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Thorpe HHA, Fontanillas P, Pham BK, Meredith JJ, Jennings MV, Courchesne-Krak NS, Vilar-Ribó L, Bianchi SB, Mutz J, Elson SL, Khokhar JY, Abdellaoui A, Davis LK, Palmer AA, Sanchez-Roige S. Genome-wide association studies of coffee intake in UK/US participants of European ancestry uncover cohort-specific genetic associations. Neuropsychopharmacology 2024:10.1038/s41386-024-01870-x. [PMID: 38858598 DOI: 10.1038/s41386-024-01870-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 06/12/2024]
Abstract
Coffee is one of the most widely consumed beverages. We performed a genome-wide association study (GWAS) of coffee intake in US-based 23andMe participants (N = 130,153) and identified 7 significant loci, with many replicating in three multi-ancestral cohorts. We examined genetic correlations and performed a phenome-wide association study across hundreds of biomarkers, health, and lifestyle traits, then compared our results to the largest available GWAS of coffee intake from the UK Biobank (UKB; N = 334,659). We observed consistent positive genetic correlations with substance use and obesity in both cohorts. Other genetic correlations were discrepant, including positive genetic correlations between coffee intake and psychiatric illnesses, pain, and gastrointestinal traits in 23andMe that were absent or negative in the UKB, and genetic correlations with cognition that were negative in 23andMe but positive in the UKB. Phenome-wide association study using polygenic scores of coffee intake derived from 23andMe or UKB summary statistics also revealed consistent associations with increased odds of obesity- and red blood cell-related traits, but all other associations were cohort-specific. Our study shows that the genetics of coffee intake associate with substance use and obesity across cohorts, but also that GWAS performed in different populations could capture cultural differences in the relationship between behavior and genetics.
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Affiliation(s)
- Hayley H A Thorpe
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Benjamin K Pham
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Julian Mutz
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | | | - Jibran Y Khokhar
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lea K Davis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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Jee C, Batsaikhan E. JNK Signaling Positively Regulates Acute Ethanol Tolerance in C. elegans. Int J Mol Sci 2024; 25:6398. [PMID: 38928105 PMCID: PMC11203441 DOI: 10.3390/ijms25126398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Alcohol use disorder (AUD) is a chronic neurobehavioral condition characterized by a cycle of tolerance development, increased consumption, and reinstated craving and seeking behaviors during withdrawal. Understanding the intricate mechanisms of AUD necessitates reliable animal models reflecting its key features. Caenorhabditis elegans (C. elegans), with its conserved nervous system and genetic tractability, has emerged as a valuable model organism to study AUD. Here, we employ an ethanol vapor exposure model in Caenorhabditis elegans, recapitulating AUD features while maintaining high-throughput scalability. We demonstrate that ethanol vapor exposure induces intoxication-like behaviors, acute tolerance, and ethanol preference, akin to mammalian AUD traits. Leveraging this model, we elucidate the conserved role of c-jun N-terminal kinase (JNK) signaling in mediating acute ethanol tolerance. Mutants lacking JNK signaling components exhibit impaired tolerance development, highlighting JNK's positive regulation. Furthermore, we detect ethanol-induced JNK activation in C. elegans. Our findings underscore the utility of C. elegans with ethanol vapor exposure for studying AUD and offer novel insights into the molecular mechanisms underlying acute ethanol tolerance through JNK signaling.
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Affiliation(s)
- Changhoon Jee
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennesse Health Science Center, Memphis, TN 38163, USA;
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Jennings MV, Martínez-Magaña JJ, Courchesne-Krak NS, Cupertino RB, Vilar-Ribó L, Bianchi SB, Hatoum AS, Atkinson EG, Giusti-Rodriguez P, Montalvo-Ortiz JL, Gelernter J, Artigas MS, Elson SL, Edenberg HJ, Fontanillas P, Palmer AA, Sanchez-Roige S. A phenome-wide association and Mendelian randomisation study of alcohol use variants in a diverse cohort comprising over 3 million individuals. EBioMedicine 2024; 103:105086. [PMID: 38580523 PMCID: PMC11121167 DOI: 10.1016/j.ebiom.2024.105086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Alcohol consumption is associated with numerous negative social and health outcomes. These associations may be direct consequences of drinking, or they may reflect common genetic factors that influence both alcohol consumption and other outcomes. METHODS We performed exploratory phenome-wide association studies (PheWAS) of three of the best studied protective single nucleotide polymorphisms (SNPs) in genes encoding ethanol metabolising enzymes (ADH1B: rs1229984-T, rs2066702-A; ADH1C: rs698-T) using up to 1109 health outcomes across 28 phenotypic categories (e.g., substance-use, mental health, sleep, immune, cardiovascular, metabolic) from a diverse 23andMe cohort, including European (N ≤ 2,619,939), Latin American (N ≤ 446,646) and African American (N ≤ 146,776) populations to uncover new and perhaps unexpected associations. These SNPs have been consistently implicated by both candidate gene studies and genome-wide association studies of alcohol-related behaviours but have not been investigated in detail for other relevant phenotypes in a hypothesis-free approach in such a large cohort of multiple ancestries. To provide insight into potential causal effects of alcohol consumption on the outcomes significant in the PheWAS, we performed univariable two-sample and one-sample Mendelian randomisation (MR) analyses. FINDINGS The minor allele rs1229984-T, which is protective against alcohol behaviours, showed the highest number of PheWAS associations across the three cohorts (N = 232, European; N = 29, Latin American; N = 7, African American). rs1229984-T influenced multiple domains of health. We replicated associations with alcohol-related behaviours, mental and sleep conditions, and cardio-metabolic health. We also found associations with understudied traits related to neurological (migraines, epilepsy), immune (allergies), musculoskeletal (fibromyalgia), and reproductive health (preeclampsia). MR analyses identified evidence of causal effects of alcohol consumption on liability for 35 of these outcomes in the European cohort. INTERPRETATION Our work demonstrates that polymorphisms in genes encoding alcohol metabolising enzymes affect multiple domains of health beyond alcohol-related behaviours. Understanding the underlying mechanisms of these effects could have implications for treatments and preventative medicine. FUNDING MVJ, NCK, SBB, SSR and AAP were supported by T32IR5226 and 28IR-0070. SSR was also supported by NIDA DP1DA054394. NCK and RBC were also supported by R25MH081482. ASH was supported by funds from NIAAA K01AA030083. JLMO was supported by VA 1IK2CX002095. JLMO and JJMM were also supported by NIDA R21DA050160. JJMM was also supported by the Kavli Postdoctoral Award for Academic Diversity. EGA was supported by K01MH121659 from the NIMH/NIH, the Caroline Wiess Law Fund for Research in Molecular Medicine and the ARCO Foundation Young Teacher-Investigator Fund at Baylor College of Medicine. MSA was supported by the Instituto de Salud Carlos III and co-funded by the European Union Found: Fondo Social Europeo Plus (FSE+) (P19/01224, PI22/00464 and CP22/00128).
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Affiliation(s)
- Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - José Jaime Martínez-Magaña
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, Orange, West Haven, CT, USA
| | | | - Renata B Cupertino
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander S Hatoum
- Department of Psychology & Brain Sciences, Washington University in St. Louis, St Louis, MO, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Paola Giusti-Rodriguez
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Janitza L Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, Orange, West Haven, CT, USA; National Center of Posttraumatic Stress Disorder, VA CT Healthcare Center, West Haven, CT, USA
| | - Joel Gelernter
- VA CT Healthcare Center, Department Psychiatry, West Haven, CT, USA; Departments Psychiatry, Genetics, and Neuroscience, Yale Univ. School of Medicine, New Haven, CT, USA
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain; Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | | | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
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Waller C, Ho A, Batzler A, Geske J, Karpyak V, Biernacka J, Winham S. Genetic correlations of alcohol consumption and alcohol use disorder with sex hormone levels in females and males. RESEARCH SQUARE 2024:rs.3.rs-3944066. [PMID: 38464231 PMCID: PMC10925434 DOI: 10.21203/rs.3.rs-3944066/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Alcohol consumption behaviors and alcohol use disorder risk and presentation differ by sex, and these complex traits are associated with blood concentrations of the steroid sex hormones, testosterone and estradiol, and their regulatory binding proteins, sex hormone binding globulin (SHBG) and albumin. Genetic variation is associated with alcohol consumption and alcohol use disorder, as well as levels of steroid sex hormones and their binding proteins. Methods To assess the contribution of genetic factors to previously described phenotypic associations between alcohol-use traits and sex-hormone levels, we estimated genetic correlations (rg) using summary statistics from prior published, large sample size genome-wide association studies (GWAS) of alcohol consumption, alcohol dependence, testosterone, estradiol, SHBG, and albumin. Results For alcohol consumption, we observed positive genetic correlation (i.e. genetic effects in the same direction) with total testosterone in males (rg = 0.084, p = 0.007) and trends toward positive genetic correlation with bioavailable testosterone (rg = 0.060, p = 0.084) and SHBG in males (rg = 0.056, p = 0.086) and with albumin in a sex-combined cohort (rg = 0.082, p = 0.015); however in females, we observed positive genetic correlation with SHBG (rg = 0.089, p = 0.004) and a trend toward negative genetic correlation (i.e. genetic effects in opposite directions) with bioavailable testosterone (rg = -0.064, p = 0.032). For alcohol dependence, we observed a trend toward negative genetic correlation with total testosterone in females (rg = -0.106, p = 0.024) and positive genetic correlation with BMI-adjusted SHBG in males (rg = 0.119, p = 0.017). Several of these genetic correlations differed between females and males and were not in the same direction as the corresponding phenotypic associations. Conclusions Findings suggest that shared genetic effects may contribute to positive associations of alcohol consumption with albumin in both sexes, as well as positive associations between alcohol consumption and bioavailable testosterone and between alcohol dependence and SHBG in males. However, relative contributions of heritable and environmental factors to associations between alcohol-use traits and sex-hormone levels may differ by sex, with genetic factors contributing more in males and environmental factors contributing more in females.
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Miller AP, Gizer IR. Neurogenetic and multi-omic sources of overlap among sensation seeking, alcohol consumption, and alcohol use disorder. Addict Biol 2024; 29:e13365. [PMID: 38380706 PMCID: PMC10882188 DOI: 10.1111/adb.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/26/2023] [Accepted: 11/26/2023] [Indexed: 02/22/2024]
Abstract
Sensation seeking is bidirectionally associated with levels of alcohol consumption in both adult and adolescent samples, and shared neurobiological and genetic influences may in part explain these associations. Links between sensation seeking and alcohol use disorder (AUD) may primarily manifest via increased alcohol consumption rather than through direct effects on increasing problems and consequences. Here the overlap among sensation seeking, alcohol consumption, and AUD was examined using multivariate modelling approaches for genome-wide association study (GWAS) summary statistics in conjunction with neurobiologically informed analyses at multiple levels of investigation. Meta-analytic and genomic structural equation modelling (GenomicSEM) approaches were used to conduct GWAS of sensation seeking, alcohol consumption, and AUD. Resulting summary statistics were used in downstream analyses to examine shared brain tissue enrichment of heritability and genome-wide evidence of overlap (e.g., stratified GenomicSEM, RRHO, genetic correlations with neuroimaging phenotypes), and to identify genomic regions likely contributing to observed genetic overlap across traits (e.g., H-MAGMA and LAVA). Across approaches, results supported shared neurogenetic architecture between sensation seeking and alcohol consumption characterised by overlapping enrichment of genes expressed in midbrain and striatal tissues and variants associated with increased cortical surface area. Alcohol consumption and AUD evidenced overlap in relation to variants associated with decreased frontocortical thickness. Finally, genetic mediation models provided evidence of alcohol consumption mediating associations between sensation seeking and AUD. This study extends previous research by examining critical sources of neurogenetic and multi-omic overlap among sensation seeking, alcohol consumption, and AUD which may underlie observed phenotypic associations.
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Affiliation(s)
- Alex P. Miller
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Ian R. Gizer
- Department of Psychological SciencesUniversity of MissouriColumbiaMissouriUSA
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Ho B, Thompson A, Jorgensen AL, Pirmohamed M. Role of fatty liver index in risk-stratifying comorbid disease outcomes in non-alcoholic fatty liver disease. JHEP Rep 2023; 5:100896. [PMID: 37928746 PMCID: PMC10624587 DOI: 10.1016/j.jhepr.2023.100896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 11/07/2023] Open
Abstract
Background & Aims Population screening for non-alcoholic fatty liver disease (NAFLD) and associated comorbidities remains an unaddressed clinical need. We aimed to assess the utility of the fatty liver index (FLI) for risk stratification of NAFLD and related comorbidities using the UK Biobank. Methods Electronic health records and liver MRI-proton density fat fraction (PDFF) were used to define NAFLD cases. FLI was calculated and individuals with high alcohol intake and other liver diseases were excluded. Using listwise deletion analysis, the area under receiver-operating characteristic curve (AUROC) of FLI for NAFLD risk was determined. Thereafter, time-dependent covariate-adjusted Cox regression models were used to estimate FLI's risk stratification potential for comorbidities of interest. Results FLI was derived for 327,800 individuals with a median age of 58 (IQR 51.5-64.5), of whom 59.8% were females. Using Perspectum Diagnostics and AMRA protocols as references, FLI identified the risk of NAFLD with AUROCs (95% CI, n) of 0.858 (0.848-0.867, n = 7,566) and 0.851 (0.844-0.856, n = 10,777), respectively. Intermediate and high-risk FLI was associated with increased cardiometabolic and malignant disease. In the first 3 years, high-risk FLI conferred an increased risk (adjusted hazard ratio, 95% CI) of ischaemic heart disease (2.14, 1.94-2.36), hypertension (2.84, 2.70-2.98), type 2 diabetes mellitus (4.55, 4.04-5.12), dyslipidaemia (2.48, 2.32-2.64), ischaemic stroke (1.31, 1.20-1.42) and hepatic malignancy (1.69, 1.23-2.30). FLI was not associated with risk of extrahepatic malignancy but was associated with a higher risk of specific cancers (colon, upper gastrointestinal and breast). All-cause mortality was similarly stratified by FLI, independently of non-invasive fibrosis scores. Conclusions FLI identifies NAFLD and holds potential for the risk stratification of cardiometabolic and malignant disease outcomes (including some extrahepatic malignancies), as well as all-cause mortality. Its use in population screening for primary and secondary prevention of NAFLD should be considered. Impact and implications Our analysis using the UK Biobank study shows the potential of the fatty liver index as a risk stratification tool for identifying the risk of developing NAFLD, ischaemic heart disease, ischaemic stroke, type 2 diabetes mellitus, hypertension, hyperlipidaemia, hepatic malignancy, specific metabolism-related malignancies and all-cause mortality. These results suggest that the fatty liver index should be considered as a non-invasive steatosis score that may help guide primary prevention strategies for NAFLD and related outcomes.
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Affiliation(s)
- Brian Ho
- Wolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andrew Thompson
- Wolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Health Analytics, Lane Clark & Peacock LLP, London, UK
| | - Andrea L Jorgensen
- Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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O'Farrell F, Aleyakpo B, Mustafa R, Jiang X, Pinto RC, Elliott P, Tzoulaki I, Dehghan A, Loh SHY, Barclay JW, Martins LM, Pazoki R. Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis. Sci Rep 2023; 13:20616. [PMID: 37996473 PMCID: PMC10667215 DOI: 10.1038/s41598-023-47371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD.
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Affiliation(s)
- Felix O'Farrell
- Cardiovascular and Metabolic Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, London, UB8 3PH, UK
| | | | - Rima Mustafa
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- UK Dementia Research Institute, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Xiyun Jiang
- Cardiovascular and Metabolic Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, London, UB8 3PH, UK
| | - Rui Climaco Pinto
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- UK Dementia Research Institute, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- British Heart Foundation Centre of Research Excellence, Imperial College London, Du Cane Road, W12 0NN, UK
- National Institute for Health Research, Imperial Biomedical Research Centre, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Health Data Research UK at Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Centre for Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
- UK Dementia Research Institute, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Samantha H Y Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Jeff W Barclay
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - L Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Raha Pazoki
- Cardiovascular and Metabolic Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, London, UB8 3PH, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- Division of Biomedical Sciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University, London, UB8 3PH, UK.
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8
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Thorpe HHA, Fontanillas P, Pham BK, Meredith JJ, Jennings MV, Courchesne-Krak NS, Vilar-Ribó L, Bianchi SB, Mutz J, Elson SL, Khokhar JY, Abdellaoui A, Davis LK, Palmer AA, Sanchez-Roige S. Genome-Wide Association Studies of Coffee Intake in UK/US Participants of European Ancestry Uncover Gene-Cohort Influences. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.09.23295284. [PMID: 37745582 PMCID: PMC10516045 DOI: 10.1101/2023.09.09.23295284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Coffee is one of the most widely consumed beverages. We performed a genome-wide association study (GWAS) of coffee intake in US-based 23andMe participants (N=130,153) and identified 7 significant loci, with many replicating in three multi-ancestral cohorts. We examined genetic correlations and performed a phenome-wide association study across thousands of biomarkers and health and lifestyle traits, then compared our results to the largest available GWAS of coffee intake from UK Biobank (UKB; N=334,659). The results of these two GWAS were highly discrepant. We observed positive genetic correlations between coffee intake and psychiatric illnesses, pain, and gastrointestinal traits in 23andMe that were absent or negative in UKB. Genetic correlations with cognition were negative in 23andMe but positive in UKB. The only consistent observations were positive genetic correlations with substance use and obesity. Our study shows that GWAS in different cohorts could capture cultural differences in the relationship between behavior and genetics.
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Affiliation(s)
- Hayley H A Thorpe
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Benjamin K Pham
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Mariela V Jennings
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sevim B Bianchi
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Julian Mutz
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - 23andMe Research Team
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Sarah L Elson
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Jibran Y Khokhar
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lea K Davis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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9
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Miller AP, Gizer IR. Neurogenetic and multi-omic sources of overlap among sensation seeking, alcohol consumption, and alcohol use disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.30.23290733. [PMID: 37333128 PMCID: PMC10274973 DOI: 10.1101/2023.05.30.23290733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Sensation seeking is bidirectionally associated with levels of alcohol consumption in both adult and adolescent samples and shared neurobiological and genetic influences may in part explain this association. Links between sensation seeking and alcohol use disorder (AUD) may primarily manifest via increased alcohol consumption rather than through direct effects on increasing problems and consequences. Here the overlap between sensation seeking, alcohol consumption, and AUD was examined using multivariate modeling approaches for genome-wide association study (GWAS) summary statistics in conjunction with neurobiologically-informed analyses at multiple levels of investigation. Meta-analytic and genomic structural equation modeling (GenomicSEM) approaches were used to conduct GWAS of sensation seeking, alcohol consumption, and AUD. Resulting summary statistics were used in downstream analyses to examine shared brain tissue enrichment of heritability and genome-wide evidence of overlap (e.g., stratified GenomicSEM, RRHO, genetic correlations with neuroimaging phenotypes) and to identify genomic regions likely contributing to observed genetic overlap across traits (e.g., HMAGMA, LAVA). Across approaches, results supported shared neurogenetic architecture between sensation seeking and alcohol consumption characterized by overlapping enrichment of genes expressed in midbrain and striatal tissues and variants associated with increased cortical surface area. Alcohol consumption and AUD evidenced overlap in relation to variants associated with decreased frontocortical thickness. Finally, genetic mediation models provided evidence of alcohol consumption mediating associations between sensation seeking and AUD. This study extends previous research by examining critical sources of neurogenetic and multi-omic overlap among sensation seeking, alcohol consumption, and AUD which may underlie observed phenotypic associations.
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Affiliation(s)
- Alex P. Miller
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Ian R. Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, MO, United States
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10
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Seemiller LR, Goldberg LR, Garcia-Trevizo P, Gould TJ. Interstrain differences in adolescent fear conditioning after acute alcohol exposure. Brain Res Bull 2023; 194:35-44. [PMID: 36681252 PMCID: PMC10921434 DOI: 10.1016/j.brainresbull.2023.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Adolescent sensitivity to alcohol is a predictor of continued alcohol use and misuse later in life. Thus, it is important to understand the many factors that can impact alcohol sensitivity. Data from our laboratory suggested that susceptibility to alcohol-associated contextual fear learning deficits varied among adolescent and adult mice from two mouse strains. To investigate the extent of genetic background's influences on adolescent learning after alcohol exposure, we examined how 9 inbred mouse strains differed in vulnerability to alcohol-induced contextual and cued fear conditioning deficits. We demonstrated significant strain- and sex-dependent effects of acute alcohol exposure on adolescent fear learning, with alcohol having most pronounced effects on contextual fear learning. Female adolescents were more susceptible than males to alcohol-induced impairments in contextual, but not cued, fear learning, independent of genetic background. Heritability for contextual and cued fear learning after alcohol exposure was estimated to be 31 % and 18 %, respectively. Learning data were compared to Blood Ethanol Concentrations (BEC) to assess whether strain differences in alcohol metabolism contributed to strain differences in learning after alcohol exposure. There were no clear relationships between BEC and learning outcomes, suggesting that strains differed in learning outcomes for reasons other than strain differences in alcohol metabolism. Genetic analyses revealed polymorphisms across strains in notable genes, such as Chrna7, a promising genetic candidate for susceptibility to alcohol-induced fear conditioning deficits. These results are the first to demonstrate the impact of genetic background on alcohol-associated fear learning deficits during adolescence and suggest that the mechanisms underlying this sensitivity are distinct from alcohol metabolism.
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Affiliation(s)
- Laurel R Seemiller
- Department of Biobehavioral Health, Penn State University, University Park, PA, USA
| | - Lisa R Goldberg
- Department of Biobehavioral Health, Penn State University, University Park, PA, USA
| | | | - Thomas J Gould
- Department of Biobehavioral Health, Penn State University, University Park, PA, USA.
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11
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A Genome-Wide Association Study Reveals a BDNF-Centered Molecular Network Associated with Alcohol Dependence and Related Clinical Measures. Biomedicines 2022; 10:biomedicines10123007. [PMID: 36551763 PMCID: PMC9775455 DOI: 10.3390/biomedicines10123007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33 × 10-8 calculated with the Yates-corrected χ2 test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWASs of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network, where BDNF is the most significant hub gene. This study indicates that several genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The study also reveals a central role of BDNF in the pathogenesis of AD.
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12
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Yu X, Lophatananon A, Mekli K, Burns A, Muir KR, Guo H. A suggested shared aetiology of dementia - a colocalization study. Neurobiol Aging 2022; 117:71-82. [PMID: 35675752 DOI: 10.1016/j.neurobiolaging.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/11/2022]
Abstract
Identification of shared causal genes between dementia and its related clinical outcomes can help understand shared aetiology and multimorbidity surrounding dementia. We performed the HyPrColoc colocalization analysis to detect possible shared causal genes between dementia or Alzheimer's disease (AD) and 5 selected traits: stroke, diabetes, atherosclerosis, cholesterol level, and alcohol consumption within 601 dementia or AD associated genetic regions using summary results of the UK Biobank genome-wide association studies. Functional analysis was performed on the candidate causal genes to explore potential biological pathways. Rs150562240 in the LPIN3 gene was identified as a candidate shared causal variant across dementia, AD and atherosclerosis. Evidence for pairwise colocalization between dementia and stroke, dementia (or AD) and atherosclerosis, and dementia (or AD) and diabetes was found in 2, 6 and 2 genetic regions respectively. Colocalization signals between diabetes and the other 3 non-dementia/AD traits were detected in 5 regions. The colocalization evidence shown in our study suggested shared aetiology between dementia and related diseases such as stroke, atherosclerosis, and diabetes.
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Affiliation(s)
- Xinzhu Yu
- Centre for Biostatistics, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Artitaya Lophatananon
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Krisztina Mekli
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Alistair Burns
- Division of Neuroscience and Experimental Psychology, School of Social Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Kenneth R Muir
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Hui Guo
- Centre for Biostatistics, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK.
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13
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Chang XW, Sun Y, Muhai JN, Li YY, Chen Y, Lu L, Chang SH, Shi J. Common and distinguishing genetic factors for substance use behavior and disorder: an integrated analysis of genomic and transcriptomic studies from both human and animal studies. Addiction 2022; 117:2515-2529. [PMID: 35491750 DOI: 10.1111/add.15908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Genomic and transcriptomic findings greatly broaden the biological knowledge regarding substance use. However, systematic convergence and comparison evidence of genome-wide findings is lacking for substance use. Here, we combined all the genome-wide findings from both substance use behavior and disorder (SUBD) and identified common and distinguishing genetic factors for different SUBDs. METHODS Systemic literature search for genome-wide association (GWAS) and RNA-seq studies of alcohol/nicotine/drug use behavior (partially meets or not reported diagnostic criteria) and alcohol use behavior and disorder (AUBD), nicotine use behavior and disorder (NUBD) and drug use behavior and disorder (DUBD) was performed using PubMed and the GWAS catalog. Drug use was focused upon cannabis, opioid, cocaine and methamphetamine use. GWAS studies required case-control or case/cohort samples. RNA-seq studies were based on brain tissues. The genes which contained significant single nucleotide polymorphism (P ≤ 1 × 10-6 ) in GWAS and reported as significant in RNA-seq studies were extracted. Pathway enrichment was performed by using Metascape. Gene interaction networks were identified by using the Protein Interaction Network Analysis database. RESULTS Total SUBD-related 2910 genes were extracted from 75 GWAS studies (2 773 889 participants) and 17 RNA-seq studies. By overlapping the genes and pathways of AUBD, NUBD and DUBD, four shared genes (CACNB2, GRIN2B, PLXDC2 and PKNOX2), four shared pathways [two Gene Ontology (GO) terms of 'modulation of chemical synaptic transmission', 'regulation of trans-synaptic signaling', two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of 'dopaminergic synapse', 'cocaine addiction'] were identified (significantly higher than random, P < 1 × 10-5 ). The top shared KEGG pathways (Benjamini-Hochberg-corrected P-value < 0.05) in the pairwise comparison of AUBD versus DUBD, NUBD versus DUBD, AUBD versus NUBD were 'Epstein-Barr virus infection', 'protein processing in endoplasmic reticulum' and 'neuroactive ligand-receptor interaction', respectively. We also identified substance-specific genetic factors: i.e. ADH1B and ALDH2 were unique for AUBD, while CHRNA3 and CHRNA4 were unique for NUBD. CONCLUSIONS This systematic review identifies the shared and unique genes and pathways for alcohol, nicotine and drug use behaviors and disorders at the genome-wide level and highlights critical biological processes for the common and distinguishing vulnerability of substance use behaviors and disorders.
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Affiliation(s)
- Xiang-Wen Chang
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Yan Sun
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Jia-Na Muhai
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Yang-Yang Li
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Yun Chen
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Lin Lu
- National Institute on Drug Dependence, Peking University, Beijing, China.,Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Su-Hua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jie Shi
- National Institute on Drug Dependence, Peking University, Beijing, China.,Beijing Key Laboratory of Drug Dependence Research, Peking University, Beijing, China.,The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China.,The Key Laboratory for Neuroscience of the Ministry of Education and Health, Peking University, Beijing, China
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14
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Hou Z, Ding Q, Li Y, Zhao Z, Yan F, Li Y, Wang X, Xu J, Chen W, Wu G, Ruan X, Zhao L. Intestinal epithelial β Klotho is a critical protective factor in alcohol-induced intestinal barrier dysfunction and liver injury. EBioMedicine 2022; 82:104181. [PMID: 35908416 PMCID: PMC9352463 DOI: 10.1016/j.ebiom.2022.104181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 10/26/2022] Open
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15
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The potential effects of HECTD4 variants on fasting glucose and triglyceride levels in relation to prevalence of type 2 diabetes based on alcohol intake. Arch Toxicol 2022; 96:2487-2499. [PMID: 35713687 PMCID: PMC9325801 DOI: 10.1007/s00204-022-03325-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022]
Abstract
Excessive alcohol intake is an important cause of major public health problem in East Asian countries. Growing evidence suggests that genetic factors are associated with alcohol consumption and the risk for alcohol-associated disease, and these factors contribute to the risk of developing chronic diseases, including diabetes. This study aims to investigate the association of type 2 diabetes with genetic polymorphisms within HECTD4 based on alcohol exposure. We performed a genome-wide association study involving the cohorts of the KoGES-HEXA study (n = 50,028) and Ansan and Ansung study (n = 7,980), both of which are prospective cohort studies in Korea. The top three single-nucleotide polymorphisms (SNPs) of the HECTD4 gene, specifically rs77768175, rs2074356 and rs11066280, were found to be significantly associated with alcohol consumption. We found that individuals carrying the variant allele in these SNPs had lower fasting blood glucose, triglyceride, and GGT levels than those with the wild-type allele. Multiple logistic regression showed that statistically significant associations of HECTD4 gene polymorphisms with an increased risk of type 2 diabetes were found in drinkers. Namely, these SNPs were associated with decreased odds of diabetes in the presence of alcohol consumption. As a result of examining the effect of alcohol on the expression of the HECTD4 gene, ethanol increased the expression of HECTD4 in cells, but the level was decreased by NAC treatment. Similar results were obtained from liver samples of mice treated with alcohol. Moreover, a loss of HECTD4 resulted in reduced levels of CYP2E1 and lipogenic gene expression in ethanol-treated cells, while the level of ALDH2 expression increased, indicating a reduction in ethanol-induced hepatotoxicity.
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16
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Wang C, Martins-Bach AB, Alfaro-Almagro F, Douaud G, Klein JC, Llera A, Fiscone C, Bowtell R, Elliott LT, Smith SM, Tendler BC, Miller KL. Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging. Nat Neurosci 2022; 25:818-831. [PMID: 35606419 PMCID: PMC9174052 DOI: 10.1038/s41593-022-01074-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/11/2022] [Indexed: 12/17/2022]
Abstract
A key aim in epidemiological neuroscience is identification of markers to assess brain health and monitor therapeutic interventions. Quantitative susceptibility mapping (QSM) is an emerging magnetic resonance imaging technique that measures tissue magnetic susceptibility and has been shown to detect pathological changes in tissue iron, myelin and calcification. We present an open resource of QSM-based imaging measures of multiple brain structures in 35,273 individuals from the UK Biobank prospective epidemiological study. We identify statistically significant associations of 251 phenotypes with magnetic susceptibility that include body iron, disease, diet and alcohol consumption. Genome-wide associations relate magnetic susceptibility to 76 replicating clusters of genetic variants with biological functions involving iron, calcium, myelin and extracellular matrix. These patterns of associations include relationships that are unique to QSM, in particular being complementary to T2* signal decay time measures. These new imaging phenotypes are being integrated into the core UK Biobank measures provided to researchers worldwide, creating the potential to discover new, non-invasive markers of brain health.
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Affiliation(s)
- Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Aurea B Martins-Bach
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Fidel Alfaro-Almagro
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Gwenaëlle Douaud
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Johannes C Klein
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Alberto Llera
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Nijmegen, the Netherlands
| | - Cristiana Fiscone
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Richard Bowtell
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Lloyd T Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Benjamin C Tendler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
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17
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Schaschl H, Göllner T, Morris DL. Positive selection acts on regulatory genetic variants in populations of European ancestry that affect ALDH2 gene expression. Sci Rep 2022; 12:4563. [PMID: 35296751 PMCID: PMC8927298 DOI: 10.1038/s41598-022-08588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
ALDH2 is a key enzyme in alcohol metabolism that protects cells from acetaldehyde toxicity. Using iHS, iSAFE and FST statistics, we identified regulatory acting variants affecting ALDH2 gene expression under positive selection in populations of European ancestry. Several SNPs (rs3184504, rs4766578, rs10774625, rs597808, rs653178, rs847892, rs2013002) that function as eQTLs for ALDH2 in various tissues showed evidence of strong positive selection. Very large pairwise FST values indicated high genetic differentiation at these loci between populations of European ancestry and populations of other global ancestries. Estimating the timing of positive selection on the beneficial alleles suggests that these variants were recently adapted approximately 3000-3700 years ago. The derived beneficial alleles are in complete linkage disequilibrium with the derived ALDH2 promoter variant rs886205, which is associated with higher transcriptional activity. The SNPs rs4766578 and rs847892 are located in binding sequences for the transcription factor HNF4A, which is an important regulatory element of ALDH2 gene expression. In contrast to the missense variant ALDH2 rs671 (ALDH2*2), which is common only in East Asian populations and is associated with greatly reduced enzyme activity and alcohol intolerance, the beneficial alleles of the regulatory variants identified in this study are associated with increased expression of ALDH2. This suggests adaptation of Europeans to higher alcohol consumption.
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Affiliation(s)
- Helmut Schaschl
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Tobias Göllner
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - David L Morris
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, Great Maze Pond, London, SE1 9RT, UK
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18
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Salim C, Kan AK, Batsaikhan E, Patterson EC, Jee C. Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. Sci Rep 2022; 12:1804. [PMID: 35110557 PMCID: PMC8810865 DOI: 10.1038/s41598-022-05256-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
Despite the catastrophic consequences of alcohol abuse, alcohol use disorders (AUD) and comorbidities continue to strain the healthcare system, largely due to the effects of alcohol-seeking behavior. An improved understanding of the molecular basis of alcohol seeking will lead to enriched treatments for these disorders. Compulsive alcohol seeking is characterized by an imbalance between the superior drive to consume alcohol and the disruption or erosion in control of alcohol use. To model the development of compulsive engagement in alcohol seeking, we simultaneously exploited two distinct and conflicting Caenorhabditis elegans behavioral programs, ethanol preference and avoidance of aversive stimulus. We demonstrate that the C. elegans model recapitulated the pivotal features of compulsive alcohol seeking in mammals, specifically repeated attempts, endurance, and finally aversion-resistant alcohol seeking. We found that neuropeptide signaling via SEB-3, a CRF receptor-like GPCR, facilitates the development of ethanol preference and compels animals to seek ethanol compulsively. Furthermore, our functional genomic approach and behavioral elucidation suggest that the SEB-3 regulates another neuropeptidergic signaling, the neurokinin receptor orthologue TKR-1, to facilitate compulsive ethanol-seeking behavior.
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Affiliation(s)
- Chinnu Salim
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Ann Ke Kan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Enkhzul Batsaikhan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - E Clare Patterson
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Changhoon Jee
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA.
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19
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Indirect Genetic Effects of ADIPOQ Variants on Lipid Levels in a Sibling Study of a Rural Chinese Population. Genes (Basel) 2022; 13:genes13010161. [PMID: 35052501 PMCID: PMC8774628 DOI: 10.3390/genes13010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 01/25/2023] Open
Abstract
Variations in lipid levels are the result of combinations of genetic and environmental factors. We aim to investigate the indirect effect between siblings of the three polymorphisms of ADIPOQ on serum lipid levels in rural Chinese populations. A total of 2571 sibling pairs were enrolled as study participants. A generalized estimating equation was used to accommodate a family-based design. We used stratified analysis to detect sex combination differences in the indirect genetic effect. We found a significant association between the number of altered risk alleles of rs182052 and ego lipid levels of TG (β = 0.177, P = 0.003), TC (β = 0.140, P = 0.004) and LDL-C (β = 0.098, P = 0.014). Ego and altered genotypes of rs182052 demonstrated a joint effect on ego lipid levels of TC (β = 0.212, P = 0.019), HDL-C (β = 0.099, P = 0.002) and LDL-C (β = 0.177, P = 0.013) in recessive inheritance mode. In opposite-sex siblings, the altered GG genotype of rs182052 increased the ego lipid levels. Thus, our findings demonstrate that ADIPOQ has an indirect genetic effect on lipid levels in sibling pairs, and there are sex-combination differences in the indirect genetic effect in siblings.
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20
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Zhang H, Lu D, Li Q, Lu F, Zhang J, Wang Z, Lu X, Wang J. Identification of Six Prognostic Genes in EGFR-Mutant Lung Adenocarcinoma Using Structure Network Algorithms. Front Genet 2021; 12:755245. [PMID: 34868228 PMCID: PMC8635158 DOI: 10.3389/fgene.2021.755245] [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: 08/08/2021] [Accepted: 10/25/2021] [Indexed: 01/31/2023] Open
Abstract
This study aims to determine hub genes related to the incidence and prognosis of EGFR-mutant (MT) lung adenocarcinoma (LUAD) with weighted gene coexpression network analysis (WGCNA). From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we used 253 EGFR-MT LUAD samples and 38 normal lung tissue samples. At the same time, GSE19188 was additionally included to verify the accuracy of the predicted gene. To discover differentially expressed genes (DEGs), the R package “limma” was used. The R packages “WGCNA” and “survival” were used to perform WGCNA and survival analyses, respectively. The functional analysis was carried out with the R package “clusterProfiler.” In total, 1450 EGFR-MT–specific DEGs were found, and 7 tumor-related modules were marked with WGCNA. We found 6 hub genes in DEGs that overlapped with the tumor-related modules, and the overexpression level of B3GNT3 was significantly associated with the worse OS (overall survival) of the EGFR-MT LUAD patients (p < 0.05). Functional analysis of the hub genes showed the metabolism and protein synthesis–related terms added value. In conclusion, we used WGCNA to identify hub genes in the development of EGFR-MT LUAD. The established prognostic factors could be used as clinical biomarkers. To confirm the mechanism of those genes in EGFR-MT LUAD, further molecular research is required.
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Affiliation(s)
- Haomin Zhang
- Department of Hematology, The Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Disease, Beijing, China
| | - Di Lu
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Qinglun Li
- College of Science, University of Shanghai for Science and Technology, Beijing, China
| | - Fengfeng Lu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Key Laboratory of Neuropsychopharmacology, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Jundong Zhang
- Department of Hematology, The Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Disease, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Zining Wang
- Department of Hematology, The Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Disease, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Xuechun Lu
- Department of Hematology, The Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Disease, Beijing, China
| | - Jinliang Wang
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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21
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Lira SS, Ahammad I. A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. Sci Rep 2021; 11:23212. [PMID: 34853389 PMCID: PMC8636637 DOI: 10.1038/s41598-021-02715-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
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Affiliation(s)
- Samia Sultana Lira
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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22
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Abstract
Substance use disorders (SUDs) are conditions in which the use of legal or illegal substances, such as nicotine, alcohol or opioids, results in clinical and functional impairment. SUDs and, more generally, substance use are genetically complex traits that are enormously costly on an individual and societal basis. The past few years have seen remarkable progress in our understanding of the genetics, and therefore the biology, of substance use and abuse. Various studies - including of well-defined phenotypes in deeply phenotyped samples, as well as broadly defined phenotypes in meta-analysis and biobank samples - have revealed multiple risk loci for these common traits. A key emerging insight from this work establishes a biological and genetic distinction between quantity and/or frequency measures of substance use (which may involve low levels of use without dependence), versus symptoms related to physical dependence.
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23
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Fedorenko OY, Mikhalitskaya EV, Toshchakova VA, Loonen AJM, Bokhan NA, Ivanova SA. Association of PIP4K2A Polymorphisms with Alcohol Use Disorder. Genes (Basel) 2021; 12:genes12101642. [PMID: 34681036 PMCID: PMC8535504 DOI: 10.3390/genes12101642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Alcohol use disorder (AUD) not only influences individuals and families but also has a lasting social impact on communities at the national level. Dopaminergic neurotransmission is involved in excessive alcohol consumption. Phosphatidylinositol-5-phosphate-4-kinase type 2 α (PIP4K2A) plays an important role in the regulation of ascending dopamine pathways. In this study; we determined possible associations between nine polymorphisms in PIP4K2A and AUD in Russian men. Methods: 279 Russian men with AUD were investigated. The control group consisted of 222 healthy men from the general Russian population. Genotyping of DNA samples for nine polymorphic variants of PIP4K2A was carried out by the Applied Biosystems™ QuantStudio™ 5 Real-Time PCR System with use of the TaqMan1 Validated SNP Genotyping Assay (Applied Biosystems; CIIIA). Results: Carriage of the PIP4K2A rs2230469*TT/T genotype/allele was a relative risk factor for developing AUD in men (p = 0.026 and p = 0.0084 accordingly). Moreover; men with AUD had a higher frequency of PIP4K2A rs746203*T allele (p = 0.023) compared to healthy men. Conclusions: For the first time; we demonstrated different PIP4K2A polymorphisms to be associated with AUD presumably due to dopamine system modulation resulting from regulation of the lateral habenula.
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Affiliation(s)
- Olga Yu. Fedorenko
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia; (E.V.M.); (V.A.T.); (N.A.B.); (S.A.I.)
- Division for Control and Diagnostics, School of Non-Destructive Testing and Security, National Research Tomsk Polytechnic University, 634050 Tomsk, Russia
- Correspondence:
| | - Ekaterina V. Mikhalitskaya
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia; (E.V.M.); (V.A.T.); (N.A.B.); (S.A.I.)
| | - Valentina A. Toshchakova
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia; (E.V.M.); (V.A.T.); (N.A.B.); (S.A.I.)
| | - Anton J. M. Loonen
- PharmacoTherapy, Epidemiology and Economics, Groningen Research Institute of Pharmacy, University of Groningen, 9713AV Groningen, The Netherlands;
| | - Nikolay A. Bokhan
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia; (E.V.M.); (V.A.T.); (N.A.B.); (S.A.I.)
- Department of Psychotherapy and Psychological Counseling, National Research Tomsk State University, 634050 Tomsk, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, 634050 Tomsk, Russia
| | - Svetlana A. Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia; (E.V.M.); (V.A.T.); (N.A.B.); (S.A.I.)
- Division for Control and Diagnostics, School of Non-Destructive Testing and Security, National Research Tomsk Polytechnic University, 634050 Tomsk, Russia
- Department of Psychiatry, Addictology and Psychotherapy, Siberian State Medical University, 634050 Tomsk, Russia
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24
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Exploring the Role of Alcohol Metabolizing Genotypes in a 12-Week Clinical Trial of Naltrexone for Alcohol Use Disorder. Biomolecules 2021; 11:biom11101495. [PMID: 34680127 PMCID: PMC8533258 DOI: 10.3390/biom11101495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 10/03/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The efficacy of naltrexone in the treatment of alcohol use disorder (AUD) has been associated with a set of variables not directly related with the expression of opioid receptors. All the variables have been found to be highly associated with AUD itself or more severe clinical levels of AUD. Objectives: Given the high association between alcohol metabolizing enzymes (AME) and the outcome of AUD, the present study aims to investigate the role of AME genotype variants in the treatment of AUD with naltrexone. Methods: We carried out a 12-week longitudinal clinical trial based on the treatment of AUD patients with naltrexone (N = 101), stratified by different alcohol metabolization genotypes. Genotyping was performed after the inclusion of the patients in the study, based on the individual presence of single nucleotide polymorphisms (SNPs) in the ADH (alcohol dehydrogenase)1B (ADH1B*2 and ADH1B*3), ADH1C (ADHC*1) and ALDH (aldehyde dehydrogenase) 2 (ALDH2*2) genes. The outcome of alcohol use has been monitored employing the timeline follow-back during the treatment. Results: The ADH1C*1 (Ile350Val, rs698) and ALDH2*2 (Glu504Lys, rs671) polymorphisms were associated with a better response to naltrexone treatment, whereas the ADH1B*3 (Arg370Cys, rs2066702) allelic variant showed a negative outcome. Conclusions: The present study explores a genomic setting for the treatment of AUD with naltrexone. According to our findings, the association between ADH1C*1 and ALDH2*2 variants and better outcomes suggests a successful treatment, whereas the ADH1B*3 mutated allele might lead to an unsuccessful treatment. Further studies should be performed to investigate the relationship between alcohol metabolizing genotypes, the family history of alcohol use disorders and the effect of naltrexone on the outcomes. Genotyping may be a valuable tool for precision-medicine and individualized approach, especially in the context of alcohol use disorders. The small number of subjects was the main limitation of the present study.
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25
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Seemiller LR, Gould TJ. Adult and adolescent C57BL/6J and DBA/2J mice are differentially susceptible to fear learning deficits after acute ethanol or MK-801 treatment. Behav Brain Res 2021; 410:113351. [PMID: 33974921 PMCID: PMC8403488 DOI: 10.1016/j.bbr.2021.113351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022]
Abstract
Ethanol and other drugs of abuse disrupt learning and memory processes, creating problems associated with drug use and addiction. Understanding individual factors that determine susceptibility to drug-induced cognitive deficits, such as genetic background, age, and sex, is important for prevention and treatment. Comparison of adolescent and adult mice of both sexes across inbred mouse strains can reveal age, sex, and genetic contributions to phenotypes. We treated adolescent and adult, male and female, C57BL/6J and DBA/2J inbred mice with ethanol (1 g/kg or 1.5 g/kg) or MK-801 (0.05 mg/kg or 0.1 mg/kg), an NMDA receptor antagonist, prior to fear conditioning training. Contextual and cued fear retention were tested one day and eight or nine days after training. After ethanol exposure, adult C57BL/6J mice experienced greater deficits in contextual learning than adult DBA/2J mice. C57BL/6 J adolescents were less susceptible to ethanol-induced contextual learning disruptions than C57BL/6J adults, and adolescent males of both strains exhibited greater ethanol-induced contextual learning deficits than adolescent females. After MK-801 exposure, adolescent C57BL/6J mice experienced more severe contextual learning deficits than adolescent DBA/2J mice. Both ethanol and MK-801 had greater effects on contextual learning than cued learning. Collectively, we demonstrate that genetic background contributes to contextual and cued learning outcomes after ethanol or MK-801 exposure. Further, we report age-dependent drug sensitivities that are strain-, sex-, and drug-specific, suggesting that age, sex, and genetic background interact to determine contextual and cued learning impairments after ethanol or MK-801 exposure.
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Affiliation(s)
- L R Seemiller
- Department of Biobehavioral Health, Penn State University, 219 Biobehavioral Health Building, University Park, PA, 16801, United States
| | - T J Gould
- Department of Biobehavioral Health, Penn State University, 219 Biobehavioral Health Building, University Park, PA, 16801, United States.
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26
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Thompson A, King K, Morris AP, Pirmohamed M. Assessing the impact of alcohol consumption on the genetic contribution to mean corpuscular volume. Hum Mol Genet 2021; 30:2040-2051. [PMID: 34104963 PMCID: PMC8522631 DOI: 10.1093/hmg/ddab147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
The relationship between the genetic loci that influence mean corpuscular volume (MCV) and those associated with excess alcohol drinking are unknown. We used white British participants from the UK Biobank (n = 362 595) to assess the association between alcohol consumption and MCV, and whether this was modulated by genetic factors. Multivariable regression was applied to identify predictors of MCV. GWAS, with and without stratification for alcohol consumption, determined how genetic variants influence MCV. SNPs in ADH1B, ADH1C and ALDH1B were used to construct a genetic score to test the assumption that acetaldehyde formation is an important determinant of MCV. Additional investigations using mendelian randomisation and phenome-wide association analysis were conducted. Increasing alcohol consumption by 40 g/week resulted in a 0.30% (95% CI: 0.30 to 0.31%) increase in MCV (P < 1.0x10-320). Unstratified (irrespective of alcohol intake) GWAS identified 212 loci associated with MCV, of which 108 were novel. There was no heterogeneity of allelic effects by drinking status. No association was found between MCV and the genetic score generated from alcohol metabolising genes. Mendelian randomisation demonstrated a causal effect for alcohol on MCV. Seventy-one SNP-outcome pairs reached statistical significance in phenome-wide association analysis, with evidence of shared genetic architecture for MCV and thyroid dysfunction, and mineral metabolism disorders. MCV increases linearly with alcohol intake in a causal manner. Many genetic loci influence MCV, with new loci identified in this analysis that provide novel biological insights. However, there was no interaction between alcohol consumption and the allelic variants associated with MCV.
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Affiliation(s)
- Andrew Thompson
- Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,MRC Centre for Drug Safety Science, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Liverpool Centre for Alcohol Research, University of Liverpool, Liverpool, UK
| | - Katharine King
- Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,MRC Centre for Drug Safety Science, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK.,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,MRC Centre for Drug Safety Science, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Liverpool Centre for Alcohol Research, University of Liverpool, Liverpool, UK.,Liverpool University Hospital, Liverpool, UK.,Liverpool Health Partners, Liverpool, UK
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27
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Sterken MG, van Wijk MH, Quamme EC, Riksen JAG, Carnell L, Mathies LD, Davies AG, Kammenga JE, Bettinger JC. Transcriptional analysis of the response of C. elegans to ethanol exposure. Sci Rep 2021; 11:10993. [PMID: 34040055 PMCID: PMC8155136 DOI: 10.1038/s41598-021-90282-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/07/2021] [Indexed: 11/30/2022] Open
Abstract
Ethanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved in the physiological response to ethanol, including direct ethanol targets, were regulated at 8 h of exposure. This longer exposure to ethanol also resulted in the regulation of genes involved in cilia function, which is consistent with an important role for the effects of ethanol on cilia in the deleterious effects of chronic ethanol consumption in humans. Finally, we found that food deprivation for an 8-h period induced gene expression changes that were somewhat ameliorated by the presence of ethanol, supporting previous observations that worms can use ethanol as a calorie source.
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Affiliation(s)
- Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Marijke H van Wijk
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Elizabeth C Quamme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Box 980613, Richmond, VA, 23298, USA
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Lucinda Carnell
- Department of Biological Sciences, Central Washington University, Ellensburg, WA, 98926, USA
| | - Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Box 980613, Richmond, VA, 23298, USA
- Virginia Commonwealth University Alcohol Research Center, Richmond, VA, USA
| | - Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Box 980613, Richmond, VA, 23298, USA
- Virginia Commonwealth University Alcohol Research Center, Richmond, VA, USA
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Box 980613, Richmond, VA, 23298, USA.
- Virginia Commonwealth University Alcohol Research Center, Richmond, VA, USA.
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28
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Fan X, Liu Z, Poulsen KL, Wu X, Miyata T, Dasarathy S, Rotroff DM, Nagy LE. Alcohol Consumption Is Associated with Poor Prognosis in Obese Patients with COVID-19: A Mendelian Randomization Study Using UK Biobank. Nutrients 2021; 13:1592. [PMID: 34068824 PMCID: PMC8152000 DOI: 10.3390/nu13051592] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acute and chronic alcohol abuse has adverse impacts on both the innate and adaptive immune response, which may result in reduced resistance to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and promote the progression of coronavirus disease 2019 (COVID-19). However, there are no large population-based data evaluating potential causal associations between alcohol consumption and COVID-19. METHODS We conducted a Mendelian randomization study using data from UK Biobank to explore the association between alcohol consumption and risk of SARS-CoV-2 infection and serious clinical outcomes in patients with COVID-19. A total of 12,937 participants aged 50-83 who tested for SARS-CoV-2 between 16 March to 27 July 2020 (12.1% tested positive) were included in the analysis. The exposure factor was alcohol consumption. Main outcomes were SARS-CoV-2 positivity and death in COVID-19 patients. We generated allele scores using three genetic variants (rs1229984 (Alcohol Dehydrogenase 1B, ADH1B), rs1260326 (Glucokinase Regulator, GCKR), and rs13107325 (Solute Carrier Family 39 Member 8, SLC39A8)) and applied the allele scores as the instrumental variables to assess the effect of alcohol consumption on outcomes. Analyses were conducted separately for white participants with and without obesity. RESULTS Of the 12,937 participants, 4496 were never or infrequent drinkers and 8441 were frequent drinkers. Both logistic regression and Mendelian randomization analyses found no evidence that alcohol consumption was associated with risk of SARS-CoV-2 infection in participants either with or without obesity (All q > 0.10). However, frequent drinking, especially heavy drinking (HR = 2.07, 95%CI 1.24-3.47; q = 0.054), was associated with higher risk of death in patients with obesity and COVID-19, but not in patients without obesity. Notably, the risk of death in frequent drinkers with obesity increased slightly with the average amount of alcohol consumed weekly (All q < 0.10). CONCLUSIONS Our findings suggest that alcohol consumption has adverse effects on the progression of COVID-19 in white participants with obesity, but was not associated with susceptibility to SARS-CoV-2 infection.
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Affiliation(s)
- Xiude Fan
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710049, China;
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710049, China;
| | - Kyle L. Poulsen
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
| | - Xiaoqin Wu
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
| | - Tatsunori Miyata
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Laura E. Nagy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA; (X.F.); (K.L.P.); (X.W.); (T.M.); (S.D.)
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
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29
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Curtis D. Investigation of Association of Rare, Functional Genetic Variants With Heavy Drinking and Problem Drinking in Exome Sequenced UK Biobank Participants. Alcohol Alcohol 2021; 57:421-428. [PMID: 33893496 PMCID: PMC9270990 DOI: 10.1093/alcalc/agab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/29/2022] Open
Abstract
Aims The study aimed to identify specific genes and functional genetic variants affecting susceptibility to two alcohol-related phenotypes: heavy drinking and problem drinking. Methods Phenotypic and exome sequence data were downloaded from the UK Biobank. Reported drinks in the last 24 hours were used to define heavy drinking, while responses to a mental health questionnaire defined problem drinking. Gene-wise weighted burden analysis was applied, with genetic variants which were rarer and/or had a more severe functional effect being weighted more highly. Additionally, previously reported variants of interest were analysed inidividually. Results Of exome sequenced subjects, for heavy drinking, there were 8166 cases and 84,461 controls, while for problem drinking, there were 7811 cases and 59,606 controls. No gene was formally significant after correction for multiple testing, but three genes possibly related to autism were significant at P < 0.001, FOXP1, ARHGAP33 and CDH9, along with VGF which may also be of psychiatric interest. Well established associations with rs1229984 in ADH1B and rs671 in ALDH2 were confirmed, but previously reported variants in ALDH1B1 and GRM3 were not associated with either phenotype. Conclusions This large study fails to conclusively implicate any novel genes or variants. It is possible that more definitive results will be obtained when sequence data for the remaining UK Biobank participants become available and/or if data can be obtained for a more extreme phenotype such as alcohol dependence disorder. This research has been conducted using the UK Biobank Resource.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, UCL, Darwin Building, Gower Street, London WC1E 6BT, UK.,Centre for Psychiatry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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30
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Converging vulnerability factors for compulsive food and drug use. Neuropharmacology 2021; 196:108556. [PMID: 33862029 DOI: 10.1016/j.neuropharm.2021.108556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
Highly palatable foods and substance of abuse have intersecting neurobiological, metabolic and behavioral effects relevant for understanding vulnerability to conditions related to food (e.g., obesity, binge eating disorder) and drug (e.g., substance use disorder) misuse. Here, we review data from animal models, clinical populations and epidemiological evidence in behavioral, genetic, pathophysiologic and therapeutic domains. Results suggest that consumption of highly palatable food and drugs of abuse both impact and conversely are regulated by metabolic hormones and metabolic status. Palatable foods high in fat and/or sugar can elicit adaptation in brain reward and withdrawal circuitry akin to substances of abuse. Intake of or withdrawal from palatable food can impact behavioral sensitivity to drugs of abuse and vice versa. A robust literature suggests common substrates and roles for negative reinforcement, negative affect, negative urgency, and impulse control deficits, with both highly palatable foods and substances of abuse. Candidate genetic risk loci shared by obesity and alcohol use disorders have been identified in molecules classically associated with both metabolic and motivational functions. Finally, certain drugs may have overlapping therapeutic potential to treat obesity, diabetes, binge-related eating disorders and substance use disorders. Taken together, data are consistent with the hypotheses that compulsive food and substance use share overlapping, interacting substrates at neurobiological and metabolic levels and that motivated behavior associated with feeding or substance use might constitute vulnerability factors for one another. This article is part of the special issue on 'Vulnerabilities to Substance Abuse'.
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31
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Hade AC, Philips MA, Reimann E, Jagomäe T, Eskla KL, Traks T, Prans E, Kõks S, Vasar E, Väli M. Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. Brain Sci 2021; 11:435. [PMID: 33805312 PMCID: PMC8066746 DOI: 10.3390/brainsci11040435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The Mediodorsal (MD) thalamus that represents a fundamental subcortical relay has been underrepresented in the studies focusing on the molecular changes in the brains of subjects with alcohol use disorder (AUD). In the current study, MD thalamic regions from AUD subjects and controls were analyzed with Affymetrix Clariom S human microarray. Long-term alcohol use induced a significant (FDR ≤ 0.05) upregulation of 2802 transcripts and downregulation of 1893 genes in the MD thalamus of AUD subjects. A significant upregulation of GRIN1 (glutamate receptor NMDA type 1) and FTO (alpha-ketoglutarate dependent dioxygenase) was confirmed in western blot analysis. Immunohistochemical staining revealed similar heterogenous distribution of GRIN1 in the thalamic nuclei of both AUD and control subjects. The most prevalent functional categories of upregulated genes were related to glutamatergic and GABAergic neurotransmission, cellular metabolism, and neurodevelopment. The prevalent gene cluster among down-regulated genes was immune system mediators. Forty-two differentially expressed genes, including FTO, ADH1B, DRD2, CADM2, TCF4, GCKR, DPP6, MAPT and CHRH1, have been shown to have strong associations (FDR p < 10-8) with AUD or/and alcohol use phenotypes in recent GWA studies. Despite a small number of subjects, we were able to detect robust molecular changes in the mediodorsal thalamus caused by alcohol emphasizing the importance of deeper brain structures such as diencephalon, in the development of AUD-related dysregulation of neurocircuitry.
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Affiliation(s)
- Andreas-Christian Hade
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia;
| | - Toomas Jagomäe
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Tanel Traks
- Department of Dermatology and Venerology, Institute of Clinical Medicine, University of Tartu, 51010 Tartu, Estonia;
| | - Ele Prans
- Department of Anaesthesiology and Intensive Care, Tartu University Hospital, 50406 Tartu, Estonia;
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Marika Väli
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
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Lu Y, Guo Y, Lin H, Wang Z, Zheng L. Genetically determined tobacco and alcohol use and risk of atrial fibrillation. BMC Med Genomics 2021; 14:73. [PMID: 33750369 PMCID: PMC7944892 DOI: 10.1186/s12920-021-00915-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The causality between the use of alcohol and cigarettes and atrial fibrillation (AF) remains controversial. We conducted a Mendelian randomization (MR) study to evaluate the association of genetic variants related to tobacco and alcohol use with AF. METHODS Single nucleotide polymorphisms (SNPs) related to smoking initiation (N = 374), age at initiation of regular smoking (N = 10), cigarettes per day (N = 55), and smoking cessation (N = 24) were derived from a genome-wide association studies (GWAS) of tobacco use (N = 1.2 million individuals). SNPs related to heavy alcohol use (N = 6) were derived from a GWAS of UK biobank (N = 125,249 individuals). The genetically matching instrumented variables were obtained from the GWAS of AF (N = 588,190 individuals). The estimates between tobacco and alcohol use and AF were combined by inverse-variance weighted (IVW), simple median, weighted median, MR-robust adjusted profile score method, MR-PRESSO, and multivariable MR. RESULTS A total of 65,446 AF patients and 522,744 referents were included. In the IVW analysis, the odds ratio per one-unit increase of smoking initiation was 1.11 (95% CI, 1.06-1.16; P = 3.35 × 10-6) for AF. Genetically predicted age at initiation of regular smoking, cigarettes per day and smoking cessation were not associated with AF. The IVW estimate showed that heavy alcohol consumption increased AF risk (OR, 1.11; 95% CI, 1.04-1.18; P = 0.001). The results were consistent in complementary analyses and multivariable MR. CONCLUSION Our MR study indicated that regular smoking was associated with increased risk of AF, no matter the age at initiation of regular smoking, or the number of cigarettes smoked per day. Genetically predicted heavy alcohol consumption increased the risk of AF.
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Affiliation(s)
- Yunlong Lu
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Yan Guo
- Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Hefeng Lin
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Zhen Wang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Liangrong Zheng
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
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Corpas M, Megy K, Mistry V, Metastasio A, Lehmann E. Whole Genome Interpretation for a Family of Five. Front Genet 2021; 12:535123. [PMID: 33763108 PMCID: PMC7982663 DOI: 10.3389/fgene.2021.535123] [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: 02/14/2020] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Although best practices have emerged on how to analyse and interpret personal genomes, the utility of whole genome screening remains underdeveloped. A large amount of information can be gathered from various types of analyses via whole genome sequencing including pathogenicity screening, genetic risk scoring, fitness, nutrition, and pharmacogenomic analysis. We recognize different levels of confidence when assessing the validity of genetic markers and apply rigorous standards for evaluation of phenotype associations. We illustrate the application of this approach on a family of five. By applying analyses of whole genomes from different methodological perspectives, we are able to build a more comprehensive picture to assist decision making in preventative healthcare and well-being management. Our interpretation and reporting outputs provide input for a clinician to develop a healthcare plan for the individual, based on genetic and other healthcare data.
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Affiliation(s)
- Manuel Corpas
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, United Kingdom.,Institute of Continuing Education Madingley Hall Madingley, University of Cambridge, Cambridge, United Kingdom.,Facultad de Ciencias de la Salud, Universidad Internacional de La Rioja, Madrid, Spain
| | - Karyn Megy
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge & National Health Service (NHS) Blood and Transplant, Cambridge, United Kingdom
| | | | - Antonio Metastasio
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, United Kingdom.,Camden and Islington NHS Foundation Trust, London, United Kingdom
| | - Edmund Lehmann
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, United Kingdom
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Klaus K, Vaht M, Pennington K, Harro J. Interactive effects of DRD2 rs6277 polymorphism, environment and sex on impulsivity in a population-representative study. Behav Brain Res 2021; 403:113131. [PMID: 33444693 DOI: 10.1016/j.bbr.2021.113131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/31/2020] [Accepted: 01/07/2021] [Indexed: 11/17/2022]
Abstract
Previous research has shown that dopaminergic dysregulation and early life stress interact to impact on aspects of impulse control. This study aimed to explore the potentially interactive effects of the rs6277 polymorphism of the dopamine D2 receptor gene (DRD2), stressful or supportive environment and sex on behavioural and self-reported measures of impulsivity, as well as alcohol use - a condition characterised by a deficit in impulse control. The sample consisted of the younger cohort (n = 583) of the longitudinal Estonian Children Personality, Behaviour and Health Study. The results showed that the CC homozygotes (suggested to have decreased striatal D2 receptor availability) who had experienced stressful life events (SLE) or maltreatment in the family prior to age 15 showed higher self-reported maladaptive impulsivity at age 15. The genotype-SLE interaction and further association with sex was also evident in the frequency of alcohol use at age 15. Lack of warmth in the family contributed to significantly higher levels of thoughtlessness and more frequent alcohol use in CC carriers at age 25, whereas family support was associated with lower thoughtlessness scores in CC males, which may suggest a protective effect of supportive family environment in this group. Together the findings suggest that DRD2 rs6277 polymorphism, in interaction with environmental factors experienced in childhood and youth may affect facets of impulsivity. Future work should aim to further clarify the sex and age-specific effects of stressful and supportive environment on the development of neuronal systems that are compromised in disorders characterised by deficits in impulse control.
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Affiliation(s)
- K Klaus
- School of Psychology, University of Lincoln, Brayford Wharf, Lincoln, LN5 7AT, England, UK; MRC Cognition and Brain Sciences Unit, University of Cambridge, 15 Chaucer Road, Cambridge, CB3 0HH, England, UK.
| | - M Vaht
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - K Pennington
- School of Psychology, University of Lincoln, Brayford Wharf, Lincoln, LN5 7AT, England, UK
| | - J Harro
- Faculty of Science and Technology, Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
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Fan X, Liu Z, Poulsen KL, Wu X, Miyata T, Dasarathy S, Rotroff DM, Nagy LE. Alcohol Consumption is Associated with Poor Prognosis in Obese Patients with COVID-19: a Mendelian Randomization Study using UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.25.20238915. [PMID: 33269370 PMCID: PMC7709191 DOI: 10.1101/2020.11.25.20238915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Background Acute and chronic alcohol abuse have adverse impacts on both the innate and adaptive immune response, which may result in reduced resistance to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and promote the progression of coronavirus disease 2019 (COVID-19). However, there are no large population-based data evaluating potential causal associations between alcohol consumption and COVID-19. Method We conducted a Mendelian randomization study using data from UK Biobank to explore the association between alcohol consumption and risk of SARS-CoV-2 infection and serious clinical outcomes in patients with COVID-19. A total of 12,937 participants aged 50-83 who tested for SARS-CoV-2 between 16 March to 27 July 2020 (12.1% tested positive) were included in the analysis. The exposure factor was alcohol consumption. Main outcomes were SARS-CoV-2 positivity and death in COVID-19 patients. We generated weighted and unweighted allele scores using three genetic variants (rs1229984, rs1260326, and rs13107325) and applied the allele scores as the instrumental variables to assess the effect of alcohol consumption on outcomes. Analyses were conducted separately for white participates with and without obesity. Results Of the 12,937 participants, 4,496 were never or infrequent drinkers and 8,441 were frequent drinkers. (including 1,156 light drinkers, 3,795 moderate drinkers, and 3,490 heavy drinkers). Both logistic regression and Mendelian randomization analyses found no evidence that alcohol consumption was associated with risk of SARS-CoV-2 infection in participants either with (OR=0.963, 95%CI 0.800-1.159; q =1.000) or without obesity (OR=0.891, 95%CI 0.755-1.053; q =.319). However, frequent drinking (HR=1.565, 95%CI 1.012-2.419; q =.079), especially heavy drinking (HR=2.071, 95%CI 1.235-3.472; q =.054), was associated with higher risk of death in patients with obesity and COVID-19, but not in patients without obesity. Notably, the risk of death in frequent drinkers with obesity increased slightly with the average amount of alcohol consumed weekly (HR=1.480, 95%CI 1.059-2.069; q =.099). Conclusions Our findings suggested alcohol consumption may had adverse effects on the progression of COVID-19 in white participants with obesity, but was not associate with susceptibility to SARS-CoV-2 infection.
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Affiliation(s)
- Xiude Fan
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Kyle L Poulsen
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Xiaoqin Wu
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Tatsunori Miyata
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH
| | - Laura E. Nagy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH
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Antibody-mediated activation of the FGFR1/Klothoβ complex corrects metabolic dysfunction and alters food preference in obese humans. Proc Natl Acad Sci U S A 2020; 117:28992-29000. [PMID: 33139537 PMCID: PMC7682391 DOI: 10.1073/pnas.2012073117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fibroblast growth factor 21 (FGF21) controls metabolic organ homeostasis and eating behavior via FGF receptor 1/Klothoβ (FGFR1/KLB) complexes. Here we show that a bispecific anti-FGFR1/KLB agonist antibody, BFKB8488A, mimics the actions of FGF21 in monkeys and humans. BFKB8488A induced marked weight loss in obese monkeys while elevating expression of FGFR1 target genes in adipose tissue. A clinical study in overweight human participants demonstrated that a single dose of BFKB8488A caused transient body weight reduction, sustained improvement in cardiometabolic parameters, and a trend toward reduction in preference for sweet taste and carbohydrate intake. These data suggest that antibody-mediated activation of the FGFR1/KLB complex in humans recapitulates the effects of FGF21 and can be used as therapy for obesity-related metabolic defects. Fibroblast growth factor 21 (FGF21) controls metabolic organ homeostasis and eating/drinking behavior via FGF receptor 1/Klothoβ (FGFR1/KLB) complexes expressed in adipocytes, pancreatic acinar cells, and the nervous system in mice. Chronic administration of recombinant FGF21 or engineered variants improves metabolic health in rodents, nonhuman primates, and humans; however, the rapid turnover of these molecules limits therapeutic utility. Here we show that the bispecific anti-FGFR1/KLB agonist antibody BFKB8488A induced marked weight loss in obese cynomolgus monkeys while elevating serum adiponectin and the adipose expression of FGFR1 target genes, demonstrating its action as an FGF21 mimetic. In a randomized, placebo-controlled, single ascending-dose study in overweight/obese human participants, subcutaneous BFKB8488A injection caused transient body weight reduction, sustained improvement in cardiometabolic parameters, and a trend toward reduction in preference for sweet taste and carbohydrate intake. These data suggest that specific activation of the FGFR1/KLB complex in humans can be used as therapy for obesity-related metabolic defects.
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Bohnsack JP, Pandey SC. Histone modifications, DNA methylation, and the epigenetic code of alcohol use disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:1-62. [PMID: 33461661 DOI: 10.1016/bs.irn.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality. Despite AUD's substantial contributions to lost economic productivity and quality of life, there are only a limited number of approved drugs for treatment of AUD in the United States. This chapter will update progress made on the epigenetic basis of AUD, with particular focus on histone post-translational modifications and DNA methylation and how these two epigenetic mechanisms interact to contribute to neuroadaptive processes leading to initiation, maintenance and progression of AUD pathophysiology. We will also evaluate epigenetic therapeutic strategies that have arisen from preclinical models of AUD and epigenetic biomarkers that have been discovered in human populations with AUD.
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Affiliation(s)
- John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.
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Gupta I, Dandavate R, Gupta P, Agrawal V, Kapoor M. Recent advances in genetic studies of alcohol use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:27-34. [PMID: 33344068 PMCID: PMC7748121 DOI: 10.1007/s40142-020-00185-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Alcohol use disorder (AUD) is a complex genetic disorder with very high heritability. This polygenic disorder not only results in increased morbidity and mortality, it is also a substantial social and economic burden on families and the nation. For past three decades, several genetic studies were conducted to identify genes and pathways associated with AUD. This review aims to summarize past efforts and recent advances in genetic association studies of AUD and related traits. RECENT FINDINGS Initial genetic association studies achieved a limted success and suffered from low power due to small sample sizes. AUD is a polygenic trait and data from several thousands individuals was required to identify the genetic factors of small effect sizes. The scenario changed recently with technological advances and significant reduction in cost of the genome wide association analyses (GWAS). This enabled researchers to generate genomic data on mega biobanks and cohorts with access to extensive clinical and non-clinical phenotypes. Public access to data from biobanks and collaborative efforts of researchers lead to identification of several novel loci associated with AUDs and related traits. Efforts are now underway to identify the causal variants under the GWAS loci to identify target genes and biological mechanisms underpining AUDs. Many GWAS variants occur in promoter or enhancer regions of the genes and are involved in regulation of gene expression of causal genes. This, large amounts of "omics" data from projects such as "ENCODE", RoadMap and GTEx is also helping researchers to integrate "multi-omics" data to interpret functional significance of GWAS variants. SUMMARY With current review, we aim to present the recent advances in genetic and molecular studies of AUDs. Recent successes in genetic studies of AUDs will definetely motivate researchers and lead to better therapeutic interventions for this complex disorder.
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Affiliation(s)
| | - Rohan Dandavate
- Indian Institute of Science Education and Research, Bhopal, India
| | - Pallavi Gupta
- Indian Institute of Science Education and Research, Bhopal, India
| | - Viplav Agrawal
- Indian Institute of Science Education and Research, Bhopal, India
| | - Manav Kapoor
- Icahn School of Medicine at Mount Sinai, New york, USA
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