role, with NR1D1, in an additional feedback loop for the circadian rhythm machinery. METHODS In this study, we assessed the relationships between sleep duration and SNPs in the circadian clock genes NR1D1, RORA, and RORB in the Taiwan Biobank with a sample of 10,112 Taiwanese subjects. RESULTS From our data, we revealed a novel significant association in sleep duration with the rs75981965 SNP (P = 9.93 × 10-5) in the RORA gene that has not been previously identified. The association of sleep duration with this SNP remained significant after performing Bonferroni correction. RORA is a potential candidate for sleep duration as RORA has been suggested to play a key role in the regulation of sleep disorders. Additionally, we pinpointed the effects of interactions between RORA rs75981965 and environmental factors such as tea consumption (P = 0.0015), coffee consumption (P = 0.0029), physical activity (P = 0.011), alcohol consumption (P = 0.0146), and smoking (P = 0.0223) in influencing sleep duration. We also found interactions between RORA and NR1D1 (P = 0.0023) as well as between RORA and RORB (P = 0.0061) in affecting sleep duration. CONCLUSIONS Our results indicate that the circadian clock gene RORA may contribute to sleep duration independently as well as through gene-gene and gene-environment interactions in the Taiwanese population.
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Affiliation(s)
- Sheue-Jane Hou
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Psychiatry, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan; Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan; Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, 02215, USA
| | - Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA; Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
| | - Tsuo-Hung Lan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Psychiatry, Taichung Veterans General Hospital, Taichung, Taiwan; Tsaotun Psychiatric Center, Ministry of Health and Welfare, Nantou, Taiwan.
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10
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Lin E, Lin CH, Lane HY. Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches. Int J Mol Sci 2020; 21:ijms21030969. [PMID: 32024055 PMCID: PMC7037937 DOI: 10.3390/ijms21030969] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/25/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
A growing body of evidence now suggests that precision psychiatry, an interdisciplinary field of psychiatry, precision medicine, and pharmacogenomics, serves as an indispensable foundation of medical practices by offering the accurate medication with the accurate dose at the accurate time to patients with psychiatric disorders. In light of the latest advancements in artificial intelligence and machine learning techniques, numerous biomarkers and genetic loci associated with psychiatric diseases and relevant treatments are being discovered in precision psychiatry research by employing neuroimaging and multi-omics. In this review, we focus on the latest developments for precision psychiatry research using artificial intelligence and machine learning approaches, such as deep learning and neural network algorithms, together with multi-omics and neuroimaging data. Firstly, we review precision psychiatry and pharmacogenomics studies that leverage various artificial intelligence and machine learning techniques to assess treatment prediction, prognosis prediction, diagnosis prediction, and the detection of potential biomarkers. In addition, we describe potential biomarkers and genetic loci that have been discovered to be associated with psychiatric diseases and relevant treatments. Moreover, we outline the limitations in regard to the previous precision psychiatry and pharmacogenomics studies. Finally, we present a discussion of directions and challenges for future research.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA;
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Chieh-Hsin Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence: (C.-H.L.); (H.-Y.L.)
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Psychiatry, China Medical University Hospital, Taichung 40402, Taiwan
- Brain Disease Research Center, China Medical University Hospital, Taichung 40402, Taiwan
- Department of Psychology, College of Medical and Health Sciences, Asia University, Taichung 41354, Taiwan
- Correspondence: (C.-H.L.); (H.-Y.L.)
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Lin E, Kuo PH, Liu YL, Yang AC, Tsai SJ. Association and Interaction Effects of Interleukin-12 Related Genes and Physical Activity on Cognitive Aging in Old Adults in the Taiwanese Population. Front Neurol 2019; 10:1065. [PMID: 31649612 PMCID: PMC6795278 DOI: 10.3389/fneur.2019.01065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/20/2019] [Indexed: 01/03/2023] Open
Abstract
Evidence suggests that the neuro-inflammation mechanisms associated with interleukin-12 (IL-12) may be linked to Alzheimer's diseases and cognitive aging. In this study, we speculate that single nucleotide polymorphisms (SNPs) in IL-12-associated genes, such as IL12A, IL12B, IL12RB1, and IL12RB2 genes, could be associated with cognitive aging individually and/or via complicated interactions in the elder Taiwanese population. There were totally 3,730 Taiwanese individuals with age ≥60 years from the Taiwan Biobank. Mini-Mental State Examination (MMSE) was analyzed for all participants. We employed MMSE scores to assess cognitive functions. Our analysis revealed that the IL12A gene (including rs116910715, rs78902931, and rs78569420), the IL12B gene (including rs730691), and the IL12RB2 gene (including rs3790558, rs4655538, rs75699623, and rs1874396) were associated with cognitive aging. Among these SNPs, the association with the IL12RB2 rs3790558 SNP remained significant after performing Bonferroni correction (P = 6.87 × 10−4). Additionally, we found that interactions between the IL12A and IL12RB2 genes influenced cognitive aging (P = 0.022). Finally, we pinpointed the effects of interactions between IL12A, IL12B, and IL12RB2 with physical activity (P < 0.001, = 0.002, and < 0.001, respectively). Our study suggests that the IL-12-associated genes may contribute to susceptibility to cognitive aging independently as well as through gene-gene and gene-physical activity interactions.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA, United States.,Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, United States.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Hsinchu, Taiwan
| | - Albert C Yang
- Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, United States.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
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12
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Lin E, Kuo PH, Liu YL, Yang AC, Tsai SJ. Polymorphisms of the DNA repair gene EXO1 modulate cognitive aging in old adults in a Taiwanese population. DNA Repair (Amst) 2019; 78:1-6. [PMID: 30928815 DOI: 10.1016/j.dnarep.2019.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 12/15/2022]
Abstract
Evidence indicates that the age-related neuropathological mechanisms associated with DNA repair genes may contribute to cognitive aging and Alzheimer's disease. In this study, we hypothesize that single nucleotide polymorphisms (SNPs) within 155 DNA repair genes may be linked to cognitive aging independently and/or through complex interactions in an older Taiwanese population. A total of 3,730 Taiwanese subjects aged over 60 years from the Taiwan Biobank were analyzed. Mini-Mental State Examination (MMSE) was administered to all subjects, and MMSE scores were used to measure cognitive functions. Our data showed that out of 1,652 SNPs, the rs1776181 (P = 1.47 × 10-5), rs1776177 (P = 8.42 × 10-7), rs1635510 (P = 7.97 × 10-6), and rs2526698 (P = 7.06 × 10-6) SNPs in the EXO1 gene were associated with cognitive aging. The association with these SNP remained significant after performing Bonferroni correction. Additionally, we found that interactions between the EXO1 and RAD51C genes influenced cognitive aging (P = 0.002). Finally, we pinpointed the influence of interactions between EXO1 and physical activity (P < 0.001) as well as between DCLRE1C and physical activity (P < 0.001). Our study indicated that DNA repair genes may contribute to susceptibility in cognitive aging independently as well as through gene-gene and gene-physical interactions.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA; Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan; Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, 02215, USA; Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan; Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan.
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13
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Machine Learning in Neural Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1192:127-137. [DOI: 10.1007/978-981-32-9721-0_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Gjerstad MD, Alves G, Maple-Grødem J. Excessive Daytime Sleepiness and REM Sleep Behavior Disorders in Parkinson's Disease: A Narrative Review on Early Intervention With Implications to Neuroprotection. Front Neurol 2018; 9:961. [PMID: 30487775 PMCID: PMC6246656 DOI: 10.3389/fneur.2018.00961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/25/2018] [Indexed: 11/13/2022] Open
Abstract
Sleep contributes to the consolidation of our memory and facilitates learning. Short term sleep deprivation temporarily reduces mnestic capacity, whereas long lasting sleep deprivation is associated with structural changes in the hippocampus and cortical areas. However, it is unknown whether early intervention and treatment of sleep disorders could have a neuroprotective effect. In neurodegenerative diseases sleep disorders can occur at preclinical stages and are frequently observed in patients with established Parkinson's disease (PD) and other α-synucleinopathies. REM sleep behavior disorder (RBD) is recognized as a hallmark for the development of α-synucleinopathies and may predict early cognitive decline, while excessive daytime sleepiness (EDS) is present in 12% of patients with PD before treatment initiation and increases continuously over time, causing substantial restrictions for the patients' social life. In more advanced disease, EDS is associated with dementia. Even though well recognized, limited attention has been given to genetics or the treatment of RBD and EDS in early PD. Systematic screening and early intervention can be expected to increase the patients' quality of life, but it remains unclear if this will also impact disease progression. Intervention studies in preclinical and early stages of α-synucleinopathies are needed to increase our understanding of the underlying pathomechanisms and may also provide important inroads to help clarify whether sleep disturbances are secondary to the neurodegenerative process or also contribute to disease exacerbation.
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Affiliation(s)
- Michaela D Gjerstad
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Neurology, Stavanger University Hospital, Stavanger, Norway
| | - Guido Alves
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Neurology, Stavanger University Hospital, Stavanger, Norway
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
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Tsai SJ. Critical Issues in BDNF Val66Met Genetic Studies of Neuropsychiatric Disorders. Front Mol Neurosci 2018; 11:156. [PMID: 29867348 PMCID: PMC5962780 DOI: 10.3389/fnmol.2018.00156] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/24/2018] [Indexed: 12/20/2022] Open
Abstract
Neurotrophins have been implicated in the pathophysiology of many neuropsychiatric diseases. Brain-derived neurotrophic factor (BDNF) is the most abundant and widely distributed neurotrophin in the brain. Its Val66Met polymorphism (refSNP Cluster Report: rs6265) is a common and functional single-nucleotide polymorphism (SNP) affecting the activity-dependent release of BDNF. BDNF Val66Met transgenic mice have been generated, which may provide further insight into the functional impact of this polymorphism in the brain. Considering the important role of BDNF in brain function, more than 1,100 genetic studies have investigated this polymorphism in the past 15 years. Although these studies have reported some encouraging positive findings initially, most of the findings cannot be replicated in following studies. These inconsistencies in BDNF Val66Met genetic studies may be attributed to many factors such as age, sex, environmental factors, ethnicity, genetic model used for analysis, and gene–gene interaction, which are discussed in this review. We also discuss the results of recent studies that have reported the novel functions of this polymorphism. Because many BDNF polymorphisms and non-genetic factors have been implicated in the complex traits of neuropsychiatric diseases, the conventional genetic association-based method is limited to address these complex interactions. Future studies should apply data mining and machine learning techniques to determine the genetic role of BDNF in neuropsychiatric diseases.
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Affiliation(s)
- Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
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16
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Lin E, Kuo PH, Liu YL, Yang AC, Tsai SJ. Transforming growth factor-β signaling pathway-associated genes SMAD2 and TGFBR2 are implicated in metabolic syndrome in a Taiwanese population. Sci Rep 2017; 7:13589. [PMID: 29051557 PMCID: PMC5648797 DOI: 10.1038/s41598-017-14025-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/05/2017] [Indexed: 01/18/2023] Open
Abstract
The transforming growth factor-β (TGF-β) signaling pathway and its relevant genes have been correlated with an increased risk of developing various hallmarks of metabolic syndrome (MetS). In this study, we assessed whether the TGF-β signaling pathway-associated genes of SMAD family member 2 (SMAD2), SMAD3, SMAD4, transforming growth factor beta 1 (TGFB1), TGFB2, TGFB3, transforming growth factor beta receptor 1 (TGFBR1), and TGFBR2 are associated with MetS and its individual components independently, through complex interactions, or both in a Taiwanese population. A total of 3,000 Taiwanese subjects from the Taiwan Biobank were assessed. Metabolic traits such as waist circumference, triglyceride, high-density lipoprotein cholesterol, systolic and diastolic blood pressure, and fasting glucose were measured. Our results showed a significant association of MetS with the two single nucleotide polymorphisms (SNPs) of SMAD2 rs11082639 and TGFBR2 rs3773651. The association of MetS with these SNPs remained significant after performing Bonferroni correction. Moreover, we identified the effect of SMAD2 rs11082639 on high waist circumference. We also found that an interaction between the SMAD2 rs11082639 and TGFBR2 rs3773651 SNPs influenced MetS. Our findings indicated that the TGF-β signaling pathway-associated genes of SMAD2 and TGFBR2 may contribute to the risk of MetS independently and through gene-gene interactions.
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Affiliation(s)
- Eugene Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
- Vita Genomics, Inc., Taipei, Taiwan.
- TickleFish Systems Corporation, Seattle, WA, USA.
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.
- Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan.
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Lin E, Kuo PH, Liu YL, Yang AC, Tsai SJ. Detection of susceptibility loci on APOA5 and COLEC12 associated with metabolic syndrome using a genome-wide association study in a Taiwanese population. Oncotarget 2017; 8:93349-93359. [PMID: 29212154 PMCID: PMC5706800 DOI: 10.18632/oncotarget.20967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022] Open
Abstract
Background Although the association of single nucleotide polymorphisms (SNPs) with metabolic syndrome (MetS) has been reported in various populations in several genome-wide association studies (GWAS), the data is not conclusive. In this GWAS study, we assessed whether SNPs are associated with MetS and its individual components independently and/or through complex interactions in a Taiwanese population. Methods A total of 10,300 Taiwanese subjects were assessed in this study. Metabolic traits such as waist circumference, triglyceride, high-density lipoprotein (HDL) cholesterol, systolic and diastolic blood pressure, and fasting glucose were measured. Results Our data showed an association of MetS at the genome-wide significance level (P < 8.6 x 10-8) with two SNPs, including the rs662799 SNP in the apolipoprotein A5 (APOA5) gene and the rs16944558 SNP in the collectin subfamily member 12 (COLEC12) gene. Moreover, we identified the effect of APOA5 rs662799 on triglyceride and HDL, the effect of rs1106475 in the actin filament associated protein 1 like 2 (AFAP1L2) gene on systolic blood pressure, and the effect of rs17667932 in the mediator complex subunit 30 (MED30) gene on fasting glucose. Additionally, we found that an interaction between the APOA5 rs662799 and COLEC12 rs16944558 SNPs influenced MetS, high triglyceride, and low HDL. Conclusions Our study indicates that the APOA5 and COLEC12 genes may contribute to the risk of MetS and its individual components independently as well as through gene-gene interactions.
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Affiliation(s)
- Eugene Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Vita Genomics, Inc., Taipei, Taiwan.,TickleFish Systems Corporation, Seattle, WA, USA
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan.,Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
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Lin E, Kuo PH, Liu YL, Yang AC, Kao CF, Tsai SJ. Effects of circadian clock genes and health-related behavior on metabolic syndrome in a Taiwanese population: Evidence from association and interaction analysis. PLoS One 2017; 12:e0173861. [PMID: 28296937 PMCID: PMC5352001 DOI: 10.1371/journal.pone.0173861] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/28/2017] [Indexed: 12/12/2022] Open
Abstract
Increased risk of developing metabolic syndrome (MetS) has been associated with the circadian clock genes. In this study, we assessed whether 29 circadian clock-related genes (including ADCYAP1, ARNTL, ARNTL2, BHLHE40, CLOCK, CRY1, CRY2, CSNK1D, CSNK1E, GSK3B, HCRTR2, KLF10, NFIL3, NPAS2, NR1D1, NR1D2, PER1, PER2, PER3, REV1, RORA, RORB, RORC, SENP3, SERPINE1, TIMELESS, TIPIN, VIP, and VIPR2) are associated with MetS and its individual components independently and/or through complex interactions in a Taiwanese population. We also analyzed the interactions between environmental factors and these genes in influencing MetS and its individual components. A total of 3,000 Taiwanese subjects from the Taiwan Biobank were assessed in this study. Metabolic traits such as waist circumference, triglyceride, high-density lipoprotein cholesterol, systolic and diastolic blood pressure, and fasting glucose were measured. Our data showed a nominal association of MetS with several single nucleotide polymorphisms (SNPs) in five key circadian clock genes including ARNTL, GSK3B, PER3, RORA, and RORB; but none of these SNPs persisted significantly after performing Bonferroni correction. Moreover, we identified the effect of GSK3B rs2199503 on high fasting glucose (P = 0.0002). Additionally, we found interactions among the ARNTL rs10832020, GSK3B rs2199503, PER3 rs10746473, RORA rs8034880, and RORB rs972902 SNPs influenced MetS (P < 0.001 ~ P = 0.002). Finally, we investigated the influence of interactions between ARNTL rs10832020, GSK3B rs2199503, PER3 rs10746473, and RORB rs972902 with environmental factors such as alcohol consumption, smoking status, and physical activity on MetS and its individual components (P < 0.001 ~ P = 0.002). Our study indicates that circadian clock genes such as ARNTL, GSK3B, PER3, RORA, and RORB genes may contribute to the risk of MetS independently as well as through gene-gene and gene-environment interactions.
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Affiliation(s)
- Eugene Lin
- Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Vita Genomics, Inc., Taipei, Taiwan
- TickleFish Systems Corporation, Seattle, Western Australia, United States of America
- * E-mail: (EL); (SJT)
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C. Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
| | - Chung-Feng Kao
- Department of Agronomy, College of Agriculture & Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
- * E-mail: (EL); (SJT)
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Lin CH, Lin E, Lane HY. Genetic Biomarkers on Age-Related Cognitive Decline. Front Psychiatry 2017; 8:247. [PMID: 29209239 PMCID: PMC5702307 DOI: 10.3389/fpsyt.2017.00247] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/07/2017] [Indexed: 12/29/2022] Open
Abstract
With ever-increasing elder populations, age-related cognitive decline, which is characterized as a gradual decline in cognitive capacity in the aging process, has turned out to be a mammoth public health concern. Since genetic information has become increasingly important to explore the biological mechanisms of cognitive decline, the search for genetic biomarkers of cognitive aging has received much attention. There is growing evidence that single-nucleotide polymorphisms (SNPs) within the ADAMTS9, BDNF, CASS4, COMT, CR1, DNMT3A, DTNBP1, REST, SRR, TOMM40, circadian clock, and Alzheimer's diseases-associated genes may contribute to susceptibility to cognitive aging. In this review, we first illustrated evidence of the genetic contribution to disease susceptibility to age-related cognitive decline in recent studies ranging from approaches of candidate genes to genome-wide association studies. We then surveyed a variety of association studies regarding age-related cognitive decline with consideration of gene-gene and gene-environment interactions. Finally, we highlighted their limitations and future directions. In light of advances in precision medicine and multi-omics technologies, future research in genomic medicine promises to lead to innovative ideas that are relevant to disease prevention and novel drugs for cognitive aging.
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Affiliation(s)
- Chieh-Hsin Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center for General Education, Cheng Shiu University, Kaohsiung, Taiwan
| | - Eugene Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Electrical Engineering, University of Washington, Seattle, WA, United States.,TickleFish Systems Corporation, Seattle, WA, United States
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Psychiatry, Brain Disease Research Center, China Medical University Hospital, Taichung, Taiwan
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