1
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Barr PB, Neale Z, Chatzinakos C, Schulman J, Mullins N, Zhang J, Chorlian DB, Kamarajan C, Kinreich S, Pandey AK, Pandey G, Saenz de Viteri S, Acion L, Bauer L, Bucholz KK, Chan G, Dick DM, Edenberg HJ, Foroud T, Goate A, Hesselbrock V, Johnson EC, Kramer J, Lai D, Plawecki MH, Salvatore JE, Wetherill L, Agrawal A, Porjesz B, Meyers JL. Clinical, genomic, and neurophysiological correlates of lifetime suicide attempts among individuals with an alcohol use disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.04.28.23289173. [PMID: 37162915 PMCID: PMC10168504 DOI: 10.1101/2023.04.28.23289173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Research has identified clinical, genomic, and neurophysiological markers associated with suicide attempts (SA) among individuals with psychiatric illness. However, there is limited research among those with an alcohol use disorder (AUD), despite their disproportionately higher rates of SA. We examined lifetime SA in 4,068 individuals with DSM-IV alcohol dependence from the Collaborative Study on the Genetics of Alcoholism (23% lifetime suicide attempt; 53% female; mean age: 38). Within participants with an AUD diagnosis, we explored risk across other clinical conditions, polygenic scores (PGS) for comorbid psychiatric problems, and neurocognitive functioning for lifetime suicide attempt. Participants with an AUD who had attempted suicide had greater rates of trauma exposure, major depressive disorder, post-traumatic stress disorder, and other substance use disorders compared to those who had not attempted suicide. Polygenic scores for suicide attempt, depression, and PTSD were associated with reporting a suicide attempt (ORs = 1.22 - 1.44). Participants who reported a SA also had decreased right hemispheric frontal-parietal theta and decreased interhemispheric temporal-parietal alpha electroencephalogram resting-state coherences relative to those who did not, but differences were small. Overall, individuals with an AUD who report a lifetime suicide attempt appear to experience greater levels of trauma, have more severe comorbidities, and carry polygenic risk for a variety of psychiatric problems. Our results demonstrate the need to further investigate suicide attempts in the presence of substance use disorders.
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Affiliation(s)
- Peter B. Barr
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- VA New York Harbor Healthcare System, Brooklyn, NY
- Institute for Genomics in Health (IGH), SUNY Downstate Health Sciences University, Brooklyn, NY
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Zoe Neale
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- VA New York Harbor Healthcare System, Brooklyn, NY
- Institute for Genomics in Health (IGH), SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Chris Chatzinakos
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- VA New York Harbor Healthcare System, Brooklyn, NY
- Institute for Genomics in Health (IGH), SUNY Downstate Health Sciences University, Brooklyn, NY
| | | | - Niamh Mullins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jian Zhang
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - David B. Chorlian
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Chella Kamarajan
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Sivan Kinreich
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Ashwini K. Pandey
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Gayathri Pandey
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | | | - Laura Acion
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Lance Bauer
- Department of Psychiatry, School of Medicine, University of Connecticut, Farmington, CT
| | - Kathleen K. Bucholz
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO
| | - Grace Chan
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA
- Department of Psychiatry, School of Medicine, University of Connecticut, Farmington, CT
| | - Danielle M. Dick
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ
- Rutgers Addiction Research Center, Rutgers University, Piscataway, NJ
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN
| | - Alison Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Victor Hesselbrock
- Department of Psychiatry, School of Medicine, University of Connecticut, Farmington, CT
| | - Emma C. Johnson
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO
| | - John Kramer
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN
| | - Martin H. Plawecki
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN
| | - Jessica E. Salvatore
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN
| | - Arpana Agrawal
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Jacquelyn L. Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- VA New York Harbor Healthcare System, Brooklyn, NY
- Institute for Genomics in Health (IGH), SUNY Downstate Health Sciences University, Brooklyn, NY
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY
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2
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Barr P, Neale Z, Chatzinakos C, Schulman J, Mullins N, Zhang J, Chorlian D, Kamarajan C, Kinreich S, Pandey A, Pandey G, de Viteri SS, Acion L, Bauer L, Bucholz K, Chan G, Dick D, Edenberg H, Foroud T, Goate A, Hesselbrock V, Johnson E, Kramer J, Lai D, Plawecki M, Salvatore J, Wetherill L, Agrawal A, Porjesz B, Meyers J. Clinical, genomic, and neurophysiological correlates of lifetime suicide attempts among individuals with alcohol dependence. RESEARCH SQUARE 2024:rs.3.rs-3894892. [PMID: 38405959 PMCID: PMC10889049 DOI: 10.21203/rs.3.rs-3894892/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Research has identified clinical, genomic, and neurophysiological markers associated with suicide attempts (SA) among individuals with psychiatric illness. However, there is limited research among those with an alcohol use disorder (AUD), despite their disproportionately higher rates of SA. We examined lifetime SA in 4,068 individuals with DSM-IV alcohol dependence from the Collaborative Study on the Genetics of Alcoholism (23% lifetime suicide attempt; 53% female; 17% Admixed African American ancestries; mean age: 38). We 1) conducted a genome-wide association study (GWAS) of SA and performed downstream analyses to determine whether we could identify specific biological pathways of risk, and 2) explored risk in aggregate across other clinical conditions, polygenic scores (PGS) for comorbid psychiatric problems, and neurocognitive functioning between those with AD who have and have not reported a lifetime suicide attempt. The GWAS and downstream analyses did not produce any significant associations. Participants with an AUD who had attempted suicide had greater rates of trauma exposure, major depressive disorder, post-traumatic stress disorder, and other substance use disorders compared to those who had not attempted suicide. Polygenic scores for suicide attempt, depression, and PTSD were associated with reporting a suicide attempt (ORs = 1.22-1.44). Participants who reported a SA also had decreased right hemispheric frontal-parietal theta and decreased interhemispheric temporal-parietal alpha electroencephalogram resting-state coherences relative to those who did not, but differences were small. Overall, individuals with alcohol dependence who report SA appear to experience a variety of severe comorbidities and elevated polygenic risk for SA. Our results demonstrate the need to further investigate suicide attempts in the presence of substance use disorders.
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Affiliation(s)
- Peter Barr
- SUNY Downstate Health Sciences University
| | - Zoe Neale
- SUNY Downstate Health Sciences University
| | | | | | | | | | | | | | | | - Ashwini Pandey
- State University of New York Downstate Health Sciences University
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacquelyn Meyers
- State University of New York (SUNY) Downstate Health Sciences University
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3
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Chen AB, Yu X, Thapa KS, Gao H, Reiter JL, Xuei X, Tsai AP, Landreth GE, Lai D, Wang Y, Foroud TM, Tischfield JA, Edenberg HJ, Liu Y. Functional 3'-UTR Variants Identify Regulatory Mechanisms Impacting Alcohol Use Disorder and Related Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578270. [PMID: 38370821 PMCID: PMC10871301 DOI: 10.1101/2024.01.31.578270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Although genome-wide association studies (GWAS) have identified loci associated with alcohol consumption and alcohol use disorder (AUD), they do not identify which variants are functional. To approach this, we evaluated the impact of variants in 3' untranslated regions (3'-UTRs) of genes in loci associated with substance use and neurological disorders using a massively parallel reporter assay (MPRA) in neuroblastoma and microglia cells. Functionally impactful variants explained a higher proportion of heritability of alcohol traits than non-functional variants. We identified genes whose 3'UTR activities are associated with AUD and alcohol consumption by combining variant effects from MPRA with GWAS results. We examined their effects by evaluating gene expression after CRISPR inhibition of neuronal cells and stratifying brain tissue samples by MPRA-derived 3'-UTR activity. A pathway analysis of differentially expressed genes identified inflammation response pathways. These analyses suggest that variation in response to inflammation contributes to the propensity to increase alcohol consumption.
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Affiliation(s)
- Andy B. Chen
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xuhong Yu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kriti S. Thapa
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Hongyu Gao
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jill L Reiter
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Xiaoling Xuei
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andy P. Tsai
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gary E. Landreth
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dongbing Lai
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yue Wang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Tatiana M. Foroud
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Howard J. Edenberg
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana
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Johnson EC, Salvatore JE, Lai D, Merikangas AK, Nurnberger JI, Tischfield JA, Xuei X, Kamarajan C, Wetherill L, Rice JP, Kramer JR, Kuperman S, Foroud T, Slesinger PA, Goate AM, Porjesz B, Dick DM, Edenberg HJ, Agrawal A. The collaborative study on the genetics of alcoholism: Genetics. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12856. [PMID: 37387240 PMCID: PMC10550788 DOI: 10.1111/gbb.12856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/02/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
This review describes the genetic approaches and results from the family-based Collaborative Study on the Genetics of Alcoholism (COGA). COGA was designed during the linkage era to identify genes affecting the risk for alcohol use disorder (AUD) and related problems, and was among the first AUD-focused studies to subsequently adopt a genome-wide association (GWAS) approach. COGA's family-based structure, multimodal assessment with gold-standard clinical and neurophysiological data, and the availability of prospective longitudinal phenotyping continues to provide insights into the etiology of AUD and related disorders. These include investigations of genetic risk and trajectories of substance use and use disorders, phenome-wide association studies of loci of interest, and investigations of pleiotropy, social genomics, genetic nurture, and within-family comparisons. COGA is one of the few AUD genetics projects that includes a substantial number of participants of African ancestry. The sharing of data and biospecimens has been a cornerstone of the COGA project, and COGA is a key contributor to large-scale GWAS consortia. COGA's wealth of publicly available genetic and extensive phenotyping data continues to provide a unique and adaptable resource for our understanding of the genetic etiology of AUD and related traits.
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Affiliation(s)
- Emma C. Johnson
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Jessica E. Salvatore
- Department of Psychiatry, Robert Wood Johnson Medical SchoolRutgers UniversityPiscatawayNew JerseyUSA
| | - Dongbing Lai
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Alison K. Merikangas
- Department of Biomedical and Health InformaticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - John I. Nurnberger
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of PsychiatryIndiana University School of MedicineIndianapolisIndianaUSA
| | | | - Xiaoling Xuei
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Chella Kamarajan
- Department of Psychiatry and Behavioral SciencesState University of New York Health Sciences UniversityBrooklynNew YorkUSA
| | - Leah Wetherill
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | | | - John P. Rice
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - John R. Kramer
- Department of Psychiatry, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Samuel Kuperman
- Department of Psychiatry, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Tatiana Foroud
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Paul A. Slesinger
- Departments of Neuroscience and Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Alison M. Goate
- Departments of Genetics and Genomic Sciences, Neuroscience, and NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral SciencesState University of New York Health Sciences UniversityBrooklynNew YorkUSA
| | - Danielle M. Dick
- Department of Psychiatry, Robert Wood Johnson Medical SchoolRutgers UniversityPiscatawayNew JerseyUSA
| | - Howard J. Edenberg
- Department of Medical & Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Biochemistry and Molecular BiologyIndiana UniversityIndianapolisIndianaUSA
| | - Arpana Agrawal
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
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5
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Agrawal A, Brislin SJ, Bucholz KK, Dick D, Hart RP, Johnson EC, Meyers J, Salvatore J, Slesinger P, Almasy L, Foroud T, Goate A, Hesselbrock V, Kramer J, Kuperman S, Merikangas AK, Nurnberger JI, Tischfield J, Edenberg HJ, Porjesz B. The Collaborative Study on the Genetics of Alcoholism: Overview. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12864. [PMID: 37736010 PMCID: PMC10550790 DOI: 10.1111/gbb.12864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
Alcohol use disorders (AUD) are commonly occurring, heritable and polygenic disorders with etiological origins in the brain and the environment. To outline the causes and consequences of alcohol-related milestones, including AUD, and their related psychiatric comorbidities, the Collaborative Study on the Genetics of Alcoholism (COGA) was launched in 1989 with a gene-brain-behavior framework. COGA is a family based, diverse (~25% self-identified African American, ~52% female) sample, including data on 17,878 individuals, ages 7-97 years, in 2246 families of which a proportion are densely affected for AUD. All participants responded to questionnaires (e.g., personality) and the Semi-Structured Assessment for the Genetics of Alcoholism (SSAGA) which gathers information on psychiatric diagnoses, conditions and related behaviors (e.g., parental monitoring). In addition, 9871 individuals have brain function data from electroencephalogram (EEG) recordings while 12,009 individuals have been genotyped on genome-wide association study (GWAS) arrays. A series of functional genomics studies examine the specific cellular and molecular mechanisms underlying AUD. This overview provides the framework for the development of COGA as a scientific resource in the past three decades, with individual reviews providing in-depth descriptions of data on and discoveries from behavioral and clinical, brain function, genetic and functional genomics data. The value of COGA also resides in its data sharing policies, its efforts to communicate scientific findings to the broader community via a project website and its potential to nurture early career investigators and to generate independent research that has broadened the impact of gene-brain-behavior research into AUD.
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Affiliation(s)
- Arpana Agrawal
- Department of PsychiatryWashington University School of Medicine in St. LouisSt. LouisMissouriUSA
| | - Sarah J. Brislin
- Department of PsychiatryRutgers Robert Wood Johnson Medical SchoolPiscatawayNew JerseyUSA
| | - Kathleen K. Bucholz
- Department of PsychiatryWashington University School of Medicine in St. LouisSt. LouisMissouriUSA
| | - Danielle Dick
- Department of PsychiatryRutgers Robert Wood Johnson Medical SchoolPiscatawayNew JerseyUSA
| | - Ronald P. Hart
- Department of Cell Biology and NeuroscienceRutgers UniversityPiscatawayNew JerseyUSA
| | - Emma C. Johnson
- Department of PsychiatryWashington University School of Medicine in St. LouisSt. LouisMissouriUSA
| | - Jacquelyn Meyers
- Department of Psychiatry and Behavioral SciencesSUNY Downstate Health Sciences UniversityBrooklynNew YorkUSA
| | - Jessica Salvatore
- Department of PsychiatryRutgers Robert Wood Johnson Medical SchoolPiscatawayNew JerseyUSA
| | - Paul Slesinger
- Department of Neuroscience & Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Laura Almasy
- Department of Biomedical and Health InformaticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Tatiana Foroud
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Victor Hesselbrock
- Department of PsychiatryUniversity of Connecticut School of MedicineFarmingtonConnecticutUSA
| | - John Kramer
- Department of PsychiatryUniversity of Iowa Carver College of MedicineIowa CityIowaUSA
| | - Samuel Kuperman
- Department of PsychiatryUniversity of Iowa Carver College of MedicineIowa CityIowaUSA
| | - Alison K. Merikangas
- Department of Biomedical and Health InformaticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Jay Tischfield
- Department of GeneticsRutgers UniversityPiscatawayNew JerseyUSA
| | - Howard J. Edenberg
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral SciencesSUNY Downstate Health Sciences UniversityBrooklynNew YorkUSA
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6
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Lai D, Schwantes-An TH, Abreu M, Chan G, Hesselbrock V, Kamarajan C, Liu Y, Meyers JL, Nurnberger JI, Plawecki MH, Wetherill L, Schuckit M, Zhang P, Edenberg HJ, Porjesz B, Agrawal A, Foroud T. Gene-based polygenic risk scores analysis of alcohol use disorder in African Americans. Transl Psychiatry 2022; 12:266. [PMID: 35790736 PMCID: PMC9256707 DOI: 10.1038/s41398-022-02029-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWAS) in admixed populations such as African Americans (AA) have limited sample sizes, resulting in poor performance of polygenic risk scores (PRS). Based on the observations that many disease-causing genes are shared between AA and European ancestry (EA) populations, and some disease-causing variants are located within the boundaries of these genes, we proposed a novel gene-based PRS framework (PRSgene) by using variants located within disease-associated genes. Using the AA GWAS of alcohol use disorder (AUD) from the Million Veteran Program and the EA GWAS of problematic alcohol use as the discovery GWAS, we identified 858 variants from 410 genes that were AUD-related in both AA and EA. PRSgene calculated using these variants were significantly associated with AUD in three AA target datasets (P-values ranged from 7.61E-05 to 6.27E-03; Betas ranged from 0.15 to 0.21) and outperformed PRS calculated using all variants (P-values ranged from 7.28E-03 to 0.16; Betas ranged from 0.06 to 0.18). PRSgene were also associated with AUD in an EA target dataset (P-value = 0.02, Beta = 0.11). In AA, individuals in the highest PRSgene decile had an odds ratio of 1.76 (95% CI: 1.32-2.34) to develop AUD compared to those in the lowest decile. The 410 genes were enriched in 54 Gene Ontology biological processes, including ethanol oxidation and processes involving the synaptic system, which are known to be AUD-related. In addition, 26 genes were targets of drugs used to treat AUD or other diseases that might be considered for repurposing to treat AUD. Our study demonstrated that the gene-based PRS had improved performance in evaluating AUD risk in AA and provided new insight into AUD genetics.
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marco Abreu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Grace Chan
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Psychiatry, University of Iowa, Carver College of Medicine, Iowa City, IA, USA
| | - Victor Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Chella Kamarajan
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jacquelyn L Meyers
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - John I Nurnberger
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Martin H Plawecki
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marc Schuckit
- Department of Psychiatry, University of California, San Diego Medical School, San Diego, CA, USA
| | - Pengyue Zhang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
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7
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Parker CC, Philip VM, Gatti DM, Kasparek S, Kreuzman AM, Kuffler L, Mansky B, Masneuf S, Sharif K, Sluys E, Taterra D, Taylor WM, Thomas M, Polesskaya O, Palmer AA, Holmes A, Chesler EJ. Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population. Alcohol Clin Exp Res 2022; 46:941-960. [PMID: 35383961 DOI: 10.1111/acer.14825] [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: 09/01/2021] [Revised: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND A strong predictor for the development of alcohol use disorder (AUD) is altered sensitivity to the intoxicating effects of alcohol. Individual differences in the initial sensitivity to alcohol are controlled in part by genetic factors. Mice offer a powerful tool to elucidate the genetic basis of behavioral and physiological traits relevant to AUD, but conventional experimental crosses have only been able to identify large chromosomal regions rather than specific genes. Genetically diverse, highly recombinant mouse populations make it possible to observe a wider range of phenotypic variation, offer greater mapping precision, and thus increase the potential for efficient gene identification. METHODS We have taken advantage of the Diversity Outbred (DO) mouse population to identify and precisely map quantitative trait loci (QTL) associated with ethanol sensitivity. We phenotyped 798 male J:DO mice for three measures of ethanol sensitivity: ataxia, hypothermia, and loss of the righting response. We used high-density MegaMUGA and GigaMUGA to obtain genotypes ranging from 77,808 to 143,259 SNPs. We also performed RNA sequencing in striatum to map expression QTLs and identify gene expression-trait correlations. We then applied a systems genetic strategy to identify narrow QTLs and construct the network of correlations that exists between DNA sequence, gene expression values, and ethanol-related phenotypes to prioritize our list of positional candidate genes. RESULTS We observed large amounts of phenotypic variation with the DO population and identified suggestive and significant QTLs associated with ethanol sensitivity on chromosomes 1, 2, and 16. The implicated regions were narrow (4.5-6.9 Mb in size) and each QTL explained ~4-5% of the variance. CONCLUSIONS Our results can be used to identify alleles that contribute to AUD in humans, elucidate causative biological mechanisms, or assist in the development of novel therapeutic interventions.
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Affiliation(s)
- Clarissa C Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Vivek M Philip
- Center for Computational Sciences, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Daniel M Gatti
- Center for Computational Sciences, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Steven Kasparek
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Andrew M Kreuzman
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Lauren Kuffler
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Benjamin Mansky
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Sophie Masneuf
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Kayvon Sharif
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Erica Sluys
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Dominik Taterra
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Walter M Taylor
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Mary Thomas
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Elissa J Chesler
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
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Cormand B, Cabana-Domínguez J, Forero DA, Fernàndez-Castillo N. Genomics and epigenomics of substance use disorders: An introduction. Am J Med Genet B Neuropsychiatr Genet 2021; 186:125-127. [PMID: 33973715 DOI: 10.1002/ajmg.b.32844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia, Spain
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