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Wang R, Su Y, O'Donnell K, Caron J, Meaney M, Meng X, Li Y. Differential interactions between gene expressions and stressors across the lifespan in major depressive disorder. J Affect Disord 2024; 362:688-697. [PMID: 39029669 DOI: 10.1016/j.jad.2024.07.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/05/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Both genetic predispositions and exposures to stressors have collectively contributed to the development of major depressive disorder (MDD). To deep dive into their roles in MDD, our study aimed to examine which susceptible gene expression interacts with various dimensions of stressors in the MDD risk among a large population cohort. METHODS Data analyzed were from a longitudinal community-based cohort from Southwest Montreal, Canada (N = 1083). Latent profile models were used to identify distinct patterns of stressors for the study cohort. A transcriptome-wide association study (TWAS) method was performed to examine the interactive effects of three dimensions of stressors (threat, deprivation, and cumulative lifetime stress) and gene expression on the MDD risk in a total of 48 tissues from GTEx. Additional analyses were also conducted to further explore and specify these associations including colocalization, and fine-mapping analyses, in addition to enrichment analysis investigations based on TWAS. RESULTS We identified 3321 genes linked to MDD at the nominal p-value <0.05 and found that different patterns of stressors can amplify the genetic susceptibility to MDD. We also observed specific genes and pathways that interacted with deprivation and cumulative lifetime stressors, particularly in specific brain tissues including basal ganglia, prefrontal cortex, brain amygdala, brain cerebellum, brain cortex, and the whole blood. Colocalization analysis also identified these genes as having a high probability of sharing MDD causal variants. LIMITATIONS The study cohort was composed exclusively of individuals of Caucasians, which restricts the generalizability of the findings to other ethnic population groups. CONCLUSIONS The findings of the study unveiled significant interactions between potential tissue-specific gene expression × stressors in the MDD risk and shed light on the intricate etiological attributes of gene expression and specific stressors across the lifespan in MDD. These genetic and environmental attributes in MDD corroborate the vulnerability-stress theory and direct future stress research to have a closer examination of genetic predisposition and potential involvements of omics studies to specify the intricate relationships between genes and stressful environments.
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Affiliation(s)
- Ruiyang Wang
- Department of Financial and Risk Engineering, New York University, NY, NYC, USA; Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Yingying Su
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Kieran O'Donnell
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada; Yale Child Study Center, Department of Obstetrics Gynecology & Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA; Child & Brain Development Program, CIFAR, Toronto, ON, Canada
| | - Jean Caron
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Michael Meaney
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Xiangfei Meng
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada.
| | - Yue Li
- School of Computer Science, McGill University, Montreal, QC, Canada.
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Bledsoe X, Gamazon ER. A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health. Am J Hum Genet 2024; 111:1559-1572. [PMID: 38925120 DOI: 10.1016/j.ajhg.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Regulation of gene expression is a vital component of neurological homeostasis. Cataloging the consequences of endogenous gene expression on the physical structure and connectivity of the brain offers a means of unifying trait-associated genetic variation with trait-associated neurological features. We perform tissue-specific transcriptome-wide association studies (TWASs) on over 3,400 neuroimaging phenotypes in the UK Biobank (N = 33,224) using our joint-tissue imputation (JTI)-TWAS method. We identify highly significant associations between predicted expression for 7,192 genes and a wide variety of measures of the brain derived from magnetic resonance imaging (MRI). Our approach generates reproducible results in internal and external replication datasets. Genetically determined expression alone is sufficient for high-fidelity reconstruction of brain structure and organization. We demonstrate complementary benefits of cross-tissue and single-tissue analyses toward an integrated neurobiology and provide evidence that gene expression outside the central nervous system provides unique insights into brain health. As an application, we provide evidence suggesting that the genetically regulated expression of schizophrenia risk genes causally affects over 73% of neurological phenotypes that are altered in individuals with schizophrenia (as identified by neuroimaging studies). Imaging features associated with neuropsychiatric traits can provide valuable insights into underlying pathophysiology. By linking neuroimaging-derived phenotypes with expression levels of specific genes, this resource represents a powerful gene prioritization schema that can improve our understanding of brain function, development, and disease. The use of multiple different cortical and subcortical atlases in the resource facilitates direct integration of these data with findings from a diverse range of clinical neuroimaging studies.
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Affiliation(s)
- Xavier Bledsoe
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Memory & Alzheimer's Center, Nashville, TN, USA.
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Li X, Fernandes BS, Liu A, Lu Y, Chen J, Zhao Z, Dai Y. GRPa-PRS: A risk stratification method to identify genetically-regulated pathways in polygenic diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.06.19.23291621. [PMID: 37425929 PMCID: PMC10327215 DOI: 10.1101/2023.06.19.23291621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background Polygenic risk scores (PRS) are tools used to evaluate an individual's susceptibility to polygenic diseases based on their genetic profile. A considerable proportion of people carry a high genetic risk but evade the disease. On the other hand, some individuals with a low risk of eventually developing the disease. We hypothesized that unknown counterfactors might be involved in reversing the PRS prediction, which might provide new insights into the pathogenesis, prevention, and early intervention of diseases. Methods We built a novel computational framework to identify genetically-regulated pathways (GRPas) using PRS-based stratification for each cohort. We curated two AD cohorts with genotyping data; the discovery (disc) and the replication (rep) datasets include 2722 and 2854 individuals, respectively. First, we calculated the optimized PRS model based on the three recent AD GWAS summary statistics for each cohort. Then, we stratified the individuals by their PRS and clinical diagnosis into six biologically meaningful PRS strata, such as AD cases with low/high risk and cognitively normal (CN) with low/high risk. Lastly, we imputed individual genetically-regulated expression (GReX) and identified differential GReX and GRPas between risk strata using gene-set enrichment and variational analyses in two models, with and without APOE effects. An orthogonality test was further conducted to verify those GRPas are independent of PRS risk. To verify the generalizability of other polygenic diseases, we further applied a default model of GRPa-PRS for schizophrenia (SCZ). Results For each stratum, we conducted the same procedures in both the disc and rep datasets for comparison. In AD, we identified several well-known AD-related pathways, including amyloid-beta clearance, tau protein binding, and astrocyte response to oxidative stress. Additionally, we discovered resilience-related GRPs that are orthogonal to AD PRS, such as the calcium signaling pathway and divalent inorganic cation homeostasis. In SCZ, pathways related to mitochondrial function and muscle development were highlighted. Finally, our GRPa-PRS method identified more consistent differential pathways compared to another variant-based pathway PRS method. Conclusions We developed a framework, GRPa-PRS, to systematically explore the differential GReX and GRPas among individuals stratified by their estimated PRS. The GReX-level comparison among those strata unveiled new insights into the pathways associated with disease risk and resilience. Our framework is extendable to other polygenic complex diseases.
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Affiliation(s)
- Xiaoyang Li
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brisa S. Fernandes
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Andi Liu
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yimei Lu
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Daskalakis NP, Iatrou A, Chatzinakos C, Jajoo A, Snijders C, Wylie D, DiPietro CP, Tsatsani I, Chen CY, Pernia CD, Soliva-Estruch M, Arasappan D, Bharadwaj RA, Collado-Torres L, Wuchty S, Alvarez VE, Dammer EB, Deep-Soboslay A, Duong DM, Eagles N, Huber BR, Huuki L, Holstein VL, Logue ΜW, Lugenbühl JF, Maihofer AX, Miller MW, Nievergelt CM, Pertea G, Ross D, Sendi MSE, Sun BB, Tao R, Tooke J, Wolf EJ, Zeier Z, Berretta S, Champagne FA, Hyde T, Seyfried NT, Shin JH, Weinberger DR, Nemeroff CB, Kleinman JE, Ressler KJ. Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood. Science 2024; 384:eadh3707. [PMID: 38781393 PMCID: PMC11203158 DOI: 10.1126/science.adh3707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
The molecular pathology of stress-related disorders remains elusive. Our brain multiregion, multiomic study of posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) included the central nucleus of the amygdala, hippocampal dentate gyrus, and medial prefrontal cortex (mPFC). Genes and exons within the mPFC carried most disease signals replicated across two independent cohorts. Pathways pointed to immune function, neuronal and synaptic regulation, and stress hormones. Multiomic factor and gene network analyses provided the underlying genomic structure. Single nucleus RNA sequencing in dorsolateral PFC revealed dysregulated (stress-related) signals in neuronal and non-neuronal cell types. Analyses of brain-blood intersections in >50,000 UK Biobank participants were conducted along with fine-mapping of the results of PTSD and MDD genome-wide association studies to distinguish risk from disease processes. Our data suggest shared and distinct molecular pathology in both disorders and propose potential therapeutic targets and biomarkers.
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Affiliation(s)
- Nikolaos P. Daskalakis
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Artemis Iatrou
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Chris Chatzinakos
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, 11203, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, 11209, USA
| | - Aarti Jajoo
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Clara Snijders
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Dennis Wylie
- Center for Biomedical Research Support, The University of Texas at Austin; Austin, TX, 78712, USA
| | - Christopher P. DiPietro
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Ioulia Tsatsani
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Psychiatry and Neuropsychology, School for Mental Health, and Neuroscience (MHeNs), Maastricht University, Maastricht, 6229 ER, The Netherlands
| | | | - Cameron D. Pernia
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Marina Soliva-Estruch
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Psychiatry and Neuropsychology, School for Mental Health, and Neuroscience (MHeNs), Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Dhivya Arasappan
- Center for Biomedical Research Support, The University of Texas at Austin; Austin, TX, 78712, USA
| | - Rahul A. Bharadwaj
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Stefan Wuchty
- Departments of Computer Science, University of Miami, Miami, FL, 33146, USA
- Department of Biology, University of Miami, Miami, FL, 33146, USA
| | - Victor E. Alvarez
- Department of Neurology, Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- VA Bedford Healthcare System, Bedford, MA, 01730, USA
- National Posttraumatic Stress Disorder Brain Bank, VA Boston Healthcare System, Boston, MA, 02130, USA
| | - Eric B Dammer
- Department of Biochemistry, Center for Neurodegenerative Disease, Emory School of Medicine; Atlanta GA, 30329, USA
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Duc M. Duong
- Department of Biochemistry, Center for Neurodegenerative Disease, Emory School of Medicine; Atlanta GA, 30329, USA
| | - Nick Eagles
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Bertrand R. Huber
- Department of Neurology, Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- National Posttraumatic Stress Disorder Brain Bank, VA Boston Healthcare System, Boston, MA, 02130, USA
| | - Louise Huuki
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Vincent L Holstein
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Μark W. Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, 02130, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Biomedical Genetics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Justina F. Lugenbühl
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Psychiatry and Neuropsychology, School for Mental Health, and Neuroscience (MHeNs), Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Adam X. Maihofer
- Department of Psychiatry, University of California San Diego; La Jolla, CA, 92093, USA
- Center for Excellence in Stress and Mental Health, Veterans Affairs San Diego Healthcare System; San Diego, CA, 92161, USA
- Research Service, Veterans Affairs San Diego Healthcare System; San Diego, CA, 92161, USA
| | - Mark W. Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, 02130, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego; La Jolla, CA, 92093, USA
- Center for Excellence in Stress and Mental Health, Veterans Affairs San Diego Healthcare System; San Diego, CA, 92161, USA
- Research Service, Veterans Affairs San Diego Healthcare System; San Diego, CA, 92161, USA
| | - Geo Pertea
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Deanna Ross
- Department of Psychology, University of Texas at Austin; Austin, TX, 78712, USA
| | - Mohammad S. E Sendi
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | | | - Ran Tao
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - James Tooke
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Erika J. Wolf
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, 02130, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine; Miami, FL, 33136, USA
| | | | - Sabina Berretta
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | | | - Thomas Hyde
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Center for Neurodegenerative Disease, Emory School of Medicine; Atlanta GA, 30329, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Charles B. Nemeroff
- Department of Psychology, University of Texas at Austin; Austin, TX, 78712, USA
- Department of Psychiatry and Behavioral Sciences, University of Texas at Austin; Austin, TX, 78712, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Kerry J. Ressler
- McLean Hospital; Belmont, MA, 02478, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02115, USA
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5
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Nievergelt CM, Maihofer AX, Atkinson EG, Chen CY, Choi KW, Coleman JRI, Daskalakis NP, Duncan LE, Polimanti R, Aaronson C, Amstadter AB, Andersen SB, Andreassen OA, Arbisi PA, Ashley-Koch AE, Austin SB, Avdibegoviç E, Babić D, Bacanu SA, Baker DG, Batzler A, Beckham JC, Belangero S, Benjet C, Bergner C, Bierer LM, Biernacka JM, Bierut LJ, Bisson JI, Boks MP, Bolger EA, Brandolino A, Breen G, Bressan RA, Bryant RA, Bustamante AC, Bybjerg-Grauholm J, Bækvad-Hansen M, Børglum AD, Børte S, Cahn L, Calabrese JR, Caldas-de-Almeida JM, Chatzinakos C, Cheema S, Clouston SAP, Colodro-Conde L, Coombes BJ, Cruz-Fuentes CS, Dale AM, Dalvie S, Davis LK, Deckert J, Delahanty DL, Dennis MF, Desarnaud F, DiPietro CP, Disner SG, Docherty AR, Domschke K, Dyb G, Kulenović AD, Edenberg HJ, Evans A, Fabbri C, Fani N, Farrer LA, Feder A, Feeny NC, Flory JD, Forbes D, Franz CE, Galea S, Garrett ME, Gelaye B, Gelernter J, Geuze E, Gillespie CF, Goleva SB, Gordon SD, Goçi A, Grasser LR, Guindalini C, Haas M, Hagenaars S, Hauser MA, Heath AC, Hemmings SMJ, Hesselbrock V, Hickie IB, Hogan K, Hougaard DM, Huang H, Huckins LM, Hveem K, Jakovljević M, Javanbakht A, Jenkins GD, Johnson J, Jones I, Jovanovic T, Karstoft KI, Kaufman ML, Kennedy JL, Kessler RC, Khan A, Kimbrel NA, King AP, Koen N, Kotov R, Kranzler HR, Krebs K, Kremen WS, Kuan PF, Lawford BR, Lebois LAM, Lehto K, Levey DF, Lewis C, Liberzon I, Linnstaedt SD, Logue MW, Lori A, Lu Y, Luft BJ, Lupton MK, Luykx JJ, Makotkine I, Maples-Keller JL, Marchese S, Marmar C, Martin NG, Martínez-Levy GA, McAloney K, McFarlane A, McLaughlin KA, McLean SA, Medland SE, Mehta D, Meyers J, Michopoulos V, Mikita EA, Milani L, Milberg W, Miller MW, Morey RA, Morris CP, Mors O, Mortensen PB, Mufford MS, Nelson EC, Nordentoft M, Norman SB, Nugent NR, O'Donnell M, Orcutt HK, Pan PM, Panizzon MS, Pathak GA, Peters ES, Peterson AL, Peverill M, Pietrzak RH, Polusny MA, Porjesz B, Powers A, Qin XJ, Ratanatharathorn A, Risbrough VB, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero KJ, Rung A, Runz H, Rutten BPF, de Viteri SS, Salum GA, Sampson L, Sanchez SE, Santoro M, Seah C, Seedat S, Seng JS, Shabalin A, Sheerin CM, Silove D, Smith AK, Smoller JW, Sponheim SR, Stein DJ, Stensland S, Stevens JS, Sumner JA, Teicher MH, Thompson WK, Tiwari AK, Trapido E, Uddin M, Ursano RJ, Valdimarsdóttir U, Van Hooff M, Vermetten E, Vinkers CH, Voisey J, Wang Y, Wang Z, Waszczuk M, Weber H, Wendt FR, Werge T, Williams MA, Williamson DE, Winsvold BS, Winternitz S, Wolf C, Wolf EJ, Xia Y, Xiong Y, Yehuda R, Young KA, Young RM, Zai CC, Zai GC, Zervas M, Zhao H, Zoellner LA, Zwart JA, deRoon-Cassini T, van Rooij SJH, van den Heuvel LL, Stein MB, Ressler KJ, Koenen KC. Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder. Nat Genet 2024; 56:792-808. [PMID: 38637617 DOI: 10.1038/s41588-024-01707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Post-traumatic stress disorder (PTSD) genetics are characterized by lower discoverability than most other psychiatric disorders. The contribution to biological understanding from previous genetic studies has thus been limited. We performed a multi-ancestry meta-analysis of genome-wide association studies across 1,222,882 individuals of European ancestry (137,136 cases) and 58,051 admixed individuals with African and Native American ancestry (13,624 cases). We identified 95 genome-wide significant loci (80 new). Convergent multi-omic approaches identified 43 potential causal genes, broadly classified as neurotransmitter and ion channel synaptic modulators (for example, GRIA1, GRM8 and CACNA1E), developmental, axon guidance and transcription factors (for example, FOXP2, EFNA5 and DCC), synaptic structure and function genes (for example, PCLO, NCAM1 and PDE4B) and endocrine or immune regulators (for example, ESR1, TRAF3 and TANK). Additional top genes influence stress, immune, fear and threat-related processes, previously hypothesized to underlie PTSD neurobiology. These findings strengthen our understanding of neurobiological systems relevant to PTSD pathophysiology, while also opening new areas for investigation.
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Affiliation(s)
- Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA.
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA.
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chia-Yen Chen
- Biogen Inc.,Translational Sciences, Cambridge, MA, USA
| | - Karmel W Choi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan R I Coleman
- King's College London, National Institute for Health and Care Research Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Nikolaos P Daskalakis
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Center of Excellence in Depression and Anxiety Disorders, Belmont, MA, USA
| | - Laramie E Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Renato Polimanti
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Cindy Aaronson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ananda B Amstadter
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Soren B Andersen
- The Danish Veteran Centre, Research and Knowledge Centre, Ringsted, Denmark
| | - Ole A Andreassen
- Oslo University Hospital, Division of Mental Health and Addiction, Oslo, Norway
- University of Oslo, Institute of Clinical Medicine, Oslo, Norway
| | - Paul A Arbisi
- Minneapolis VA Health Care System, Mental Health Service Line, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | | | - S Bryn Austin
- Boston Children's Hospital, Division of Adolescent and Young Adult Medicine, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Esmina Avdibegoviç
- Department of Psychiatry, University Clinical Center of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Dragan Babić
- Department of Psychiatry, University Clinical Center of Mostar, Mostar, Bosnia and Herzegovina
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
| | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jean C Beckham
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Research, Durham VA Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center (MIRECC), Genetics Research Laboratory, Durham, NC, USA
| | - Sintia Belangero
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
- Department of Psychiatry, Universidade Federal de São Paulo, Laboratory of Integrative Neuroscience, São Paulo, Brazil
| | - Corina Benjet
- Instituto Nacional de Psiquiatraía Ramón de la Fuente Muñiz, Center for Global Mental Health, Mexico City, Mexico
| | - Carisa Bergner
- Medical College of Wisconsin, Comprehensive Injury Center, Milwaukee, WI, USA
| | - Linda M Bierer
- Department of Psychiatry, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Joanna M Biernacka
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Jonathan I Bisson
- Cardiff University, National Centre for Mental Health, MRC Centre for Psychiatric Genetics and Genomics, Cardiff, UK
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elizabeth A Bolger
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Amber Brandolino
- Department of Surgery, Division of Trauma & Acute Care Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gerome Breen
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- King's College London, NIHR Maudsley BRC, London, UK
| | - Rodrigo Affonseca Bressan
- Department of Psychiatry, Universidade Federal de São Paulo, Laboratory of Integrative Neuroscience, São Paulo, Brazil
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Richard A Bryant
- University of New South Wales, School of Psychology, Sydney, New South Wales, Australia
| | - Angela C Bustamante
- Department of Internal Medicine, University of Michigan Medical School, Division of Pulmonary and Critical Care Medicine, Ann Arbor, MI, USA
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Aarhus University, Centre for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Sigrid Børte
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, K. G. Jebsen Center for Genetic Epidemiology, Trondheim, Norway
- Oslo University Hospital, Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo, Norway
| | - Leah Cahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Joseph R Calabrese
- Case Western Reserve University, School of Medicine, Cleveland, OH, USA
- Department of Psychiatry, University Hospitals, Cleveland, OH, USA
| | | | - Chris Chatzinakos
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Division of Depression and Anxiety Disorders, Belmont, MA, USA
| | - Sheraz Cheema
- University of Toronto, CanPath National Coordinating Center, Toronto, Ontario, Canada
| | - Sean A P Clouston
- Stony Brook University, Family, Population, and Preventive Medicine, Stony Brook, NY, USA
- Stony Brook University, Public Health, Stony Brook, NY, USA
| | - Lucía Colodro-Conde
- QIMR Berghofer Medical Research Institute, Mental Health & Neuroscience Program, Brisbane, Queensland, Australia
| | - Brandon J Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Carlos S Cruz-Fuentes
- Department of Genetics, Instituto Nacional de Psiquiatraía Ramón de la Fuente Muñiz, Mexico City, Mexico
| | - Anders M Dale
- Department of Radiology, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Shareefa Dalvie
- Department of Pathology, University of Cape Town, Division of Human Genetics, Cape Town, South Africa
| | - Lea K Davis
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Jürgen Deckert
- University Hospital of Würzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Würzburg, Denmark
| | | | - Michelle F Dennis
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Research, Durham VA Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center (MIRECC), Genetics Research Laboratory, Durham, NC, USA
| | - Frank Desarnaud
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Christopher P DiPietro
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- McLean Hospital, Division of Depression and Anxiety Disorders, Belmont, MA, USA
| | - Seth G Disner
- Minneapolis VA Health Care System, Research Service Line, Minneapolis, MN, USA
- Department of Psychiatry & Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anna R Docherty
- Huntsman Mental Health Institute, Salt Lake City, UT, USA
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Katharina Domschke
- University of Freiburg, Faculty of Medicine, Centre for Basics in Neuromodulation, Freiburg, Denmark
- Department of Psychiatry and Psychotherapy, University of Freiburg, Faculty of Medicine, Freiburg, Denmark
| | - Grete Dyb
- University of Oslo, Institute of Clinical Medicine, Oslo, Norway
- Norwegian Centre for Violence and Traumatic Stress Studies, Oslo, Norway
| | - Alma Džubur Kulenović
- Department of Psychiatry, University Clinical Center of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Howard J Edenberg
- Indiana University School of Medicine, Biochemistry and Molecular Biology, Indianapolis, IN, USA
- Indiana University School of Medicine, Medical and Molecular Genetics, Indianapolis, IN, USA
| | - Alexandra Evans
- Cardiff University, National Centre for Mental Health, MRC Centre for Psychiatric Genetics and Genomics, Cardiff, UK
| | - Chiara Fabbri
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Negar Fani
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Adriana Feder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Norah C Feeny
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Janine D Flory
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - David Forbes
- Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
| | - Carol E Franz
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Sandro Galea
- Boston University School of Public Health, Boston, MA, USA
| | - Melanie E Garrett
- Duke University, Duke Molecular Physiology Institute, Durham, NC, USA
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joel Gelernter
- VA Connecticut Healthcare Center, Psychiatry Service, West Haven, CT, USA
- Department of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Elbert Geuze
- Netherlands Ministry of Defence, Brain Research and Innovation Centre, Utrecht, The Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Charles F Gillespie
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Slavina B Goleva
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, TN, USA
- National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Mental Health & Neuroscience Program, Brisbane, Queensland, Australia
| | - Aferdita Goçi
- Department of Psychiatry, University Clinical Centre of Kosovo, Prishtina, Kosovo
| | - Lana Ruvolo Grasser
- Wayne State University School of Medicine, Psychiatry and Behavioral Neurosciencess, Detroit, MI, USA
| | - Camila Guindalini
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
| | - Magali Haas
- Cohen Veterans Bioscience, New York City, NY, USA
| | - Saskia Hagenaars
- King's College London, National Institute for Health and Care Research Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Michael A Hauser
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Andrew C Heath
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Victor Hesselbrock
- University of Connecticut School of Medicine, Psychiatry, Farmington, CT, USA
| | - Ian B Hickie
- University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia
| | - Kelleigh Hogan
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - David Michael Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Analytic and Translational Genetics Unit, Boston, MA, USA
| | - Laura M Huckins
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Kristian Hveem
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, K. G. Jebsen Center for Genetic Epidemiology, Trondheim, Norway
| | - Miro Jakovljević
- Department of Psychiatry, University Hospital Center of Zagreb, Zagreb, Croatia
| | - Arash Javanbakht
- Wayne State University School of Medicine, Psychiatry and Behavioral Neurosciencess, Detroit, MI, USA
| | - Gregory D Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jessica Johnson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ian Jones
- Cardiff University, National Centre for Mental Health, Cardiff University Centre for Psychiatric Genetics and Genomics, Cardiff, UK
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Karen-Inge Karstoft
- The Danish Veteran Centre, Research and Knowledge Centre, Ringsted, Denmark
- Department of Psychology, University of Copenhagen, Copenhagen, Denmark
| | - Milissa L Kaufman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - James L Kennedy
- Centre for Addiction and Mental Health, Neurogenetics Section, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Tanenbaum Centre for Pharmacogenetics, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Alaptagin Khan
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Nathan A Kimbrel
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center (MIRECC), Genetics Research Laboratory, Durham, NC, USA
- Durham VA Health Care System, Mental Health Service Line, Durham, NC, USA
| | - Anthony P King
- The Ohio State University, College of Medicine, Institute for Behavioral Medicine Research, Columbus, OH, USA
| | - Nastassja Koen
- University of Cape Town, Department of Psychiatry & Neuroscience Institute, SA MRC Unit on Risk & Resilience in Mental Disorders, Cape Town, South Africa
| | - Roman Kotov
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - Henry R Kranzler
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kristi Krebs
- University of Tartu, Institute of Genomics, Estonian Genome Center, Tartu, Estonia
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Bruce R Lawford
- Queensland University of Technology, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Lauren A M Lebois
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Center of Excellence in Depression and Anxiety Disorders, Belmont, MA, USA
| | - Kelli Lehto
- University of Tartu, Institute of Genomics, Estonian Genome Center, Tartu, Estonia
| | - Daniel F Levey
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Catrin Lewis
- Cardiff University, National Centre for Mental Health, MRC Centre for Psychiatric Genetics and Genomics, Cardiff, UK
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Sciences, Texas A&M University College of Medicine, Bryan, TX, USA
| | - Sarah D Linnstaedt
- Department of Anesthesiology, UNC Institute for Trauma Recovery, Chapel Hill, NC, USA
| | - Mark W Logue
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Boston University School of Medicine, Psychiatry, Biomedical Genetics, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Benjamin J Luft
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Michelle K Lupton
- QIMR Berghofer Medical Research Institute, Mental Health & Neuroscience Program, Brisbane, Queensland, Australia
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Iouri Makotkine
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - Shelby Marchese
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Marmar
- New York University, Grossman School of Medicine, New York City, NY, USA
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Genetics, Brisbane, Queensland, Australia
| | - Gabriela A Martínez-Levy
- Department of Genetics, Instituto Nacional de Psiquiatraía Ramón de la Fuente Muñiz, Mexico City, Mexico
| | - Kerrie McAloney
- QIMR Berghofer Medical Research Institute, Mental Health & Neuroscience Program, Brisbane, Queensland, Australia
| | - Alexander McFarlane
- University of Adelaide, Discipline of Psychiatry, Adelaide, South Australia, Australia
| | | | - Samuel A McLean
- Department of Anesthesiology, UNC Institute for Trauma Recovery, Chapel Hill, NC, USA
- Department of Emergency Medicine, UNC Institute for Trauma Recovery, Chapel Hill, NC, USA
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Mental Health & Neuroscience Program, Brisbane, Queensland, Australia
| | - Divya Mehta
- Queensland University of Technology, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, Queensland, Australia
| | - Jacquelyn Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Elizabeth A Mikita
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Lili Milani
- University of Tartu, Institute of Genomics, Estonian Genome Center, Tartu, Estonia
| | | | - Mark W Miller
- Boston University School of Medicine, Psychiatry, Biomedical Genetics, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
| | - Rajendra A Morey
- Duke University School of Medicine, Duke Brain Imaging and Analysis Center, Durham, NC, USA
| | - Charles Phillip Morris
- Queensland University of Technology, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Aarhus University Hospital-Psychiatry, Psychosis Research Unit, Aarhus, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Aarhus University, Centre for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Aarhus University, Centre for Integrated Register-Based Research, Aarhus, Denmark
- Aarhus University, National Centre for Register-Based Research, Aarhus, Denmark
| | - Mary S Mufford
- Department of Pathology, University of Cape Town, Division of Human Genetics, Cape Town, South Africa
| | - Elliot C Nelson
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- University of Copenhagen, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Sonya B Norman
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- National Center for Post Traumatic Stress Disorder, Executive Division, White River Junction, VT, USA
| | - Nicole R Nugent
- Department of Emergency Medicine, Alpert Brown Medical School, Providence, RI, USA
- Department of Pediatrics, Alpert Brown Medical School, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Alpert Brown Medical School, Providence, RI, USA
| | - Meaghan O'Donnell
- Department of Psychiatry, University of Melbourne, Phoenix Australia, Melbourne, Victoria, Australia
| | - Holly K Orcutt
- Department of Psychology, Northern Illinois University, DeKalb, IL, USA
| | - Pedro M Pan
- Universidade Federal de São Paulo, Psychiatry, São Paulo, Brazil
| | - Matthew S Panizzon
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Gita A Pathak
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Edward S Peters
- University of Nebraska Medical Center, College of Public Health, Omaha, NE, USA
| | - Alan L Peterson
- South Texas Veterans Health Care System, Research and Development Service, San Antonio, TX, USA
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Matthew Peverill
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Robert H Pietrzak
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, West Haven, CT, USA
| | - Melissa A Polusny
- Minneapolis VA Health Care System, Mental Health Service Line, Minneapolis, MN, USA
- Department of Psychiatry & Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN, USA
- Center for Care Delivery and Outcomes Research (CCDOR), Minneapolis, MN, USA
| | - Bernice Porjesz
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Abigail Powers
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Xue-Jun Qin
- Duke University, Duke Molecular Physiology Institute, Durham, NC, USA
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Columbia University Mailmain School of Public Health, New York City, NY, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Andrea L Roberts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex O Rothbaum
- Department of Psychological Sciences, Emory University, Atlanta, GA, USA
- Department of Research and Outcomes, Skyland Trail, Atlanta, GA, USA
| | - Barbara O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Peter Roy-Byrne
- Department of Psychiatry, University of Washington, Seattle, WA, USA
| | - Kenneth J Ruggiero
- Department of Nursing, Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Ariane Rung
- Department of Epidemiology, Louisiana State University Health Sciences Center, School of Public Health, New Orleans, LA, USA
| | - Heiko Runz
- Biogen Inc., Research & Development, Cambridge, MA, USA
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, School for Mental Health and Neuroscience, Maastricht, The Netherlands
| | | | - Giovanni Abrahão Salum
- Child Mind Institute, New York City, NY, USA
- Instituto Nacional de Psiquiatria de Desenvolvimento, São Paulo, Brazil
| | - Laura Sampson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Sixto E Sanchez
- Department of Medicine, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Marcos Santoro
- Universidade Federal de São Paulo, Departamento de Bioquímica-Disciplina de Biologia Molecular, São Paulo, Brazil
| | - Carina Seah
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Stellenbosch University, SAMRC Extramural Genomics of Brain Disorders Research Unit, Cape Town, South Africa
| | - Julia S Seng
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Women's and Gender Studies, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Institute for Research on Women and Gender, Ann Arbor, MI, USA
- University of Michigan, School of Nursing, Ann Arbor, MI, USA
| | - Andrey Shabalin
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Christina M Sheerin
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Derrick Silove
- Department of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Gynecology and Obstetrics, Department of Psychiatry and Behavioral Sciences, Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Boston, MA, USA
| | - Scott R Sponheim
- Minneapolis VA Health Care System, Mental Health Service Line, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan J Stein
- University of Cape Town, Department of Psychiatry & Neuroscience Institute, SA MRC Unit on Risk & Resilience in Mental Disorders, Cape Town, South Africa
| | - Synne Stensland
- Oslo University Hospital, Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo, Norway
- Norwegian Centre for Violence and Traumatic Stress Studies, Oslo, Norway
| | - Jennifer S Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Jennifer A Sumner
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Martin H Teicher
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Developmental Biopsychiatry Research Program, Belmont, MA, USA
| | - Wesley K Thompson
- Mental Health Centre Sct. Hans, Institute of Biological Psychiatry, Roskilde, Denmark
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science, La Jolla, CA, USA
| | - Arun K Tiwari
- Centre for Addiction and Mental Health, Neurogenetics Section, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Tanenbaum Centre for Pharmacogenetics, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Edward Trapido
- Department of Epidemiology, Louisiana State University Health Sciences Center, School of Public Health, New Orleans, LA, USA
| | - Monica Uddin
- University of South Florida College of Public Health, Genomics Program, Tampa, FL, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Unnur Valdimarsdóttir
- Karolinska Institutet, Unit of Integrative Epidemiology, Institute of Environmental Medicine, Stockholm, Sweden
- University of Iceland, Faculty of Medicine, Center of Public Health Sciences, School of Health Sciences, Reykjavik, Iceland
| | - Miranda Van Hooff
- University of Adelaide, Adelaide Medical School, Adelaide, South Australia, Australia
| | - Eric Vermetten
- ARQ Nationaal Psychotrauma Centrum, Psychotrauma Research Expert Group, Diemen, The Netherlands
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
- Department of Psychiatry, New York University School of Medicine, New York City, NY, USA
| | - Christiaan H Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, The Netherlands
- Department of Anatomy and Neurosciences, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joanne Voisey
- Queensland University of Technology, School of Biomedical Sciences, Kelvin Grove, Queensland, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, Queensland, Australia
| | - Yunpeng Wang
- Department of Psychology, University of Oslo, Lifespan Changes in Brain and Cognition (LCBC), Oslo, Norway
| | - Zhewu Wang
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
- Department of Mental Health, Ralph H Johnson VA Medical Center, Charleston, SC, USA
| | - Monika Waszczuk
- Department of Psychology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Heike Weber
- University Hospital of Würzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Würzburg, Denmark
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Copenhagen University Hospital, Institute of Biological Psychiatry, Mental Health Services, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- University of Copenhagen, The Globe Institute, Lundbeck Foundation Center for Geogenetics, Copenhagen, Denmark
| | - Michelle A Williams
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Douglas E Williamson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Research, Durham VA Health Care System, Durham, NC, USA
| | - Bendik S Winsvold
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, K. G. Jebsen Center for Genetic Epidemiology, Trondheim, Norway
- Oslo University Hospital, Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Sherry Winternitz
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Christiane Wolf
- University Hospital of Würzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Würzburg, Denmark
| | - Erika J Wolf
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yan Xia
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Analytic and Translational Genetics Unit, Boston, MA, USA
| | - Ying Xiong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Rachel Yehuda
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Mental Health, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Keith A Young
- Central Texas Veterans Health Care System, Research Service, Temple, TX, USA
- Department of Psychiatry and Behavioral Sciences, Texas A&M University School of Medicine, Bryan, TX, USA
| | - Ross McD Young
- Queensland University of Technology, School of Clinical Sciences, Kelvin Grove, Queensland, Australia
- University of the Sunshine Coast, The Chancellory, Sippy Downs, Queensland, Australia
| | - Clement C Zai
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Centre for Addiction and Mental Health, Neurogenetics Section, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Tanenbaum Centre for Pharmacogenetics, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Gwyneth C Zai
- Centre for Addiction and Mental Health, Neurogenetics Section, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Tanenbaum Centre for Pharmacogenetics, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, General Adult Psychiatry and Health Systems Division, Toronto, Ontario, Canada
| | - Mark Zervas
- Cohen Veterans Bioscience, New York City, NY, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - Lori A Zoellner
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - John-Anker Zwart
- University of Oslo, Institute of Clinical Medicine, Oslo, Norway
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, K. G. Jebsen Center for Genetic Epidemiology, Trondheim, Norway
- Oslo University Hospital, Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo, Norway
| | - Terri deRoon-Cassini
- Department of Surgery, Division of Trauma & Acute Care Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sanne J H van Rooij
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Leigh L van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
- University of California San Diego, School of Public Health, La Jolla, CA, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Boston, MA, USA
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6
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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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7
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Shi JJ, Mao CY, Guo YZ, Fan Y, Hao XY, Li SJ, Tian J, Hu ZW, Li MJ, Li JD, Ma DR, Guo MN, Zuo CY, Liang YY, Xu YM, Yang J, Shi CH. Joint analysis of proteome, transcriptome, and multi-trait analysis to identify novel Parkinson's disease risk genes. Aging (Albany NY) 2024; 16:1555-1580. [PMID: 38240717 PMCID: PMC10866412 DOI: 10.18632/aging.205444] [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: 02/20/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
Genome-wide association studies (GWAS) have identified multiple risk variants for Parkinson's disease (PD). Nevertheless, how the risk variants confer the risk of PD remains largely unknown. We conducted a proteome-wide association study (PWAS) and summary-data-based mendelian randomization (SMR) analysis by integrating PD GWAS with proteome and protein quantitative trait loci (pQTL) data from human brain, plasma and CSF. We also performed a large transcriptome-wide association study (TWAS) and Fine-mapping of causal gene sets (FOCUS), leveraging joint-tissue imputation (JTI) prediction models of 22 tissues to identify and prioritize putatively causal genes. We further conducted PWAS, SMR, TWAS, and FOCUS using a multi-trait analysis of GWAS (MTAG) to identify additional PD risk genes to boost statistical power. In this large-scale study, we identified 16 genes whose genetically regulated protein abundance levels were associated with Parkinson's disease risk. We undertook a large-scale analysis of PD and correlated traits, through TWAS and FOCUS studies, and discovered 26 casual genes related to PD that had not been reported in previous TWAS. 5 genes (CD38, GPNMB, RAB29, TMEM175, TTC19) showed significant associations with PD at both the proteome-wide and transcriptome-wide levels. Our study provides new insights into the etiology and underlying genetic architecture of PD.
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Affiliation(s)
- Jing-Jing Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Ya-Zhou Guo
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Xiao-Yan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Shuang-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jie Tian
- Zhengzhou Railway Vocational and Technical College, Zhengzhou 450000, Henan, China
| | - Zheng-Wei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jia-Di Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Dong-Rui Ma
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Nan Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Chun-Yan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yuan-Yuan Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
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8
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Nievergelt CM, Maihofer AX, Atkinson EG, Chen CY, Choi KW, Coleman JR, Daskalakis NP, Duncan LE, Polimanti R, Aaronson C, Amstadter AB, Andersen SB, Andreassen OA, Arbisi PA, Ashley-Koch AE, Austin SB, Avdibegoviç E, Babic D, Bacanu SA, Baker DG, Batzler A, Beckham JC, Belangero S, Benjet C, Bergner C, Bierer LM, Biernacka JM, Bierut LJ, Bisson JI, Boks MP, Bolger EA, Brandolino A, Breen G, Bressan RA, Bryant RA, Bustamante AC, Bybjerg-Grauholm J, Bækvad-Hansen M, Børglum AD, Børte S, Cahn L, Calabrese JR, Caldas-de-Almeida JM, Chatzinakos C, Cheema S, Clouston SAP, Colodro-Conde L, Coombes BJ, Cruz-Fuentes CS, Dale AM, Dalvie S, Davis LK, Deckert J, Delahanty DL, Dennis MF, deRoon-Cassini T, Desarnaud F, DiPietro CP, Disner SG, Docherty AR, Domschke K, Dyb G, Kulenovic AD, Edenberg HJ, Evans A, Fabbri C, Fani N, Farrer LA, Feder A, Feeny NC, Flory JD, Forbes D, Franz CE, Galea S, Garrett ME, Gelaye B, Gelernter J, Geuze E, Gillespie CF, Goci A, Goleva SB, Gordon SD, Grasser LR, Guindalini C, Haas M, Hagenaars S, Hauser MA, Heath AC, Hemmings SM, Hesselbrock V, Hickie IB, Hogan K, Hougaard DM, Huang H, Huckins LM, Hveem K, Jakovljevic M, Javanbakht A, Jenkins GD, Johnson J, Jones I, Jovanovic T, Karstoft KI, Kaufman ML, Kennedy JL, Kessler RC, Khan A, Kimbrel NA, King AP, Koen N, Kotov R, Kranzler HR, Krebs K, Kremen WS, Kuan PF, Lawford BR, Lebois LAM, Lehto K, Levey DF, Lewis C, Liberzon I, Linnstaedt SD, Logue MW, Lori A, Lu Y, Luft BJ, Lupton MK, Luykx JJ, Makotkine I, Maples-Keller JL, Marchese S, Marmar C, Martin NG, MartÍnez-Levy GA, McAloney K, McFarlane A, McLaughlin KA, McLean SA, Medland SE, Mehta D, Meyers J, Michopoulos V, Mikita EA, Milani L, Milberg W, Miller MW, Morey RA, Morris CP, Mors O, Mortensen PB, Mufford MS, Nelson EC, Nordentoft M, Norman SB, Nugent NR, O'Donnell M, Orcutt HK, Pan PM, Panizzon MS, Pathak GA, Peters ES, Peterson AL, Peverill M, Pietrzak RH, Polusny MA, Porjesz B, Powers A, Qin XJ, Ratanatharathorn A, Risbrough VB, Roberts AL, Rothbaum BO, Rothbaum AO, Roy-Byrne P, Ruggiero KJ, Rung A, Runz H, Rutten BPF, de Viteri SS, Salum GA, Sampson L, Sanchez SE, Santoro M, Seah C, Seedat S, Seng JS, Shabalin A, Sheerin CM, Silove D, Smith AK, Smoller JW, Sponheim SR, Stein DJ, Stensland S, Stevens JS, Sumner JA, Teicher MH, Thompson WK, Tiwari AK, Trapido E, Uddin M, Ursano RJ, Valdimarsdóttir U, van den Heuvel LL, Van Hooff M, van Rooij SJ, Vermetten E, Vinkers CH, Voisey J, Wang Z, Wang Y, Waszczuk M, Weber H, Wendt FR, Werge T, Williams MA, Williamson DE, Winsvold BS, Winternitz S, Wolf EJ, Wolf C, Xia Y, Xiong Y, Yehuda R, Young RM, Young KA, Zai CC, Zai GC, Zervas M, Zhao H, Zoellner LA, Zwart JA, Stein MB, Ressler KJ, Koenen KC. Discovery of 95 PTSD loci provides insight into genetic architecture and neurobiology of trauma and stress-related disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.31.23294915. [PMID: 37693460 PMCID: PMC10491375 DOI: 10.1101/2023.08.31.23294915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Posttraumatic stress disorder (PTSD) genetics are characterized by lower discoverability than most other psychiatric disorders. The contribution to biological understanding from previous genetic studies has thus been limited. We performed a multi-ancestry meta-analysis of genome-wide association studies across 1,222,882 individuals of European ancestry (137,136 cases) and 58,051 admixed individuals with African and Native American ancestry (13,624 cases). We identified 95 genome-wide significant loci (80 novel). Convergent multi-omic approaches identified 43 potential causal genes, broadly classified as neurotransmitter and ion channel synaptic modulators (e.g., GRIA1, GRM8, CACNA1E ), developmental, axon guidance, and transcription factors (e.g., FOXP2, EFNA5, DCC ), synaptic structure and function genes (e.g., PCLO, NCAM1, PDE4B ), and endocrine or immune regulators (e.g., ESR1, TRAF3, TANK ). Additional top genes influence stress, immune, fear, and threat-related processes, previously hypothesized to underlie PTSD neurobiology. These findings strengthen our understanding of neurobiological systems relevant to PTSD pathophysiology, while also opening new areas for investigation.
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Bledsoe X, Gamazon ER. A Transcriptomic Atlas of the Human Brain Reveals Genetically Determined Aspects of Neuropsychiatric Health. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.10.23287072. [PMID: 36993467 PMCID: PMC10055455 DOI: 10.1101/2023.03.10.23287072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Imaging features associated with neuropsychiatric traits can provide valuable insights into underlying pathophysiology. Using data from the UK biobank, we perform tissue-specific TWAS on over 3,500 neuroimaging phenotypes to generate a publicly accessible resource detailing the neurophysiologic consequences of gene expression. As a comprehensive catalog of neuroendophenotypes, this resource represents a powerful neurologic gene prioritization schema that can improve our understanding of brain function, development, and disease. We show that our approach generates reproducible results in internal and external replication datasets. Notably, genetically determined expression alone is shown here to enable high-fidelity reconstruction of brain structure and organization. We demonstrate complementary benefits of cross-tissue and single-tissue analyses towards an integrated neurobiology and provide evidence that gene expression outside the central nervous system provides unique insights into brain health. As an application, we show that over 40% of genes previously associated with schizophrenia in the largest GWAS meta-analysis causally affect neuroimaging phenotypes noted to be altered in schizophrenic patients.
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Affiliation(s)
- Xavier Bledsoe
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
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10
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Adams DM, Reay WR, Cairns MJ. Multiomic prioritisation of risk genes for anorexia nervosa. Psychol Med 2023; 53:1-9. [PMID: 36803885 PMCID: PMC10600818 DOI: 10.1017/s0033291723000235] [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: 08/14/2022] [Revised: 01/12/2023] [Accepted: 01/23/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Anorexia nervosa (AN) is a psychiatric disorder associated with marked morbidity. Whilst AN genetic studies could identify novel treatment targets, integration of functional genomics data, including transcriptomics and proteomics, would assist to disentangle correlated signals and reveal causally associated genes. METHODS We used models of genetically imputed expression and splicing from 14 tissues, leveraging mRNA, protein, and mRNA alternative splicing weights to identify genes, proteins, and transcripts, respectively, associated with AN risk. This was accomplished through transcriptome, proteome, and spliceosome-wide association studies, followed by conditional analysis and finemapping to prioritise candidate causal genes. RESULTS We uncovered 134 genes for which genetically predicted mRNA expression was associated with AN after multiple-testing correction, as well as four proteins and 16 alternatively spliced transcripts. Conditional analysis of these significantly associated genes on other proximal association signals resulted in 97 genes independently associated with AN. Moreover, probabilistic finemapping further refined these associations and prioritised putative causal genes. The gene WDR6, for which increased genetically predicted mRNA expression was correlated with AN, was strongly supported by both conditional analyses and finemapping. Pathway analysis of genes revealed by finemapping identified the pathway regulation of immune system process (overlapping genes = MST1, TREX1, PRKAR2A, PROS1) as statistically overrepresented. CONCLUSIONS We leveraged multiomic datasets to genetically prioritise novel risk genes for AN. Multiple-lines of evidence support that WDR6 is associated with AN, whilst other prioritised genes were enriched within immune related pathways, further supporting the role of the immune system in AN.
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Affiliation(s)
- Danielle M. Adams
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - William R. Reay
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Murray J. Cairns
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
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11
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Gedik H, Peterson RE, Riley BP, Vladimirov VI, Bacanu SA. Integrative Post-Genome-Wide Association Study Analyses Relevant to Psychiatric Disorders: Imputing Transcriptome and Proteome Signals. Complex Psychiatry 2023; 9:130-144. [PMID: 37588130 PMCID: PMC10425719 DOI: 10.1159/000530223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/09/2023] [Indexed: 08/18/2023] Open
Abstract
Background The genome-wide association study (GWAS) is a common tool to identify genetic variants associated with complex traits, including psychiatric disorders (PDs). However, post-GWAS analyses are needed to extend the statistical inference to biologically relevant entities, e.g., genes, proteins, and pathways. To achieve this goal, researchers developed methods that incorporate biologically relevant intermediate molecular phenotypes, such as gene expression and protein abundance, which are posited to mediate the variant-trait association. Transcriptome-wide association study (TWAS) and proteome-wide association study (PWAS) are commonly used methods to test the association between these molecular mediators and the trait. Summary In this review, we discuss the most recent developments in TWAS and PWAS. These methods integrate existing "omic" information with the GWAS summary statistics for trait(s) of interest. Specifically, they impute transcript/protein data and test the association between imputed gene expression/protein level with phenotype of interest by using (i) GWAS summary statistics and (ii) reference transcriptomic/proteomic/genomic datasets. TWAS and PWAS are suitable as analysis tools for (i) primary association scan and (ii) fine-mapping to identify potentially causal genes for PDs. Key Messages As post-GWAS analyses, TWAS and PWAS have the potential to highlight causal genes for PDs. These prioritized genes could indicate targets for the development of novel drug therapies. For researchers attempting such analyses, we recommend Mendelian randomization tools that use GWAS statistics for both trait and reference datasets, e.g., summary Mendelian randomization (SMR). We base our recommendation on (i) being able to use the same tool for both TWAS and PWAS, (ii) not requiring the pre-computed weights (and thus easier to update for larger reference datasets), and (iii) most larger transcriptome reference datasets are publicly available and easy to transform into a compatible format for SMR analysis.
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Affiliation(s)
- Huseyin Gedik
- Integrative Life Sciences, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Roseann E. Peterson
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Brien P. Riley
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Silviu-Alin Bacanu
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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12
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Voloudakis G, Vicari JM, Venkatesh S, Hoffman GE, Dobrindt K, Zhang W, Beckmann ND, Higgins CA, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee KM, Bian J, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Lynch JA, Merad M, tenOever BR, Charney AW, Brennand KJ, Fullard JF, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. NPJ Genom Med 2022; 7:52. [PMID: 36064543 PMCID: PMC9441828 DOI: 10.1038/s41525-022-00324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/19/2022] [Indexed: 02/06/2023] Open
Abstract
Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that reduce COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX), and perturbagen signatures, we identified IL10RB as the top candidate gene target for COVID-19 host susceptibility. In a series of validation steps, we show that predicted GReX upregulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
| | - James M Vicari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Dobrindt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Wen Zhang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina A Higgins
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University, New York, NY, USA
| | - Stathis Argyriou
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | | | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Jiantao Bian
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Jennifer S Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- VA Northeast Ohio Healthcare System, Cleveland VA Medical Center, Cleveland, OH, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, OR, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Striker
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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13
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Boussaty EC, Friedman RA, Clifford RE. Hearing loss and tinnitus: association studies for complex-hearing disorders in mouse and man. Hum Genet 2022; 141:981-990. [PMID: 34318347 PMCID: PMC8792513 DOI: 10.1007/s00439-021-02317-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies (GWAS) provide an unbiased first look at genetic loci involved in aging and noise-induced sensorineural hearing loss and tinnitus. The hearing phenotype, whether audiogram-based or self-report, is regressed against genotyped information at representative single nucleotide polymorphisms (SNPs) across the genome. Findings include the fact that both hearing loss and tinnitus are polygenic disorders, with up to thousands of genes, each of effect size of < 0.02. Smaller human GWAS' were able to use objective measures and identified a few loci; however, hundreds of thousands of participants have been required for the statistical power to identify significant variants, and GWAS is unable to assess rare variants with mean allele frequency < 1%. Animal studies are required as well because of inability to access the human cochlea. Mouse GWAS builds on linkage techniques and the known phenotypic differences in auditory function between inbred strains. With the advantage that the laboratory environment can be controlled for noise and aging, the Hybrid Mouse Diversity Panel (HDMP) combines 100 strains sequenced at high resolution. Lift-over regions between mice and humans have identified over 17,000 homologous genes. Since most significant SNPs are either intergenic or in introns, and binding sites between species are poorly preserved between species, expression quantitative trait locus information is required to bring humans and mice into agreement. Transcriptome-wide analysis studies (TWAS) can prioritize putative causal genes and tissues. Diverse species, each making a distinct contribution, carry a synergistic advantage in the quest for treatment and ultimate cure of sensorineural hearing difficulties.
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Affiliation(s)
- Ely Cheikh Boussaty
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Rick Adam Friedman
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Royce E Clifford
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA.
- Research Department, VA Hospitals San Diego, San Diego, CA, USA.
- Visiting Scientist, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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14
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Daskalakis NP, Meijer OC, Ronald de Kloet E. Mineralocorticoid receptor and glucocorticoid receptor work alone and together in cell-type-specific manner: Implications for resilience prediction and targeted therapy. Neurobiol Stress 2022; 18:100455. [PMID: 35601687 PMCID: PMC9118500 DOI: 10.1016/j.ynstr.2022.100455] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
‘You can't roll the clock back and reverse the effects of experiences' Bruce McEwen used to say when explaining how allostasis labels the adaptive process. Here we will for once roll the clock back to the times that the science of the glucocorticoid hormone was honored with a Nobel prize and highlight the discovery of their receptors in the hippocampus as inroad to its current status as master regulator in control of stress coping and adaptation. Glucocorticoids operate in concert with numerous neurotransmitters, neuropeptides, and other hormones with the aim to facilitate processing of information in the neurocircuitry of stress, from anticipation and perception of a novel experience to behavioral adaptation and memory storage. This action, exerted by the glucocorticoids, is guided by two complementary receptor systems, mineralocorticoid receptors (MR) and glucocorticoid receptors (GR), that need to be balanced for a healthy stress response pattern. Here we discuss the cellular, neuroendocrine, and behavioral studies underlying the MR:GR balance concept, highlight the relevance of hypothalamic-pituitary-adrenal (HPA) -axis patterns and note the limited understanding yet of sexual dimorphism in glucocorticoid actions. We conclude with the prospect that (i) genetically and epigenetically regulated receptor variants dictate cell-type-specific transcriptome signatures of stress-related neuropsychiatric symptoms and (ii) selective receptor modulators are becoming available for more targeted treatment. These two new developments may help to ‘restart the clock’ with the prospect to support resilience.
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15
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Daskalakis NP, Schultz LM, Visoki E, Moore TM, Argabright ST, Harnett NG, DiDomenico GE, Warrier V, Almasy L, Barzilay R. Contributions of PTSD polygenic risk and environmental stress to suicidality in preadolescents. Neurobiol Stress 2021; 15:100411. [PMID: 34765698 PMCID: PMC8569631 DOI: 10.1016/j.ynstr.2021.100411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/17/2021] [Accepted: 10/23/2021] [Indexed: 11/19/2022] Open
Abstract
Suicidal ideation and attempts (i.e., suicidality) are complex behaviors driven by environmental stress, genetic susceptibility, and their interaction. Preadolescent suicidality is a major health problem with rising rates, yet its underlying biology is understudied. Here we studied effects of genetic stress susceptibility, approximated by the polygenic risk score (PRS) for post-traumatic-stress-disorder (PTSD), on preadolescent suicidality in participants from the Adolescent Brain Cognitive Development (ABCD) Study®. We further evaluated PTSD-PRS effects on suicidality in the presence of environmental stressors that are established suicide risk factors. Analyses included both European and African ancestry participants using PRS calculated based on summary statistics from ancestry-specific genome-wide association studies. In European ancestry participants (N = 4,619, n = 378 suicidal), PTSD-PRS was associated with preadolescent suicidality (odds ratio [OR] = 1.12, 95%CI 1-1.25, p = 0.038). Results in African ancestry participants (N = 1,334, n = 130 suicidal) showed a similar direction but were not statistically significant (OR = 1.21, 95%CI 0.93-1.57, p = 0.153). Sensitivity analyses using non-psychiatric polygenic score for height and using cross-ancestry PTSD-PRS did not reveal any association with suicidality, supporting the specificity of the association of ancestry-specific PTSD-PRS with suicidality. Environmental stressors were robustly associated with suicidality across ancestries with moderate effect size for negative life events and family conflict (OR 1.27-1.6); and with large effect size (OR ∼ 4) for sexual-orientation discrimination. When combined with environmental factors, PTSD-PRS showed marginal additive effects in explaining variability in suicidality, with no evidence for G × E interaction. Results support use of cross-phenotype PRS, specifically stress-susceptibility, as a genetic marker for suicidality risk early in the lifespan.
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Affiliation(s)
- Nikolaos P. Daskalakis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura M. Schultz
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- Lifespan Brain Institute, CHOP and Penn Medicine, Philadelphia, PA, USA
| | - Elina Visoki
- Lifespan Brain Institute, CHOP and Penn Medicine, Philadelphia, PA, USA
| | - Tyler M. Moore
- Lifespan Brain Institute, CHOP and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Nathaniel G. Harnett
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- Lifespan Brain Institute, CHOP and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ran Barzilay
- Lifespan Brain Institute, CHOP and Penn Medicine, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, CHOP, Philadelphia, PA, USA
- Corresponding author. 10th floor, Gates Pavilion, Hospital of the University of Pennsylvania, 34th and Spruce Street, Philadelphia, PA, 19104, USA.
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16
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Dalvie S, Chatzinakos C, Al Zoubi O, Georgiadis F, Lancashire L, Daskalakis NP. From genetics to systems biology of stress-related mental disorders. Neurobiol Stress 2021; 15:100393. [PMID: 34584908 PMCID: PMC8456113 DOI: 10.1016/j.ynstr.2021.100393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 01/20/2023] Open
Abstract
Many individuals will be exposed to some form of traumatic stress in their lifetime which, in turn, increases the likelihood of developing stress-related disorders such as post-traumatic stress disorder (PTSD), major depressive disorder (MDD) and anxiety disorders (ANX). The development of these disorders is also influenced by genetics and have heritability estimates ranging between ∼30 and 70%. In this review, we provide an overview of the findings of genome-wide association studies for PTSD, depression and ANX, and we observe a clear genetic overlap between these three diagnostic categories. We go on to highlight the results from transcriptomic and epigenomic studies, and, given the multifactorial nature of stress-related disorders, we provide an overview of the gene-environment studies that have been conducted to date. Finally, we discuss systems biology approaches that are now seeing wider utility in determining a more holistic view of these complex disorders.
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Affiliation(s)
- Shareefa Dalvie
- South African Medical Research Council (SAMRC), Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC), Unit on Child & Adolescent Health, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Chris Chatzinakos
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Obada Al Zoubi
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Foivos Georgiadis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Lee Lancashire
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Data Science, Cohen Veterans Bioscience, New York, USA
| | - Nikolaos P. Daskalakis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
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17
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Chatzinakos C, Lee D, Cai N, Vladimirov VI, Webb BT, Riley BP, Flint J, Kendler KS, Ressler KJ, Daskalakis NP, Bacanu S. Increasing the resolution and precision of psychiatric genome-wide association studies by re-imputing summary statistics using a large, diverse reference panel. Am J Med Genet B Neuropsychiatr Genet 2021; 186:16-27. [PMID: 33576176 PMCID: PMC8247874 DOI: 10.1002/ajmg.b.32834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 12/30/2022]
Abstract
Genotype imputation across populations of mixed ancestry is critical for optimal discovery in large-scale genome-wide association studies (GWAS). Methods for direct imputation of GWAS summary-statistics were previously shown to be practically as accurate as summary statistics produced after raw genotype imputation, while incurring orders of magnitude lower computational burden. Given that direct imputation needs a precise estimation of linkage-disequilibrium (LD) and that most of the methods using a small reference panel for example, ~2,500-subject coming from the 1000 Genome-Project, there is a great need for much larger and more diverse reference panels. To accurately estimate the LD needed for an exhaustive analysis of any cosmopolitan cohort, we developed DISTMIX2. DISTMIX2: (a) uses a much larger and more diverse reference panel compared to traditional reference panels, and (b) can estimate weights of ethnic-mixture based solely on Z-scores, when allele frequencies are not available. We applied DISTMIX2 to GWAS summary-statistics from the psychiatric genetic consortium (PGC). DISTMIX2 uncovered signals in numerous new regions, with most of these findings coming from the rarer variants. Rarer variants provide much sharper location for the signals compared with common variants, as the LD for rare variants extends over a lower distance than for common ones. For example, while the original PGC post-traumatic stress disorder GWAS found only 3 marginal signals for common variants, we now uncover a very strong signal for a rare variant in PKN2, a gene associated with neuronal and hippocampal development. Thus, DISTMIX2 provides a robust and fast (re)imputation approach for most psychiatric GWAS-studies.
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Affiliation(s)
- Chris Chatzinakos
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Donghyung Lee
- Department of StatisticsMiami UniversityOxfordOhioUSA
| | - Na Cai
- Translational Genetics GroupHelmholtz InstituteMunichGermany
| | | | - Bradley T. Webb
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Brien P. Riley
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Jonathan Flint
- Center for Neurobehavioral GeneticsSemel Institute for Neuroscience and Human Behavior, University of CaliforniaLos AngelesCaliforniaUSA
| | - Kenneth S. Kendler
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Kerry J. Ressler
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
| | - Nikolaos P. Daskalakis
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Silviu‐Alin Bacanu
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
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Chatzinakos C, Georgiadis F, Lee D, Cai N, Vladimirov VI, Docherty A, Webb BT, Riley BP, Flint J, Kendler KS, Daskalakis NP, Bacanu S. TWAS pathway method greatly enhances the number of leads for uncovering the molecular underpinnings of psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet 2020; 183:454-463. [PMID: 32954640 PMCID: PMC7756231 DOI: 10.1002/ajmg.b.32823] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/13/2020] [Accepted: 08/15/2020] [Indexed: 01/29/2023]
Abstract
Genetic signal detection in genome-wide association studies (GWAS) is enhanced by pooling small signals from multiple Single Nucleotide Polymorphism (SNP), for example, across genes and pathways. Because genes are believed to influence traits via gene expression, it is of interest to combine information from expression Quantitative Trait Loci (eQTLs) in a gene or genes in the same pathway. Such methods, widely referred to as transcriptomic wide association studies (TWAS), already exist for gene analysis. Due to the possibility of eliminating most of the confounding effects of linkage disequilibrium (LD) from TWAS gene statistics, pathway TWAS methods would be very useful in uncovering the true molecular basis of psychiatric disorders. However, such methods are not yet available for arbitrarily large pathways/gene sets. This is possibly due to the quadratic (as a function of the number of SNPs) computational burden for computing LD across large chromosomal regions. To overcome this obstacle, we propose JEPEGMIX2-P, a novel TWAS pathway method that (a) has a linear computational burden, (b) uses a large and diverse reference panel (33 K subjects), (c) is competitive (adjusts for background enrichment in gene TWAS statistics), and (d) is applicable as-is to ethnically mixed-cohorts. To underline its potential for increasing the power to uncover genetic signals over the commonly used nontranscriptomics methods, for example, MAGMA, we applied JEPEGMIX2-P to summary statistics of most large meta-analyses from Psychiatric Genetics Consortium (PGC). While our work is just the very first step toward clinical translation of psychiatric disorders, PGC anorexia results suggest a possible avenue for treatment.
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Affiliation(s)
- Chris Chatzinakos
- Mclean HospitalHarvard UniversityCambridgeMassachusettsUSA,Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Foivos Georgiadis
- Mclean HospitalHarvard UniversityCambridgeMassachusettsUSA,Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Donghyung Lee
- Department of StatisticsUniversity of MiamiOxfordOhioUSA
| | - Na Cai
- Helmholtz Zentrum München, Helmholtz Pioneer CampusNeuherbergGermany
| | | | - Anna Docherty
- Department of PsychiatryUniversity of UtahSalt LakeUtahUSA
| | - Bradley T. Webb
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Brien P. Riley
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human BehaviorUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Kenneth S. Kendler
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Nikolaos P. Daskalakis
- Mclean HospitalHarvard UniversityCambridgeMassachusettsUSA,Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Silviu‐Alin Bacanu
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
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