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Wani AH, Katrinli S, Zhao X, Daskalakis NP, Zannas AS, Aiello AE, Baker DG, Boks MP, Brick LA, Chen CY, Dalvie S, Fortier C, Geuze E, Hayes JP, Kessler RC, King AP, Koen N, Liberzon I, Lori A, Luykx JJ, Maihofer AX, Milberg W, Miller MW, Mufford MS, Nugent NR, Rauch S, Ressler KJ, Risbrough VB, Rutten BPF, Stein DJ, Stein MB, Ursano RJ, Verfaellie MH, Vermetten E, Vinkers CH, Ware EB, Wildman DE, Wolf EJ, Nievergelt CM, Logue MW, Smith AK, Uddin M. Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts. BMC Med Genomics 2024; 17:235. [PMID: 39334086 PMCID: PMC11429352 DOI: 10.1186/s12920-024-02002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Incorporating genomic data into risk prediction has become an increasingly popular approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. METHODS Elastic Net was used to develop three risk score models using a discovery dataset (n = 1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. RESULTS The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy = 89%) using 3728 features and MoRSAE (accuracy = 84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta = 0.6839, p=0.006), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta = 1.92; MoRS, beta = 1.99 and MoRSAE, beta = 1.77) displayed a significant (p < 0.001) predictive power for post-deployment PTSD. CONCLUSION The inclusion of exposure variables adds to the predictive power of MRS. Classification-based MRS may be useful in predicting risk of future PTSD in populations with anticipated trauma exposure. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting PTSD and, relatedly, improve their performance in independent cohorts.
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Affiliation(s)
- Agaz H Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Xiang Zhao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - 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
- Center of Excellence in Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Anthony S Zannas
- University of North Carolina at Chapel Hill, Carolina Stress Initiative, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison E Aiello
- Robert N Butler Columbia Aging Center, Department of Epidemiology, Columbia University, New York, NY, 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
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht, UT, Netherlands
| | - Leslie A Brick
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Chia-Yen Chen
- Biogen Inc., Translational Sciences, Cambridge, MA, USA
| | - Shareefa Dalvie
- Department of Pathology, University of Cape Town, Cape Town, Western Province, South Africa
- Division of Human Genetics, University of Cape Town, Cape Town, Western Province, South Africa
| | - Catherine Fortier
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, TRACTS/GRECC, Boston, MA, USA
| | - Elbert Geuze
- Brain Research and Innovation Centre, Netherlands Ministry of Defence, Utrecht, UT, Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
| | - Jasmeet P Hayes
- Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Anthony P King
- The Ohio State University, College of Medicine, Institute for Behavioral Medicine Research, Columbus, OH, USA
| | - Nastassja Koen
- Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- SA MRC Unit On Risk & Resilience in Mental Disorders, University of Cape Town, Cape Town, Western Province, South Africa
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Sciences, Texas A&M University College of Medicine, Bryan, TX, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
| | - 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
| | | | - Mark W Miller
- Boston University School of Medicine, Psychiatry, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
| | - Mary S Mufford
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
| | - Nicole R Nugent
- Department of Emergency Medicine, Warren Alpert Brown Medical School, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Brown Medical School, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Brown Medical School, Providence, RI, USA
| | - Sheila Rauch
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
- Joseph Maxwell Cleland Atlanta Veterans Affairs Medical Center, Mental Health Service Line, Atlanta, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- McLean Hospital, Belmont, MA, 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
| | - Bart P F Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, Maastricht, Limburg, Netherlands
| | - Dan J Stein
- Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- SA MRC Unit On Risk & Resilience in Mental Disorders, University of Cape Town, Cape Town, Western Province, 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
- School of Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Mieke H Verfaellie
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- VA Boston Healthcare System, Memory Disorders Research Center, Boston, MA, USA
| | - Eric Vermetten
- Department of Psychiatry, Leiden University Medical Center, Leiden, ZH, Netherlands
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Christiaan H Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, Holland, Netherlands
- Department of Anatomy and Neurosciences, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, Holland, Netherlands
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, Holland, Netherlands
| | - Erin B Ware
- Survey Research Center, University of Michigan, Institute for Social Research, Ann Arbor, MI, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - 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
| | - 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
| | - Mark W Logue
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Boston University School of Medicine, Psychiatry, Biomedical Genetics, Boston, MA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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Katrinli S, Wani AH, Maihofer AX, Ratanatharathorn A, Daskalakis NP, Montalvo-Ortiz J, Núñez-Ríos DL, Zannas AS, Zhao X, Aiello AE, Ashley-Koch AE, Avetyan D, Baker DG, Beckham JC, Boks MP, Brick LA, Bromet E, Champagne FA, Chen CY, Dalvie S, Dennis MF, Fatumo S, Fortier C, Galea S, Garrett ME, Geuze E, Grant G, Hauser MA, Hayes JP, Hemmings SM, Huber BR, Jajoo A, Jansen S, Kessler RC, Kimbrel NA, King AP, Kleinman JE, Koen N, Koenen KC, Kuan PF, Liberzon I, Linnstaedt SD, Lori A, Luft BJ, Luykx JJ, Marx CE, McLean SA, Mehta D, Milberg W, Miller MW, Mufford MS, Musanabaganwa C, Mutabaruka J, Mutesa L, Nemeroff CB, Nugent NR, Orcutt HK, Qin XJ, Rauch SAM, Ressler KJ, Risbrough VB, Rutembesa E, Rutten BPF, Seedat S, Stein DJ, Stein MB, Toikumo S, Ursano RJ, Uwineza A, Verfaellie MH, Vermetten E, Vinkers CH, Ware EB, Wildman DE, Wolf EJ, Young RM, Zhao Y, van den Heuvel LL, Uddin M, Nievergelt CM, Smith AK, Logue MW. Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: A meta-analysis of 23 military and civilian cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310422. [PMID: 39072012 PMCID: PMC11275670 DOI: 10.1101/2024.07.15.24310422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background The occurrence of post-traumatic stress disorder (PTSD) following a traumatic event is associated with biological differences that can represent the susceptibility to PTSD, the impact of trauma, or the sequelae of PTSD itself. These effects include differences in DNA methylation (DNAm), an important form of epigenetic gene regulation, at multiple CpG loci across the genome. Moreover, these effects can be shared or specific to both central and peripheral tissues. Here, we aim to identify blood DNAm differences associated with PTSD and characterize the underlying biological mechanisms by examining the extent to which they mirror associations across multiple brain regions. Methods As the Psychiatric Genomics Consortium (PGC) PTSD Epigenetics Workgroup, we conducted the largest cross-sectional meta-analysis of epigenome-wide association studies (EWASs) of PTSD to date, involving 5077 participants (2156 PTSD cases and 2921 trauma-exposed controls) from 23 civilian and military studies. PTSD diagnosis assessments were harmonized following the standardized guidelines established by the PGC-PTSD Workgroup. DNAm was assayed from blood using either Illumina HumanMethylation450 or MethylationEPIC (850K) BeadChips. A common QC pipeline was applied. Within each cohort, DNA methylation was regressed on PTSD, sex (if applicable), age, blood cell proportions, and ancestry. An inverse variance-weighted meta-analysis was performed. We conducted replication analyses in tissue from multiple brain regions, neuronal nuclei, and a cellular model of prolonged stress. Results We identified 11 CpG sites associated with PTSD in the overall meta-analysis (1.44e-09 < p < 5.30e-08), as well as 14 associated in analyses of specific strata (military vs civilian cohort, sex, and ancestry), including CpGs in AHRR and CDC42BPB . Many of these loci exhibit blood-brain correlation in methylation levels and cross-tissue associations with PTSD in multiple brain regions. Methylation at most CpGs correlated with their annotated gene expression levels. Conclusions This study identifies 11 PTSD-associated CpGs, also leverages data from postmortem brain samples, GWAS, and genome-wide expression data to interpret the biology underlying these associations and prioritize genes whose regulation differs in those with PTSD.
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Polakkattil BK, Vellichirammal NN, Nair IV, Nair CM, Banerjee M. Methylome-wide and meQTL analysis helps to distinguish treatment response from non-response and pathogenesis markers in schizophrenia. Front Psychiatry 2024; 15:1297760. [PMID: 38516266 PMCID: PMC10954811 DOI: 10.3389/fpsyt.2024.1297760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
Schizophrenia is a complex condition with entwined genetic and epigenetic risk factors, posing a challenge to disentangle the intermixed pathological and therapeutic epigenetic signatures. To resolve this, we performed 850K methylome-wide and 700K genome-wide studies on the same set of schizophrenia patients by stratifying them into responders, non-responders, and drug-naïve patients. The key genes that signified the response were followed up using real-time gene expression studies to understand the effect of antipsychotics at the gene transcription level. The study primarily implicates hypermethylation in therapeutic response and hypomethylation in the drug-non-responsive state. Several differentially methylated sites and regions colocalized with the schizophrenia genome-wide association study (GWAS) risk genes and variants, supporting the convoluted gene-environment association. Gene ontology and protein-protein interaction (PPI) network analyses revealed distinct patterns that differentiated the treatment response from drug resistance. The study highlights the strong involvement of several processes related to nervous system development, cell adhesion, and signaling in the antipsychotic response. The ability of antipsychotic medications to alter the pathology by modulating gene expression or methylation patterns is evident from the general increase in the gene expression of response markers and histone modifiers and the decrease in class II human leukocyte antigen (HLA) genes following treatment with varying concentrations of medications like clozapine, olanzapine, risperidone, and haloperidol. The study indicates a directional overlap of methylation markers between pathogenesis and therapeutic response, thereby suggesting a careful distinction of methylation markers of pathogenesis from treatment response. In addition, there is a need to understand the trade-off between genetic and epigenetic observations. It is suggested that methylomic changes brought about by drugs need careful evaluation for their positive effects on pathogenesis, course of disease progression, symptom severity, side effects, and refractoriness.
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Affiliation(s)
- Binithamol K. Polakkattil
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- Research Center, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Neetha N. Vellichirammal
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Indu V. Nair
- Mental Health Centre, Thiruvananthapuram, Kerala, India
| | | | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Miller MW, Wolf EJ, Zhao X, Logue MW, Hawn SE. An EWAS of dementia biomarkers and their associations with age, African ancestry, and PTSD. Clin Epigenetics 2024; 16:38. [PMID: 38431614 PMCID: PMC10908031 DOI: 10.1186/s13148-024-01649-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Large-scale cohort and epidemiological studies suggest that PTSD confers risk for dementia in later life but the biological mechanisms underlying this association remain unknown. This study examined this question by assessing the influences of PTSD, APOE ε4 genotypes, DNA methylation, and other variables on the age- and dementia-associated biomarkers Aβ40, Aβ42, GFAP, NfL, and pTau-181 measured in plasma. Our primary hypothesis was that PTSD would be associated with elevated levels of these markers. METHODS Analyses were based on data from a PTSD-enriched cohort of 849 individuals. We began by performing factor analyses of the biomarkers, the results of which identified a two-factor solution. Drawing from the ATN research framework, we termed the first factor, defined by Aβ40 and Aβ42, "Factor A" and the second factor, defined by GFAP, NfL and pTau-181, "Factor TN." Next, we performed epigenome-wide association analyses (EWAS) of the two-factor scores. Finally, using structural equation modeling (SEM), we evaluated (a) the influence of PTSD, age, APOE ε4 genotype and other covariates on levels of the ATN factors, and (b) tested the mediating influence of the EWAS-significant DNAm loci on these associations. RESULTS The Factor A EWAS identified one significant locus, cg13053408, in FANCD2OS. The Factor TN analysis identified 3 EWAS-significant associations: cg26033520 near ASCC1, cg23156469 in FAM20B, and cg15356923 in FAM19A4. The SEM showed age to be related to both factors, more so with Factor TN (β = 0.581, p < 0.001) than Factor A (β = 0.330, p < 0.001). Genotype-determined African ancestry was associated with lower Factor A (β = 0.196, p < 0.001). Contrary to our primary hypothesis, we found a modest negative bivariate correlation between PTSD and the TN factor scores (r = - 0.133, p < 0.001) attributable primarily to reduced levels of GFAP (r = - 0.128, p < 0.001). CONCLUSIONS This study identified novel epigenetic associations with ATN biomarkers and demonstrated robust age and ancestral associations that will be essential to consider in future efforts to develop the clinical applications of these tests. The association between PTSD and reduced GFAP, which has been reported previously, warrants further investigation.
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Affiliation(s)
- Mark W Miller
- National Center for PTSD, VA Boston Healthcare System (116B-2), 150 S. Huntington Avenue, Boston, MA, 02130, USA.
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA.
| | - Erika J Wolf
- National Center for PTSD, VA Boston Healthcare System (116B-2), 150 S. Huntington Avenue, Boston, MA, 02130, USA
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Xiang Zhao
- National Center for PTSD, VA Boston Healthcare System (116B-2), 150 S. Huntington Avenue, Boston, MA, 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System (116B-2), 150 S. Huntington Avenue, Boston, MA, 02130, USA
- Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Biomedical Genetics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Sage E Hawn
- National Center for PTSD, VA Boston Healthcare System (116B-2), 150 S. Huntington Avenue, Boston, MA, 02130, USA
- Department of Psychology, Old Dominion University, Norfolk, VA, 23529, USA
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Wani A, Katrinli S, Zhao X, Daskalakis N, Zannas A, Aiello A, Baker D, Boks M, Brick L, Chen CY, Dalvie S, Fortier C, Geuze E, Hayes J, Kessler R, King A, Koen N, Liberzon I, Lori A, Luykx J, Maihofer A, Milberg W, Miller M, Mufford M, Nugent N, Rauch S, Ressler K, Risbrough V, Rutten B, Stein D, Stein M, Ursano R, Verfaellie M, Ware E, Wildman D, Wolf E, Nievergelt C, Logue M, Smith A, Uddin M, Vermetten E, Vinkers C. Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts. RESEARCH SQUARE 2024:rs.3.rs-3952163. [PMID: 38410438 PMCID: PMC10896387 DOI: 10.21203/rs.3.rs-3952163/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background Incorporating genomic data into risk prediction has become an increasingly useful approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. Methods Elastic Net was used to develop three risk score models using a discovery dataset (n = 1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. Results The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy = 89%) using 3728 features and MoRSAE (accuracy = 84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta = 0.6839, p-0.003), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta = 1.92; MoRS, beta = 1.99 and MoRSAE, beta = 1.77) displayed a significant (p < 0.001) predictive power for post-deployment PTSD. Conclusion Results, especially those from the eMRS, reinforce earlier findings that methylation and trauma are interconnected and can be leveraged to increase the correct classification of those with vs. without PTSD. Moreover, our models can potentially be a valuable tool in predicting the future risk of developing PTSD. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting the condition and, relatedly, improve their performance in independent cohorts.
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Affiliation(s)
- Agaz Wani
- University of South Florida College of Public Health, Genomics Program
| | - Seyma Katrinli
- Emory University Department of Gynecology and Obstetrics
| | - Xiang Zhao
- Boston University School of Public Health
| | | | - Anthony Zannas
- University of North Carolina at Chapel Hill, Carolina Stress Initiative
| | - Allison Aiello
- Robert N Butler Columbia Aging Center, Columbia University
| | - Dewleen Baker
- University of California San Diego, Department of Psychiatry
| | - Marco Boks
- Brain Center University Medical Center Utrecht, Department of Psychiatry
| | | | | | | | | | - Elbert Geuze
- Netherlands Ministry of Defence, Brain Research and Innovation Centre
| | | | - Ronald Kessler
- Harvard Medical School, Department of Health Care Policy
| | - Anthony King
- The Ohio State University, College of Medicine, Institute for Behavioral Medicine Research
| | - Nastassja Koen
- University of Cape Town, Department of Psychiatry & Mental Health
| | - Israel Liberzon
- Texas A&M University College of Medicine, Department of Psychiatry and Behavioral Sciences
| | - Adriana Lori
- Emory University, Department of Psychiatry and Behavioral Sciences
| | - Jurjen Luykx
- UMC Utrecht Brain Center Rudolf Magnus, Department of Psychiatry
| | | | | | - Mark Miller
- Boston University School of Medicine, Psychiatry
| | | | - Nicole Nugent
- Alpert Brown Medical School, Department of Emergency Medicine
| | - Sheila Rauch
- Emory University, Department of Psychiatry & Behavioral Sciences
| | | | | | - Bart Rutten
- Maastricht Universitair Medisch Centrum, School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology
| | - Dan Stein
- University of Cape Town, Department of Psychiatry & Mental Health
| | - Murrary Stein
- University of California San Diego, Department of Psychiatry
| | - Robert Ursano
- Uniformed Services University, Department of Psychiatry
| | | | - Erin Ware
- University of Michigan, Population Studies Center
| | - Derek Wildman
- University of South Florida College of Public Health, Genomics Program
| | - Erika Wolf
- VA Boston Healthcare System, National Center for PTSD
| | | | - Mark Logue
- Boston University School of Public Health
| | - Alicia Smith
- Emory University Department of Gynecology and Obstetrics
| | - Monica Uddin
- University of South Florida College of Public Health, Genomics Program
| | - Eric Vermetten
- Leiden University Medical Center, Department of Psychiatry
| | - Christiaan Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program
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Zheng Y, Lunetta KL, Liu C, Smith AK, Sherva R, Miller MW, Logue MW. A novel principal component based method for identifying differentially methylated regions in Illumina Infinium MethylationEPIC BeadChip data. Epigenetics 2023; 18:2207959. [PMID: 37196182 PMCID: PMC10193914 DOI: 10.1080/15592294.2023.2207959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023] Open
Abstract
Differentially methylated regions (DMRs) are genomic regions with methylation patterns across multiple CpG sites that are associated with a phenotype. In this study, we proposed a Principal Component (PC) based DMR analysis method for use with data generated using the Illumina Infinium MethylationEPIC BeadChip (EPIC) array. We obtained methylation residuals by regressing the M-values of CpGs within a region on covariates, extracted PCs of the residuals, and then combined association information across PCs to obtain regional significance. Simulation-based genome-wide false positive (GFP) rates and true positive rates were estimated under a variety of conditions before determining the final version of our method, which we have named DMRPC. Then, DMRPC and another DMR method, coMethDMR, were used to perform epigenome-wide analyses of several phenotypes known to have multiple associated methylation loci (age, sex, and smoking) in a discovery and a replication cohort. Among regions that were analysed by both methods, DMRPC identified 50% more genome-wide significant age-associated DMRs than coMethDMR. The replication rate for the loci that were identified by only DMRPC was higher than the rate for those that were identified by only coMethDMR (90% for DMRPC vs. 76% for coMethDMR). Furthermore, DMRPC identified replicable associations in regions of moderate between-CpG correlation which are typically not analysed by coMethDMR. For the analyses of sex and smoking, the advantage of DMRPC was less clear. In conclusion, DMRPC is a new powerful DMR discovery tool that retains power in genomic regions with moderate correlation across CpGs.
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Affiliation(s)
- Yuanchao Zheng
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard Sherva
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Mark W. Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Mark W. Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
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7
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Cheong Y, Nishitani S, Yu J, Habata K, Kamiya T, Shiotsu D, Omori IM, Okazawa H, Tomoda A, Kosaka H, Jung M. The effects of epigenetic age and its acceleration on surface area, cortical thickness, and volume in young adults. Cereb Cortex 2022; 32:5654-5663. [PMID: 35196707 DOI: 10.1093/cercor/bhac043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 01/25/2023] Open
Abstract
DNA methylation age has been used in recent studies as an epigenetic marker of accelerated cellular aging, whose contribution to the brain structural changes was lately acknowledged. We aimed to characterize the association of epigenetic age (i.e. estimated DNA methylation age) and its acceleration with surface area, cortical thickness, and volume in healthy young adults. Using the multi-tissue method (Horvath S. DNA methylation age of human tissues and cell types. 2013. Genome Biol 14), epigenetic age was computed with saliva sample. Epigenetic age acceleration was derived from residuals after adjusting epigenetic age for chronological age. Multiple regression models were computed for 148 brain regions for surface area, cortical thickness, and volume using epigenetic age or accelerated epigenetic age as a predictor and controlling for sex. Epigenetic age was associated with surface area reduction of the left insula. It was also associated with cortical thinning and volume reduction in multiple regions, with prominent changes of cortical thickness in the left temporal regions and of volume in the bilateral orbital gyri. Finally, accelerated epigenetic age was negatively associated with right cuneus gyrus volume. Our findings suggest that understanding the mechanisms of epigenetic age acceleration in young individuals may yield valuable insights into the relationship between epigenetic aging and the cortical change and on the early development of neurocognitive pathology among young adults.
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Affiliation(s)
- Yongjeon Cheong
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu 41062, South Korea
| | - Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Eiheiji, Fukui 910-1193, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka 565-0871, Japan
| | - Jinyoung Yu
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu 41062, South Korea
| | - Kaie Habata
- Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Taku Kamiya
- Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Daichi Shiotsu
- Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Ichiro M Omori
- Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Hidehiko Okazawa
- Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan.,Biomedical Imaging Research Center, University of Fukui, Eiheiji, Fukui 910-1193, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Eiheiji, Fukui 910-1193, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka 565-0871, Japan
| | - Hirotaka Kosaka
- Research Center for Child Mental Development, University of Fukui, Eiheiji, Fukui 910-1193, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka 565-0871, Japan.,Department of Neuropsychiatry, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Fukui 910-1193, Japan
| | - Minyoung Jung
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu 41062, South Korea
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8
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Zheng Y, Lunetta KL, Liu C, Katrinli S, Smith AK, Miller MW, Logue MW. An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays. Epigenetics 2022; 17:2241-2258. [PMID: 36047742 PMCID: PMC9665129 DOI: 10.1080/15592294.2022.2115600] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/28/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Differentially methylated regions (DMRs) are genomic regions with specific methylation patterns across multiple loci that are associated with a phenotype. We examined the genome-wide false positive (GFP) rates of five widely used DMR methods: comb-p, Bumphunter, DMRcate, mCSEA and coMethDMR using both Illumina HumanMethylation450 (450 K) and MethylationEPIC (EPIC) data and simulated continuous and dichotomous null phenotypes (i.e., generated independently of methylation data). coMethDMR provided well-controlled GFP rates (~5%) except when analysing skewed continuous phenotypes. DMRcate generally had well-controlled GFP rates when applied to 450 K data except for the skewed continuous phenotype and EPIC data only for the normally distributed continuous phenotype. GFP rates for mCSEA were at least 0.096 and comb-p yielded GFP rates above 0.34. Bumphunter had high GFP rates of at least 0.35 across conditions, reaching as high as 0.95. Analysis of the performance of these methods in specific regions of the genome found that regions with higher correlation across loci had higher regional false positive rates on average across methods. Based on the false positive rates, coMethDMR is the most recommended analysis method, and DMRcate had acceptable performance when analysing 450 K data. However, as both could display higher levels of FPs for skewed continuous distributions, a normalizing transformation of skewed continuous phenotypes is suggested. This study highlights the importance of genome-wide simulations when evaluating the performance of DMR-analysis methods.
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Affiliation(s)
- Yuanchao Zheng
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Mark W. Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Mark W. Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
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9
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Pfeiffer JR, van Rooij SJH, Mekawi Y, Fani N, Jovanovic T, Michopoulos V, Smith AK, Stevens JS, Uddin M. Blood-derived deoxyribonucleic acid methylation clusters associate with adverse social exposures and endophenotypes of stress-related psychiatric illness in a trauma-exposed cohort of women. Front Psychiatry 2022; 13:892302. [PMID: 36405926 PMCID: PMC9668877 DOI: 10.3389/fpsyt.2022.892302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Adverse social exposures (ASEs) such as low income, low educational attainment, and childhood/adult trauma exposure are associated with variability in brain region measurements of gray matter volume (GMV), surface area (SA), and cortical thickness (CT). These CNS morphometries are associated with stress-related psychiatric illnesses and represent endophenotypes of stress-related psychiatric illness development. Epigenetic mechanisms, such as 5-methyl-cytosine (5mC), may contribute to the biological embedding of the environment but are understudied and not well understood. How 5mC relates to CNS endophenotypes of psychiatric illness is also unclear. In 97 female, African American, trauma-exposed participants from the Grady Trauma Project, we examined the associations of childhood trauma burden (CTQ), adult trauma burden, low income, and low education with blood-derived 5mC clusters and variability in brain region measurements in the amygdala, hippocampus, and frontal cortex subregions. To elucidate whether peripheral 5mC indexes central nervous system (CNS) endophenotypes of psychiatric illness, we tested whether 73 brain/blood correlated 5mC clusters, defined by networks of correlated 5mC probes measured on Illumina's HumanMethylation Epic Beadchip, mediated the relationship between ASEs and brain measurements. CTQ was negatively associated with rostral middle frontal gyrus (RMFG) SA (β =-0.231, p = 0.041). Low income and low education were also associated with SA or CT in a number of brain regions. Seven 5mC clusters were associated with CTQ (pmin = 0.002), two with low education (pmin = 0.010), and three with low income (pmin = 0.007). Two clusters fully mediated the relation between CTQ and RMFG SA, accounting for 47 and 35% of variability, respectively. These clusters were enriched for probes falling in DNA regulatory regions, as well as signal transduction and immune signaling gene ontology functions. Methylome-network analyses showed enrichment of macrophage migration (p = 9 × 10-8), T cell receptor complex (p = 6 × 10-6), and chemokine-mediated signaling (p = 7 × 10-4) pathway enrichment in association with CTQ. Our results support prior work highlighting brain region variability associated with ASEs, while informing a peripheral inflammation-based epigenetic mechanism of biological embedding of such exposures. These findings could also serve to potentiate increased investigation of understudied populations at elevated risk for stress-related psychiatric illness development.
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Affiliation(s)
- John R. Pfeiffer
- Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, United States
| | - Sanne J. H. van Rooij
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Yara Mekawi
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, United States
| | - Negar Fani
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, MI, United States
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Alicia K. Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer S. Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States
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10
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Occean JR, Wani AH, Donglasan J, Aiello AE, Galea S, Koenen KC, Qu A, Wildman DE, Uddin M. DNA methylation of Nuclear Factor of Activated T Cells 1 mediates the prospective relation between exposure to different traumatic event types and post-traumatic stress disorder. Psychiatry Res 2022; 311:114510. [PMID: 35349860 PMCID: PMC9018623 DOI: 10.1016/j.psychres.2022.114510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/26/2022] [Accepted: 03/12/2022] [Indexed: 11/25/2022]
Abstract
The mechanisms through which exposure to differing trauma types become biologically embedded to shape the risk for post-traumatic stress disorder (PTSD) is unclear. DNA methylation (5-mC), particularly in stress-relevant genes, may play a role in this relationship. Here, we conducted path analysis using generalized structural equation modeling to investigate whether blood-derived 5-mC in Nuclear Factor of Activated T Cells 1 (NFATC1) mediates the prospective association between each of five different trauma types ("assaultive violence", "other injury or shocking experience", "learning of trauma to loved one", "sudden, unexpected death of a close friend or relative", and "other") and lifetime PTSD. All five trauma types were significantly associated with reduced methylation at NFATC1 CpG site, cg17057218. Two of the five trauma types were significantly associated with increased methylation at NFATC1 CpG site, cg22324981. Moreover, methylation at cg17057218 significantly mediated 21-32% of the total effect for four of the five trauma types, while methylation at cg22324981 mediated 27-40% of the total effect for two of the five trauma types. These CpG sites were differentially associated with transcription factor binding sites and chromatin state signatures. NFATC1 5-mC may be a potential mechanism in the relationship between some trauma types and prospective risk for PTSD.
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Affiliation(s)
- James R Occean
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA; Present address: Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Agaz H Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Janelle Donglasan
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Allison E Aiello
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sandro Galea
- Boston University School of Public Health, Boston University, Boston, MA, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit & Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Annie Qu
- Department of Statistics, University of California Irvine, Irvine, CA, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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11
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Youssef NA. Potential Societal and Cultural Implications of Transgenerational Epigenetic Methylation of Trauma and PTSD: Pathology or Resilience? THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:171-174. [PMID: 35370497 PMCID: PMC8961703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Psychological trauma is unique in that it is an environmental event that could induce biological changes and post-traumatic stress disorder (PTSD), depression, or other mood disorders in some patients. On the other hand, there may be no psychopathology (in most cases), or even sometimes post-traumatic growth and resilience. According to the DSM-5, trauma is a prerequisite for PTSD and traumatic stress disorder, but not for depressive episodes or mood disorders, or other psychiatric conditions. This paper brings attention to the preliminary literature on transgenerational inheritance due to trauma exposure and its societal and cultural implications. There is accumulating evidence that exposure to trauma can be passed transgenerationally through epigenetic inheritance leading to changes in gene expression and possible disorders or resilience. The effects of resilience from transgenerational inheritance have not been studied, but should be, for a full understanding not only of the disease risk across generations, but also of its social and cultural implications. The epigenetic pathologic effects across generations also need further studies, as the current research is preliminary; larger replications are needed for definitive and more complete understanding. I present here a glimpse of where we are, a vision of where we should go in terms of future research direction for disease risk transmission, and recommend studies of resilience and post-traumatic growth across generations, as well as other studies related to the societal implications at the population level.
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Affiliation(s)
- Nagy A. Youssef
- To whom all correspondence should be addressed:
Nagy Youssef, MD, PhD, Director of Clinical Research, Professor of Psychiatry,
Department of Psychiatry & Behavioral Health, The Ohio State University
College of Medicine, Columbus, OH; ;
ORCID iD: https://orcid.org/0000-0002-1922-9396
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12
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Nishitani S, Kasaba R, Hiraoka D, Shimada K, Fujisawa TX, Okazawa H, Tomoda A. Epigenetic Clock Deceleration and Maternal Reproductive Efforts: Associations With Increasing Gray Matter Volume of the Precuneus. Front Genet 2022; 13:803584. [PMID: 35309114 PMCID: PMC8926035 DOI: 10.3389/fgene.2022.803584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/02/2022] [Indexed: 11/30/2022] Open
Abstract
Reproductive efforts, such as pregnancy, delivery, and interaction with children, make maternal brains optimized for child-rearing. However, extensive studies in non-human species revealed a tradeoff between reproductive effort and life expectancy. In humans, large demographic studies have shown that this is the case for the most part; however, molecular marker studies regarding aging remain controversial. There are no studies simultaneously evaluating the relationship between reproductive effort, aging, and brain structures. We therefore examined the associations between reproductive efforts (parity status, number of deliveries, motherhood period, and cumulative motherhood period), DNA methylation age (mAge) acceleration (based on Horvath’s multi-tissue clock and the skin & blood clock), and the regional gray matter volumes (obtained through brain magnetic resonance imaging (MRI) using voxel-based morphometry) in 51 mothers aged 27–46 years of children in early childhood. We found that increasing reproductive efforts were significantly associated with decelerated aging in mothers with one to four children, even after adjusting for the confounding effects in the multiple linear regression models. We also found that the left precuneus gray matter volume was larger as deceleration of aging occurred; increasing left precuneus gray matter volume, on the other hand, mediates the relationship between parity status and mAge deceleration. Our findings suggest that mothers of children in early childhood, who have had less than four children, may benefit from deceleration of aging mediated via structural changes in the precuneus.
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Affiliation(s)
- Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Hamamatsu University School of Medicine, Osaka University, Kanazawa University, Chiba University, University of Fukui, Osaka, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
- *Correspondence: Shota Nishitani, ; Akemi Tomoda,
| | - Ryoko Kasaba
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Hamamatsu University School of Medicine, Osaka University, Kanazawa University, Chiba University, University of Fukui, Osaka, Japan
| | - Daiki Hiraoka
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Koji Shimada
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Hamamatsu University School of Medicine, Osaka University, Kanazawa University, Chiba University, University of Fukui, Osaka, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Takashi X. Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Hamamatsu University School of Medicine, Osaka University, Kanazawa University, Chiba University, University of Fukui, Osaka, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Hidehiko Okazawa
- Life Science Innovation Center, University of Fukui, Fukui, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Hamamatsu University School of Medicine, Osaka University, Kanazawa University, Chiba University, University of Fukui, Osaka, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
- *Correspondence: Shota Nishitani, ; Akemi Tomoda,
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13
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Katrinli S, Maihofer AX, Wani AH, Pfeiffer JR, Ketema E, Ratanatharathorn A, Baker DG, Boks MP, Geuze E, Kessler RC, Risbrough VB, Rutten BPF, Stein MB, Ursano RJ, Vermetten E, Logue MW, Nievergelt CM, Smith AK, Uddin M. Epigenome-wide meta-analysis of PTSD symptom severity in three military cohorts implicates DNA methylation changes in genes involved in immune system and oxidative stress. Mol Psychiatry 2022; 27:1720-1728. [PMID: 34992238 PMCID: PMC9106882 DOI: 10.1038/s41380-021-01398-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/13/2021] [Accepted: 11/23/2021] [Indexed: 11/08/2022]
Abstract
Epigenetic factors modify the effects of environmental factors on biological outcomes. Identification of epigenetic changes that associate with PTSD is therefore a crucial step in deciphering mechanisms of risk and resilience. In this study, our goal is to identify epigenetic signatures associated with PTSD symptom severity (PTSS) and changes in PTSS over time, using whole blood DNA methylation (DNAm) data (MethylationEPIC BeadChip) of military personnel prior to and following combat deployment. A total of 429 subjects (858 samples across 2 time points) from three male military cohorts were included in the analyses. We conducted two different meta-analyses to answer two different scientific questions: one to identify a DNAm profile of PTSS using a random effects model including both time points for each subject, and the other to identify a DNAm profile of change in PTSS conditioned on pre-deployment DNAm. Four CpGs near four genes (F2R, CNPY2, BAIAP2L1, and TBXAS1) and 88 differentially methylated regions (DMRs) were associated with PTSS. Change in PTSS after deployment was associated with 15 DMRs, of those 2 DMRs near OTUD5 and ELF4 were also associated with PTSS. Notably, three PTSS-associated CpGs near F2R, BAIAP2L1 and TBXAS1 also showed nominal evidence of association with change in PTSS. This study, which identifies PTSD-associated changes in genes involved in oxidative stress and immune system, provides novel evidence that epigenetic differences are associated with PTSS.
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Affiliation(s)
- Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Agaz H Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - John R Pfeiffer
- Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Elizabeth Ketema
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Marco P Boks
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elbert Geuze
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Brain Research and Innovation Centre, Netherlands Ministry of Defence, Utrecht, The Netherlands
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, School for Mental Health and Neuroscience, Maastricht, The Netherlands
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- School of Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert J Ursano
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University School of Medicine, Bethesda, MD, USA
| | - Eric Vermetten
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, Leiden University Medical Center, ZA, Leiden, The Netherlands
- Research Center, Netherlands Defense Department, UT, AA Utrecht, The Netherlands
- Arq Psychotrauma Expert Group, XE, Diemen, The Netherlands
| | - Mark W Logue
- National Center for PTSD, Behavioral Science Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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14
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Epigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans. Transl Psychiatry 2022; 12:65. [PMID: 35177594 PMCID: PMC8854688 DOI: 10.1038/s41398-022-01822-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/26/2021] [Accepted: 01/14/2022] [Indexed: 01/23/2023] Open
Abstract
Posttraumatic stress disorder (PTSD) is a chronic and disabling psychiatric disorder prevalent in military veterans. Epigenetic mechanisms have been implicated in the etiology of PTSD, with DNA methylation being the most studied to identify novel molecular biomarkers associated with this disorder. We performed one of the largest single-sample epigenome-wide association studies (EWAS) of PTSD to date. Our sample included 1135 male European-American U.S. veterans who participated in the National Health and Resilience in Veterans Study (NHRVS). DNA was collected from saliva samples and the Illumina HumanMethylation EPIC BeadChip was used for the methylation analysis. PTSD was assessed using the PTSD Checklist. An EWAS was conducted using linear regression adjusted for age, cell-type proportions, first 10 principal components, and smoking status. After Bonferroni correction, we identified six genome-wide significant (GWS) CpG sites associated with past-month PTSD and three CpGs with lifetime PTSD (prange = 10-10-10-8). These CpG sites map to genes involved in immune function, transcription regulation, axonal guidance, cell signaling, and protein binding. Among these, SENP7, which is involved in transcription regulation and has been linked to risk-taking behavior and alcohol consumption in genome-wide association studies, replicated in an independent veteran cohort and was downregulated in medial orbitofrontal cortex of PTSD postmortem brain tissue. These findings suggest potential epigenetic biomarkers of PTSD that may help inform the pathophysiology of this disorder in veterans and other trauma-affected populations.
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15
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Fujisawa TX, Nishitani S, Makita K, Yao A, Takiguchi S, Hamamura S, Shimada K, Okazawa H, Matsuzaki H, Tomoda A. Association of Epigenetic Differences Screened in a Few Cases of Monozygotic Twins Discordant for Attention-Deficit Hyperactivity Disorder With Brain Structures. Front Neurosci 2022; 15:799761. [PMID: 35145374 PMCID: PMC8823258 DOI: 10.3389/fnins.2021.799761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
The present study examined the relationship between DNA methylation differences and variations in brain structures involved in the development of attention-deficit hyperactivity disorder (ADHD). First, we used monozygotic (MZ) twins discordant (2 pairs of 4 individuals, 2 boys, mean age 12.5 years) for ADHD to identify candidate DNA methylation sites involved in the development of ADHD. Next, we tried to replicate these candidates in a case-control study (ADHD: N = 18, 15 boys, mean age 10.0 years; Controls: N = 62, 40 boys, mean age 13.9 years). Finally, we examined how methylation rates at those sites relate to the degree of local structural alterations where significant differences were observed between cases and controls. As a result, we identified 61 candidate DNA methylation sites involved in ADHD development in two pairs of discordant MZ twins, among which elevated methylation at a site in the sortilin-related Vps10p domain containing receptor 2 (SorCS2) gene was replicated in the case-control study. We also observed that the ADHD group had significantly reduced gray matter volume (GMV) in the precentral and posterior orbital gyri compared to the control group and that this volume reduction was positively associated with SorCS2 methylation. Furthermore, the reduced GMV regions in children with ADHD are involved in language processing and emotional control, while SorCS2 methylation is also negatively associated with emotional behavioral problems in children. These results indicate that SorCS2 methylation might mediate a reduced GMV in the precentral and posterior orbital gyri and therefore influence the pathology of children with ADHD.
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Affiliation(s)
- Takashi X. Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- *Correspondence: Takashi X. Fujisawa,
| | - Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Kai Makita
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
| | - Akiko Yao
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Shinichiro Takiguchi
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Shoko Hamamura
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Koji Shimada
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Hidehiko Okazawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Hideo Matsuzaki
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
- *Correspondence: Takashi X. Fujisawa,
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16
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Vermetten E, Snijders C, Daskalakis NP, Rutten BPF. Revisiting the Need for a PTSD Brain Bank; Commentary on Friedman. Psychiatry 2022; 85:203-211. [PMID: 35588487 DOI: 10.1080/00332747.2022.2068938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Xue F, Tang X, Kim G, Koenen KC, Martin CL, Galea S, Wildman D, Uddin M, Qu A. Heterogeneous Mediation Analysis on Epigenomic PTSD and Traumatic Stress in a Predominantly African American Cohort. J Am Stat Assoc 2022; 117:1669-1683. [PMID: 36875798 PMCID: PMC9980467 DOI: 10.1080/01621459.2022.2089572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA methylation (DNAm) has been suggested to play a critical role in post-traumatic stress disorder (PTSD), through mediating the relationship between trauma and PTSD. However, this underlying mechanism of PTSD for African Americans still remains unknown. To fill this gap, in this article, we investigate how DNAm mediates the effects of traumatic experiences on PTSD symptoms in the Detroit Neighborhood Health Study (DNHS) (2008-2013) which involves primarily African Americans adults. To achieve this, we develop a new mediation analysis approach for high-dimensional potential DNAm mediators. A key novelty of our method is that we consider heterogeneity in mediation effects across subpopulations. Specifically, mediators in different subpopulations could have opposite effects on the outcome, and thus could be difficult to identify under a traditional homogeneous model framework. In contrast, the proposed method can estimate heterogeneous mediation effects and identifies subpopulations in which individuals share similar effects. Simulation studies demonstrate that the proposed method outperforms existing methods for both homogeneous and heterogeneous data. We also present our mediation analysis results of a dataset with 125 participants and more than 450,000 CpG sites from the DNHS study. The proposed method finds three subgroups of subjects and identifies DNAm mediators corresponding to genes such as HSP90AA1 and NFATC1 which have been linked to PTSD symptoms in literature. Our finding could be useful in future finer-grained investigation of PTSD mechanism and in the development of new treatments for PTSD.
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Affiliation(s)
- Fei Xue
- Purdue University, West Lafayette, IN
| | - Xiwei Tang
- University of Virginia, Charlottesville, VA
| | - Grace Kim
- University of Illinois College of Medicine, Chicago, IL
| | | | - Chantel L Martin
- The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Annie Qu
- University of California Irvine, Irvine, CA
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18
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Zheng Y, Garrett ME, Sun D, Clarke-Rubright EK, Haswell CC, Maihofer AX, Elman JA, Franz CE, Lyons MJ, Kremen WS, Peverill M, Sambrook K, McLaughlin KA, Davenport ND, Disner S, Sponheim SR, Andrew E, Korgaonkar M, Bryant R, Varkevisser T, Geuze E, Coleman J, Beckham JC, Kimbrel NA, Sullivan D, Miller M, Hayes J, Verfaellie M, Wolf E, Salat D, Spielberg JM, Milberg W, McGlinchey R, Dennis EL, Thompson PM, Medland S, Jahanshad N, Nievergelt CM, Ashley-Koch AE, Logue MW, Morey RA. Trauma and posttraumatic stress disorder modulate polygenic predictors of hippocampal and amygdala volume. Transl Psychiatry 2021; 11:637. [PMID: 34916497 PMCID: PMC8677780 DOI: 10.1038/s41398-021-01707-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/05/2021] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
The volume of subcortical structures represents a reliable, quantitative, and objective phenotype that captures genetic effects, environmental effects such as trauma, and disease effects such as posttraumatic stress disorder (PTSD). Trauma and PTSD represent potent exposures that may interact with genetic markers to influence brain structure and function. Genetic variants, associated with subcortical volumes in two large normative discovery samples, were used to compute polygenic scores (PGS) for the volume of seven subcortical structures. These were applied to a target sample enriched for childhood trauma and PTSD. Subcortical volume PGS from the discovery sample were strongly associated in our trauma/PTSD enriched sample (n = 7580) with respective subcortical volumes of the hippocampus (p = 1.10 × 10-20), thalamus (p = 7.46 × 10-10), caudate (p = 1.97 × 10-18), putamen (p = 1.7 × 10-12), and nucleus accumbens (p = 1.99 × 10-7). We found a significant association between the hippocampal volume PGS and hippocampal volume in control subjects from our sample, but was absent in individuals with PTSD (GxE; (beta = -0.10, p = 0.027)). This significant GxE (PGS × PTSD) relationship persisted (p < 1 × 10-19) in four out of five threshold peaks (0.024, 0.133, 0.487, 0.730, and 0.889) used to calculate hippocampal volume PGSs. We detected similar GxE (G × ChildTrauma) relationships in the amygdala for exposure to childhood trauma (rs4702973; p = 2.16 × 10-7) or PTSD (rs10861272; p = 1.78 × 10-6) in the CHST11 gene. The hippocampus and amygdala are pivotal brain structures in mediating PTSD symptomatology. Trauma exposure and PTSD modulate the effect of polygenic markers on hippocampal volume (GxE) and the amygdala volume PGS is associated with PTSD risk, which supports the role of amygdala volume as a risk factor for PTSD.
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Affiliation(s)
- Yuanchao Zheng
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Melanie E Garrett
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA
| | - Delin Sun
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
| | - Emily K Clarke-Rubright
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
| | - Courtney C Haswell
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
| | - Adam X Maihofer
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeremy A Elman
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Carol E Franz
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Michael J Lyons
- Department of Psychological and Brain Sciences, Boston University, Boston, MA, USA
| | - William S Kremen
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Matthew Peverill
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Kelly Sambrook
- Department of Psychology, Harvard University, Boston, MA, USA
| | | | - Nicholas D Davenport
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Seth Disner
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Scott R Sponheim
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, USA
| | | | - Mayuresh Korgaonkar
- Brain Dynamics Centre, Westmead Institute of Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Richard Bryant
- School of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Tim Varkevisser
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Elbert Geuze
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Jonathan Coleman
- 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
| | - Jean C Beckham
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Kimbrel
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Danielle Sullivan
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mark Miller
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Jasmeet Hayes
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mieke Verfaellie
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Erika Wolf
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - David Salat
- VA Boston Healthcare System, Jamaica Plain, MA, USA
- Department of Radiology, Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Jeffrey M Spielberg
- VA Boston Healthcare System, Jamaica Plain, MA, USA
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - William Milberg
- Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System, Boston, MA, USA
- Geriatric Research, Educational and Clinical Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Regina McGlinchey
- Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System, Boston, MA, USA
- Geriatric Research, Educational and Clinical Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Emily L Dennis
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sarah Medland
- Queensland Institute for Medical Research, Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Neda Jahanshad
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Allison E Ashley-Koch
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Departments of Psychiatry and Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Rajendra A Morey
- VISN 6 MIRECC, Durham VA Health Care System, Durham, NC, USA.
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA.
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA.
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19
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Song W, Wang W, Liu Z, Cai W, Yu S, Zhao M, Lin GN. A Comprehensive Evaluation of Cross-Omics Blood-Based Biomarkers for Neuropsychiatric Disorders. J Pers Med 2021; 11:1247. [PMID: 34945719 PMCID: PMC8703948 DOI: 10.3390/jpm11121247] [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: 10/18/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
The identification of peripheral multi-omics biomarkers of brain disorders has long been hindered by insufficient sample size and confounder influence. This study aimed to compare biomarker potential for different molecules and diseases. We leveraged summary statistics of five blood quantitative trait loci studies (N = 1980 to 22,609) and genome-wide association studies (N = 9725 to 500,199) from 14 different brain disorders, such as Schizophrenia (SCZ) and Alzheimer's Disease (AD). We applied summary-based and two-sample Mendelian Randomization to estimate the associations between blood molecules and brain disorders. We identified 524 RNA, 807 methylation sites, 29 proteins, seven cytokines, and 22 metabolites having a significant association with at least one of 14 brain disorders. Simulation analyses indicated that a cross-omics combination of biomarkers had better performance for most disorders, and different disorders could associate with different omics. We identified an 11-methylation-site model for SCZ diagnosis (Area Under Curve, AUC = 0.74) by analyzing selected candidate markers in published datasets (total N = 6098). Moreover, we constructed an 18-methylation-sites model that could predict the prognosis of elders with mild cognitive impairment (hazard ratio = 2.32). We provided an association landscape between blood cross-omic biomarkers and 14 brain disorders as well as a suggestion guide for future clinical discovery and application.
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Affiliation(s)
- Weichen Song
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Weidi Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Zhe Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Wenxiang Cai
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; (S.Y.); (M.Z.)
| | - Min Zhao
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; (S.Y.); (M.Z.)
| | - Guan Ning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
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20
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Nishitani S, Fujisawa TX, Hiraoka D, Makita K, Takiguchi S, Hamamura S, Yao A, Shimada K, Smith AK, Tomoda A. A multi-modal MRI analysis of brain structure and function in relation to OXT methylation in maltreated children and adolescents. Transl Psychiatry 2021; 11:589. [PMID: 34789725 PMCID: PMC8599663 DOI: 10.1038/s41398-021-01714-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/20/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
Child maltreatment dysregulates the brain's oxytocinergic system, resulting in dysfunctional attachment patterns. However, how the oxytocinergic system in children who are maltreated (CM) is epigenetically affected remains unknown. We assessed differences in salivary DNA methylation of the gene encoding oxytocin (OXT) between CM (n = 24) and non-CM (n = 31), alongside its impact on brain structures and functions using multi-modal brain imaging (voxel-based morphometry, diffusion tensor imaging, and task and resting-state functional magnetic resonance imaging). We found that CM showed higher promoter methylation than non-CM, and nine CpG sites were observed to be correlated with each other and grouped into one index (OXTmi). OXTmi was significantly negatively correlated with gray matter volume (GMV) in the left superior parietal lobule (SPL), and with right putamen activation during a rewarding task, but not with white matter structures. Using a random forest regression model, we investigated the sensitive period and type of maltreatment that contributed the most to OXTmi in CM, revealing that they were 5-8 years of age and physical abuse (PA), respectively. However, the presence of PA (PA+) was meant to reflect more severe cases, such as prolonged exposure to multiple types of abuse, than the absence of PA. PA+ was associated with significantly greater functional connectivity between the right putamen set as the seed and the left SPL and the left cerebellum exterior. The results suggest that OXT promoter hypermethylation may lead to the atypical development of reward and visual association structures and functions, thereby potentially worsening clinical aspects raised by traumatic experiences.
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Affiliation(s)
- Shota Nishitani
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan ,grid.163577.10000 0001 0692 8246Life Science Innovation Center, University of Fukui, Fukui, Japan ,grid.189967.80000 0001 0941 6502Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA USA
| | - Takashi X. Fujisawa
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan ,grid.163577.10000 0001 0692 8246Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Daiki Hiraoka
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.54432.340000 0004 0614 710XJapan Society for the Promotion of Science, Tokyo, Japan
| | - Kai Makita
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Shinichiro Takiguchi
- grid.413114.2Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Shoko Hamamura
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan ,grid.413114.2Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Akiko Yao
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Koji Shimada
- grid.163577.10000 0001 0692 8246Research Center for Child Mental Development, University of Fukui, Fukui, Japan ,grid.136593.b0000 0004 0373 3971Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan ,grid.163577.10000 0001 0692 8246Life Science Innovation Center, University of Fukui, Fukui, Japan ,grid.163577.10000 0001 0692 8246Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Alicia K. Smith
- grid.189967.80000 0001 0941 6502Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA USA
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan. .,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan. .,Life Science Innovation Center, University of Fukui, Fukui, Japan. .,Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan.
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21
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Abstract
Posttraumatic stress disorder (PTSD) is a complex mental disorder afflicting approximately 7% of the population. The diverse number of traumatic events and the wide array of symptom combinations leading to PTSD diagnosis contribute substantial heterogeneity to studies of the disorder. Genomic and complimentary-omic investigations have rapidly increased our understanding of the heritable risk for PTSD. In this review, we emphasize the contributions of genome-wide association, epigenome-wide association, transcriptomic, and neuroimaging studies to our understanding of PTSD etiology. We also discuss the shared risk between PTSD and other complex traits derived from studies of causal inference, co-expression, and brain morphological similarities. The investigations completed so far converge on stark contrasts in PTSD risk between sexes, partially attributed to sex-specific prevalence of traumatic experiences with high conditional risk of PTSD. To further understand PTSD biology, future studies should focus on detecting risk for PTSD while accounting for substantial cohort-level heterogeneity (e.g. civilian v. combat-exposed PTSD cases or PTSD risk among cases exposed to specific traumas), expanding ancestral diversity among study cohorts, and remaining cognizant of how these data influence social stigma associated with certain traumatic events among underrepresented minorities and/or high-risk populations.
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Affiliation(s)
- Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
- Veterans Administration Connecticut Healthcare System, West Haven, CT, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
- Veterans Administration Connecticut Healthcare System, West Haven, CT, USA
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22
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Li G, Raffield L, Logue M, Miller MW, Santos HP, O’Shea TM, Fry RC, Li Y. CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms. Epigenetics 2021; 16:851-861. [PMID: 33016200 PMCID: PMC8330997 DOI: 10.1080/15592294.2020.1827716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/08/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022] Open
Abstract
DNA methylation at CpG dinucleotides is one of the most extensively studied epigenetic marks. With technological advancements, geneticists can profile DNA methylation with multiple reliable approaches. However, profiling platforms can differ substantially in the CpGs they assess, consequently hindering integrated analysis across platforms. Here, we present CpG impUtation Ensemble (CUE), which leverages multiple classical statistical and modern machine learning methods, to impute from the Illumina HumanMethylation450 (HM450) BeadChip to the Illumina HumanMethylationEPIC (HM850) BeadChip. Data were analysed from two population cohorts with methylation measured both by HM450 and HM850: the Extremely Low Gestational Age Newborns (ELGAN) study (n = 127, placenta) and the VA Boston Posttraumatic Stress Disorder (PTSD) genetics repository (n = 144, whole blood). Cross-validation results show that CUE achieves the lowest predicted root-mean-square error (RMSE) (0.026 in PTSD) and the highest accuracy (99.97% in PTSD) compared with five individual methods tested, including k-nearest-neighbours, logistic regression, penalized functional regression, random forest, and XGBoost. Finally, among all 339,033 HM850-only CpG sites shared between ELGAN and PTSD, CUE successfully imputed 289,604 (85.4%) sites, where success was defined as RMSE < 0.05 and accuracy >95% in PTSD. In summary, CUE is a valuable tool for imputing CpG methylation from the HM450 to HM850 platform.
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Affiliation(s)
- Gang Li
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Mark Logue
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mark W. Miller
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Hudson P. Santos
- School of Nursing, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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23
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Garrett ME, Qin XJ, Mehta D, Dennis MF, Marx CE, Grant GA, Stein MB, Kimbrel NA, Beckham JC, Hauser MA, Ashley-Koch AE. Gene Expression Analysis in Three Posttraumatic Stress Disorder Cohorts Implicates Inflammation and Innate Immunity Pathways and Uncovers Shared Genetic Risk With Major Depressive Disorder. Front Neurosci 2021; 15:678548. [PMID: 34393704 PMCID: PMC8358297 DOI: 10.3389/fnins.2021.678548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/07/2021] [Indexed: 01/09/2023] Open
Abstract
Posttraumatic stress disorder (PTSD) is a complex psychiatric disorder that can develop following exposure to traumatic events. The Psychiatric Genomics Consortium PTSD group (PGC-PTSD) has collected over 20,000 multi-ethnic PTSD cases and controls and has identified both genetic and epigenetic factors associated with PTSD risk. To further investigate biological correlates of PTSD risk, we examined three PGC-PTSD cohorts comprising 977 subjects to identify differentially expressed genes among PTSD cases and controls. Whole blood gene expression was quantified with the HumanHT-12 v4 Expression BeadChip for 726 OEF/OIF veterans from the Veterans Affairs (VA) Mental Illness Research Education and Clinical Center (MIRECC), 155 samples from the Injury and Traumatic Stress (INTRuST) Clinical Consortium, and 96 Australian Vietnam War veterans. Differential gene expression analysis was performed in each cohort separately followed by meta-analysis. In the largest cohort, we performed co-expression analysis to identify modules of genes that are associated with PTSD and MDD. We then conducted expression quantitative trait loci (eQTL) analysis and assessed the presence of eQTL interactions involving PTSD and major depressive disorder (MDD). Finally, we utilized PTSD and MDD GWAS summary statistics to identify regions that colocalize with eQTLs. Although not surpassing correction for multiple testing, the most differentially expressed genes in meta-analysis were interleukin-1 beta (IL1B), a pro-inflammatory cytokine previously associated with PTSD, and integrin-linked kinase (ILK), which is highly expressed in brain and can rescue dysregulated hippocampal neurogenesis and memory deficits. Pathway analysis revealed enrichment of toll-like receptor (TLR) and interleukin-1 receptor genes, which are integral to cellular innate immune response. Co-expression analysis identified four modules of genes associated with PTSD, two of which are also associated with MDD, demonstrating common biological pathways underlying the two conditions. Lastly, we identified four genes (UBA7, HLA-F, HSPA1B, and RERE) with high probability of a shared causal eQTL variant with PTSD and/or MDD GWAS variants, thereby providing a potential mechanism by which the GWAS variant contributes to disease risk. In summary, we provide additional evidence for genes and pathways previously reported and identified plausible novel candidates for PTSD. These data provide further insight into genetic factors and pathways involved in PTSD, as well as potential regions of pleiotropy between PTSD and MDD.
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Affiliation(s)
- Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Xue Jun Qin
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Divya Mehta
- Queensland University of Technology, Centre for Genomics and Personalised Health, Faculty of Health, Institute of Health and Biomedical Innovation, Kelvin Grove, QLD, Australia
| | - Michelle F Dennis
- Durham Veterans Affairs Health Care System, Durham, NC, United States.,VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC United States.,Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Christine E Marx
- Durham Veterans Affairs Health Care System, Durham, NC, United States.,VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC United States.,Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
| | | | | | | | | | - Murray B Stein
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, CA, United States.,Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, United States.,VA San Diego Healthcare System, San Diego, CA, United States
| | - Nathan A Kimbrel
- Durham Veterans Affairs Health Care System, Durham, NC, United States.,VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC United States.,Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Jean C Beckham
- Durham Veterans Affairs Health Care System, Durham, NC, United States.,VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC United States.,Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Michael A Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
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24
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The Impact of Stress Within and Across Generations: Neuroscientific and Epigenetic Considerations. Harv Rev Psychiatry 2021; 29:303-317. [PMID: 34049337 DOI: 10.1097/hrp.0000000000000300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The impact of stress and trauma on biological systems in humans can be substantial. They can result in epigenetic changes, accelerated brain development and sexual maturation, and predisposition to psychopathology. Such modifications may be accompanied by behavioral, emotional, and cognitive overtones during one's lifetime. Exposure during sensitive periods of neural development may lead to long-lasting effects that may not be affected by subsequent environmental interventions. The cumulative effects of life stressors in an individual may affect offspring's methylome makeup and epigenetic clocks, neurohormonal modulation and stress reactivity, and physiological and reproductive development. While offspring may suffer deleterious effects from parental stress and their own early-life adversity, these factors may also confer traits that prove beneficial and enhance fitness to their own environment. This article synthesizes the data on how stress shapes biological and behavioral dimensions, drawing from preclinical and human models. Advances in this field of knowledge should potentially allow for an improved understanding of how interventions may be increasingly tailored according to individual biomarkers and developmental history.
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25
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Pfeiffer JR, Bustamante AC, Kim GS, Armstrong D, Knodt AR, Koenen KC, Hariri AR, Uddin M. Associations between childhood family emotional health, fronto-limbic grey matter volume, and saliva 5mC in young adulthood. Clin Epigenetics 2021; 13:68. [PMID: 33789736 PMCID: PMC8010979 DOI: 10.1186/s13148-021-01056-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background Poor family emotional health (FEH) during childhood is prevalent and impactful, and likely confers similar neurodevelopmental risks as other adverse social environments. Pointed FEH study efforts are underdeveloped, and the mechanisms by which poor FEH are biologically embedded are unclear. The current exploratory study examined whether variability in 5-methyl-cytosine (5mC) and fronto-limbic grey matter volume may represent pathways through which FEH may become biologically embedded. Results In 98 university students aged 18–22 years, retrospective self-reported childhood FEH was associated with right hemisphere hippocampus (b = 10.4, p = 0.005), left hemisphere amygdala (b = 5.3, p = 0.009), and right hemisphere amygdala (b = 5.8, p = 0.016) volumes. After pre-processing and filtering to 5mC probes correlated between saliva and brain, analyses showed that childhood FEH was associated with 49 5mC principal components (module eigengenes; MEs) (prange = 3 × 10–6 to 0.047). Saliva-derived 5mC MEs partially mediated the association between FEH and right hippocampal volume (Burlywood ME indirect effect b = − 111, p = 0.014), and fully mediated the FEH and right amygdala volume relationship (Pink4 ME indirect effect b = − 48, p = 0.026). Modules were enriched with probes falling in genes with immune, central nervous system (CNS), cellular development/differentiation, and metabolic functions. Conclusions Findings extend work highlighting neurodevelopmental variability associated with adverse social environment exposure during childhood by specifically implicating poor FEH, while informing a mechanism of biological embedding. FEH-associated epigenetic signatures could function as proxies of altered fronto-limbic grey matter volume associated with poor childhood FEH and inform further investigation into primarily affected tissues such as endocrine, immune, and CNS cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01056-y.
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Affiliation(s)
- J R Pfeiffer
- Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Angela C Bustamante
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Grace S Kim
- Medical Scholars Program, University of Illinois College of Medicine, Urbana, IL, USA
| | - Don Armstrong
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Annchen R Knodt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA.,Laboratory of NeuroGenetics, Duke University, Durham, NC, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Ahmad R Hariri
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA.,Laboratory of NeuroGenetics, Duke University, Durham, NC, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Suite 304, Tampa, FL, USA.
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26
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Nishitani S, Suzuki S, Ochiai K, Yao A, Fujioka T, Fujisawa TX, Tomoda A. Altered epigenetic clock in children exposed to maltreatment. Psychiatry Clin Neurosci 2021; 75:110-112. [PMID: 33305449 DOI: 10.1111/pcn.13183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan.,Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Shizuka Suzuki
- United Graduate School of Professional Development of Teachers, University of Fukui, Fukui, Japan.,Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Keiko Ochiai
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan
| | - Akiko Yao
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan
| | - Toru Fujioka
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan.,Department of Science of Human Development, Faculty of Education, Humanities and Social Sciences, University of Fukui, Fukui, Japan
| | - Takashi X Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan.,Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan.,Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan.,Life Science Innovation Center, University of Fukui, Fukui, Japan.,Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
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27
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Parade SH, Huffhines L, Daniels TE, Stroud LR, Nugent NR, Tyrka AR. A systematic review of childhood maltreatment and DNA methylation: candidate gene and epigenome-wide approaches. Transl Psychiatry 2021; 11:134. [PMID: 33608499 PMCID: PMC7896059 DOI: 10.1038/s41398-021-01207-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 01/31/2023] Open
Abstract
Childhood maltreatment is a major risk factor for chronic and severe mental and physical health problems across the lifespan. Increasing evidence supports the hypothesis that maltreatment is associated with epigenetic changes that may subsequently serve as mechanisms of disease. The current review uses a systematic approach to identify and summarize the literature related to childhood maltreatment and alterations in DNA methylation in humans. A total of 100 empirical articles were identified in our systematic review of research published prior to or during March 2020, including studies that focused on candidate genes and studies that leveraged epigenome-wide data in both children and adults. Themes arising from the literature, including consistent and inconsistent patterns of results, are presented. Several directions for future research, including important methodological considerations for future study design, are discussed. Taken together, the literature on childhood maltreatment and DNA methylation underscores the complexity of transactions between the environment and biology across development.
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Affiliation(s)
- Stephanie H Parade
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA.
- Bradley/Hasbro Children's Research Center, E. P. Bradley Hospital, East Providence, RI, USA.
| | - Lindsay Huffhines
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Bradley/Hasbro Children's Research Center, E. P. Bradley Hospital, East Providence, RI, USA
| | - Teresa E Daniels
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
| | - Laura R Stroud
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Center for Behavioral and Preventive Medicine, The Miriam Hospital, Providence, RI, USA
| | - Nicole R Nugent
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Audrey R Tyrka
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
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28
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Katrinli S, Zheng Y, Gautam A, Hammamieh R, Yang R, Venkateswaran S, Kilaru V, Lori A, Hinrichs R, Powers A, Gillespie CF, Wingo AP, Michopoulos V, Jovanovic T, Wolf EJ, McGlinchey RE, Milberg WP, Miller MW, Kugathasan S, Jett M, Logue MW, Ressler KJ, Smith AK. PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L. Brain Behav Immun 2021; 91:429-436. [PMID: 33152445 PMCID: PMC7749859 DOI: 10.1016/j.bbi.2020.10.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/09/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is characterized by intrusive thoughts, avoidance, negative alterations in cognitions and mood, and arousal symptoms that adversely affect mental and physical health. Recent evidence links changes in DNA methylation of CpG cites to PTSD. Since clusters of proximal CpGs share similar methylation signatures, identification of PTSD-associated differentially methylated regions (DMRs) may elucidate the pathways defining differential risk and resilience of PTSD. Here we aimed to identify epigenetic differences associated with PTSD. DNA methylation data profiled from blood samples using the MethylationEPIC BeadChip were used to perform a DMR analysis in 187 PTSD cases and 367 trauma-exposed controls from the Grady Trauma Project (GTP). DMRs were assessed with R package bumphunter. We identified two regions that associate with PTSD after multiple test correction. These regions were in the gene body of HLA-DPB1 and in the promoter of SPATC1L. The DMR in HLA-DPB1 was associated with PTSD in an independent cohort. Both DMRs included CpGs whose methylation associated with nearby sequence variation (meQTL) and that associated with expression of their respective genes (eQTM). This study supports an emerging literature linking PTSD risk to genetic and epigenetic variation in the HLA region.
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Affiliation(s)
- Seyma Katrinli
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | - Yuanchao Zheng
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Suresh Venkateswaran
- Emory University School of Medicine Department of Pediatrics, Division of Pediatric Gastroenterology & Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Varun Kilaru
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | - Adriana Lori
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Rebecca Hinrichs
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Abigail Powers
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Charles F Gillespie
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Aliza P Wingo
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA; Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA
| | - Vasiliki Michopoulos
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Tanja Jovanovic
- Wayne State University, Department of Psychiatry & Behavioral Neurosciences, Detroit, MI, USA
| | - Erika J Wolf
- National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Regina E McGlinchey
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, Boston, USA; VA Boston Health Care System, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - William P Milberg
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, Boston, USA; VA Boston Health Care System, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Mark W Miller
- National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Subra Kugathasan
- Emory University School of Medicine Department of Pediatrics, Division of Pediatric Gastroenterology & Children's Healthcare of Atlanta, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Marti Jett
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mark W Logue
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA; National Center for PTSD at VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA; Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Kerry J Ressler
- Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA; Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Alicia K Smith
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA; Emory University School of Medicine, Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA.
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29
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Hiraoka D, Nishitani S, Shimada K, Kasaba R, Fujisawa TX, Tomoda A. RETRACTED: Epigenetic modification of the oxytocin gene is associated with gray matter volume and trait empathy in mothers. Psychoneuroendocrinology 2021; 123:105026. [PMID: 33130408 DOI: 10.1016/j.psyneuen.2020.105026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). The Editor has concluded that the acceptance of this article was partly based upon the positive advice of an unreliable reviewer report. The report was provided to the journal by a reviewer suggested by the authors, and there were inappropriate communications between the authors and reviewer during the peer-review process. The Editor has therefore concluded that the review was not appropriate or independent. This manipulation of the peer-review process represents a clear violation of the fundamentals of peer review, our publishing policies, and publishing ethics standards. Apologies are offered to the readers of the journal that this deception was not detected during the submission process.
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Affiliation(s)
- Daiki Hiraoka
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan
| | - Koji Shimada
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan; Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Ryoko Kasaba
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan
| | - Takashi X Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan; Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan; Division of Developmental Higher Brain Functions, United Graduate School of Child Development, University of Fukui, Fukui, Japan.
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30
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Smith AK, Ratanatharathorn A, Maihofer AX, Naviaux RK, Aiello AE, Amstadter AB, Ashley-Koch AE, Baker DG, Beckham JC, Boks MP, Bromet E, Dennis M, Galea S, Garrett ME, Geuze E, Guffanti G, Hauser MA, Katrinli S, Kilaru V, Kessler RC, Kimbrel NA, Koenen KC, Kuan PF, Li K, Logue MW, Lori A, Luft BJ, Miller MW, Naviaux JC, Nugent NR, Qin X, Ressler KJ, Risbrough VB, Rutten BPF, Stein MB, Ursano RJ, Vermetten E, Vinkers CH, Wang L, Youssef NA, Uddin M, Nievergelt CM. Epigenome-wide meta-analysis of PTSD across 10 military and civilian cohorts identifies methylation changes in AHRR. Nat Commun 2020; 11:5965. [PMID: 33235198 PMCID: PMC7686485 DOI: 10.1038/s41467-020-19615-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetic differences may help to distinguish between PTSD cases and trauma-exposed controls. Here, we describe the results of the largest DNA methylation meta-analysis of PTSD to date. Ten cohorts, military and civilian, contribute blood-derived DNA methylation data from 1,896 PTSD cases and trauma-exposed controls. Four CpG sites within the aryl-hydrocarbon receptor repressor (AHRR) associate with PTSD after adjustment for multiple comparisons, with lower DNA methylation in PTSD cases relative to controls. Although AHRR methylation is known to associate with smoking, the AHRR association with PTSD is most pronounced in non-smokers, suggesting the result was independent of smoking status. Evaluation of metabolomics data reveals that AHRR methylation associated with kynurenine levels, which are lower among subjects with PTSD. This study supports epigenetic differences in those with PTSD and suggests a role for decreased kynurenine as a contributor to immune dysregulation in PTSD.
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Affiliation(s)
- Alicia K Smith
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA.
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA.
| | | | - Adam X Maihofer
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Robert K Naviaux
- University of California, The Mitochondrial and Metabolic Disease Center, Departments of Medicine, Pediatrics, and Pathology, San Diego, CA, USA
| | - Allison E Aiello
- University of North Carolina, Gillings School of Global Public Health, Department of Epidemiology, Chapel Hill, NC, USA
| | - Ananda B Amstadter
- Virginia Commonwealth University, Department of Psychiatry, Richmond, VA, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Dewleen G Baker
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Jean C Beckham
- VA Mid-Atlantic, Mental Illness Research, Education, and Clinical Center, Durham, NC, USA
- Veterans Affairs Durham Healthcare System, Durham, NC, USA
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | - Marco P Boks
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Evelyn Bromet
- State University of New York at Stony Brook, Epidemiology Research Group, Stony Brook, NY, USA
| | - Michelle Dennis
- VA Mid-Atlantic, Mental Illness Research, Education, and Clinical Center, Durham, NC, USA
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | - Sandro Galea
- Boston University, School of Public Health, Boston, MA, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Elbert Geuze
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Utrecht, The Netherlands
- Netherlands Ministry of Defence, Brain Research and Innovation Centre, Utrecht, The Netherlands
| | - Guia Guffanti
- McLean Hospital, Division of Depression and Anxiety, Belmont, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael A Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Duke University, Department of Medicine, Durham, NC, USA
| | - Seyma Katrinli
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | - Varun Kilaru
- Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA
| | | | - Nathan A Kimbrel
- VA Mid-Atlantic, Mental Illness Research, Education, and Clinical Center, Durham, NC, USA
- Veterans Affairs Durham Healthcare System, Durham, NC, USA
- Duke University Medical Center, Department of Psychiatry and Behavioral Sciences, Durham, NC, USA
| | - Karestan C Koenen
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Department of Psychiatry, Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Pei-Fen Kuan
- State University of New York at Stony Brook, Department of Applied Mathematics and Statistics, Stony Brook, NY, USA
| | - Kefeng Li
- University of California, The Mitochondrial and Metabolic Disease Center, Department of Medicine, San Diego, CA, USA
| | - Mark W Logue
- National Center for PTSD, Behavioral Science Division at VA Boston Healthcare System, Boston, MA, USA
- Boston University School of Medicine, Department of Psychiatry, Boston, MA, USA
- Boston University School of Medicine, Department of Medicine (Biomedical Genetics), Boston, MA, USA
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA
| | - Adriana Lori
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
| | - Benjamin J Luft
- State University of New York at Stony Brook, Department of Medicine, Stony Brook, NY, USA
| | - Mark W Miller
- National Center for PTSD, Behavioral Science Division at VA Boston Healthcare System, Boston, MA, USA
- Boston University School of Medicine, Department of Psychiatry, Boston, MA, USA
| | - Jane C Naviaux
- University of California, The Mitochondrial and Metabolic Disease Center, Department of Neuroscience, San Diego, CA, USA
| | - Nicole R Nugent
- Brown University, Psychiatry and Human Behavior, Department of Pediatric Research, Providence, RI, USA
| | - Xuejun Qin
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kerry J Ressler
- Emory University, Department of Psychiatry & Behavioral Sciences, Atlanta, GA, USA
- McLean Hospital, Division of Depression and Anxiety, Belmont, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Victoria B Risbrough
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Bart P F Rutten
- Maastricht University Medical Centre, School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht, The Netherlands
| | - Murray B Stein
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- University of California San Diego, Department of Family Medicine and Public Health, La Jolla, CA, USA
| | - Robert J Ursano
- Uniformed Services University School of Medicine, Center for the Study of Traumatic Stress, Bethesda, MD, USA
| | - Eric Vermetten
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Utrecht, The Netherlands
- Uniformed Services University School of Medicine, Center for the Study of Traumatic Stress, Bethesda, MD, USA
- Leiden University Medical Center, Department of Psychiatry, Leiden, The Netherlands
- Netherlands Defense Department, Research Center, Utrecht, UT, The Netherlands
- Arq Psychotrauma Expert Group, Diemen, The Netherlands
| | - Christiaan H Vinkers
- Amsterdam UMC (location VUmc), Department of Psychiatry, Amsterdam, The Netherlands
- Amsterdam UMC (location VUmc), Department of Anatomy and Neurosciences, Amsterdam, The Netherlands
| | - Lin Wang
- University of California, The Mitochondrial and Metabolic Disease Center, Department of Medicine, San Diego, CA, USA
| | - Nagy A Youssef
- Medical College of Georgia at Augusta University, Department of Psychiatry and Human Behavior and Office of Academic Affairs, Augusta, GA, USA
| | - Monica Uddin
- University of South Florida, College of Public Health, Tampa, FL, USA
| | - Caroline M Nievergelt
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Veterans Affairs Center of Excellence for Stress and Mental Health, San Diego, CA, USA
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Wolf EJ, Logue MW, Zhao X, Daskalakis NP, Morrison FG, Escarfulleri S, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Chen C, Abraham CR, Miller MW. PTSD and the klotho longevity gene: Evaluation of longitudinal effects on inflammation via DNA methylation. Psychoneuroendocrinology 2020; 117:104656. [PMID: 32438247 PMCID: PMC7293549 DOI: 10.1016/j.psyneuen.2020.104656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/04/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Longevity gene klotho (KL) is associated with age-related phenotypes including lifespan, cardiometabolic disorders, cognition, and brain morphology, in part, by conferring protection against inflammation. We hypothesized that the KL/inflammation association might be altered in the presence of psychiatric stress and operate via epigenetic pathways. We examined KL polymorphisms, and their interaction with posttraumatic stress disorder (PTSD) symptoms, in association with KL DNA methylation in blood. We further examined KL DNA methylation as a predictor of longitudinal changes in a peripheral biomarker of inflammation (C-reactive protein; CRP). METHODS The sample comprised 309 white non-Hispanic military veterans (93.5 % male; mean age: 32 years, range: 19-65; 30 % PTSD per structured diagnostic interview); 111 were reassessed approximately two years later. RESULTS Analyses revealed a methylation quantitative trait locus at rs9527025 (C370S, previously implicated in numerous studies of aging) in association with a Cytosine-phosphate-Guanine site (cg00129557; B = -.65, p = 1.29 X 10-20), located within a DNase hypersensitivity site in the body of KL. There was also a rs9527025 x PTSD severity interaction (B = .004, p = .035) on methylation at this locus such that the minor allele was associated with reduced cg00129557 methylation in individuals with few or no PTSD symptoms while this effect was attenuated in those with elevated levels of PTSD. Path models revealed that methylation at cg00129557 was inversely associated with CRP over time (B = -.14, p = .005), controlling for baseline CRP. There was also an indirect effect of rs9527025 X PTSD on subsequent CRP via cg00129557 methylation (indirect B = -.002, p = .033). CONCLUSIONS Results contribute to our understanding of the epigenetic correlates of inflammation in PTSD and suggest that KL methylation may be a mechanism by which KL genotype confers risk vs. resilience to accelerated aging in those experiencing traumatic stress.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine,Biomedical Genetics, Boston University School of Medicine
| | - Xiang Zhao
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
| | | | - Filomene G. Morrison
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
| | | | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System
| | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System
| | - Regina E. McGlinchey
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System,Department of Psychiatry, Harvard Medical School
| | - William P. Milberg
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System,Department of Psychiatry, Harvard Medical School
| | - Cidi Chen
- Department of Biochemistry, Boston University School of Medicine
| | - Carmela R. Abraham
- Department of Biochemistry, Boston University School of Medicine,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
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32
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The relationship between DNA methylation in neurotrophic genes and age as evidenced from three independent cohorts: differences by delirium status. Neurobiol Aging 2020; 94:227-235. [PMID: 32650186 DOI: 10.1016/j.neurobiolaging.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/07/2020] [Accepted: 06/06/2020] [Indexed: 12/19/2022]
Abstract
We previously reported the association between DNA methylation (DNAm) of pro-inflammatory cytokine genes and age. In addition, neurotrophic factors are known to be associated with age and neurocognitive disorders. Therefore, we hypothesized that DNAm of neurotrophic genes change with age, especially in delirium patients. DNAm was analyzed using the Illumina HumanMethylation450 or HumanMethylationEPIC BeadChip Kit in 3 independent cohorts: blood from 383 Grady Trauma Project subjects, brain from 21 neurosurgery patients, and blood from 87 inpatients with and without delirium. Both blood and brain samples showed that most of the DNAm of neurotrophic genes were positively correlated with age. Furthermore, DNAm of neurotrophic genes was more positively correlated with age in delirium cases than in non-delirium controls. These findings support our hypothesis that the neurotrophic genes may be epigenetically modulated with age, and this process may be contributing to the pathophysiology of delirium.
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33
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Logue MW, Miller MW, Wolf EJ, Huber BR, Morrison FG, Zhou Z, Zheng Y, Smith AK, Daskalakis NP, Ratanatharathorn A, Uddin M, Nievergelt CM, Ashley-Koch AE, Baker DG, Beckham JC, Garrett ME, Boks MP, Geuze E, Grant GA, Hauser MA, Kessler RC, Kimbrel NA, Maihofer AX, Marx CE, Qin XJ, Risbrough VB, Rutten BPF, Stein MB, Ursano RJ, Vermetten E, Vinkers CH, Ware EB, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Hayes JP, Verfaellie M. An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci. Clin Epigenetics 2020; 12:46. [PMID: 32171335 PMCID: PMC7071645 DOI: 10.1186/s13148-020-0820-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Previous studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD). METHODS In this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72). RESULTS The analysis of blood samples yielded one genome-wide significant association with PTSD at cg19534438 in the gene G0S2 (p = 1.19 × 10-7, padj = 0.048). This association was replicated in an independent PGC-PTSD-EWAS consortium meta-analysis of military cohorts (p = 0.0024). We also observed association with the smoking-related locus cg05575921 in AHRR despite inclusion of a methylation-based smoking score covariate (p = 9.16 × 10-6), which replicates a previously observed PGC-PTSD-EWAS association (Smith et al. 2019), and yields evidence consistent with a smoking-independent effect. The top 100 EWAS loci were then examined in the PFC data. One of the blood-based PTSD loci, cg04130728 in CHST11, which was in the top 10 loci in blood, but which was not genome-wide significant, was significantly associated with PTSD in brain tissue (in blood p = 1.19 × 10-5, padj = 0.60, in brain, p = 0.00032 with the same direction of effect). Gene set enrichment analysis of the top 500 EWAS loci yielded several significant overlapping GO terms involved in pathogen response, including "Response to lipopolysaccharide" (p = 6.97 × 10-6, padj = 0.042). CONCLUSIONS The cross replication observed in independent cohorts is evidence that DNA methylation in peripheral tissue can yield consistent and replicable PTSD associations, and our results also suggest that that some PTSD associations observed in peripheral tissue may mirror associations in the brain.
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Affiliation(s)
- Mark W. Logue
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA ,grid.475010.70000 0004 0367 5222,Biomedical Genetics, Boston University School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Mark W. Miller
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA
| | - Erika J. Wolf
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA
| | - Bertrand Russ Huber
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA
| | - Filomene G. Morrison
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA
| | - Zhenwei Zhou
- grid.189504.10000 0004 1936 7558Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Yuanchao Zheng
- grid.189504.10000 0004 1936 7558Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Alicia K. Smith
- grid.189967.80000 0001 0941 6502Department of Gynecology and Obstetrics, Emory University, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Nikolaos P. Daskalakis
- grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.240206.20000 0000 8795 072XMcLean Hospital, Belmont, MA USA ,Cohen Veterans Bioscience, Cambridge, MA USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Andrew Ratanatharathorn
- grid.21729.3f0000000419368729Department of Epidemiology, Columbia University, New York, NY USA
| | - Monica Uddin
- grid.170693.a0000 0001 2353 285XGenomics Program, University of South Florida College of Public Health, Tampa, FL USA ,grid.170693.a0000 0001 2353 285X,Global Health and Infectious Disease Research Program, University of South Florida College of Public Health, Tampa, FL USA
| | - Caroline M. Nievergelt
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA USA ,grid.410371.00000 0004 0419 2708Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Allison E. Ashley-Koch
- grid.189509.c0000000100241216Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC USA
| | - Dewleen G. Baker
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA USA ,grid.410371.00000 0004 0419 2708Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Jean C. Beckham
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC USA ,grid.410332.70000 0004 0419 9846Research, Durham VA Medical Center, Durham, NC USA ,grid.281208.10000 0004 0419 3073Genetics Research Laboratory, VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center (MIRECC), Durham, NC USA
| | - Melanie E. Garrett
- grid.189509.c0000000100241216Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC USA
| | - Marco P. Boks
- grid.7692.a0000000090126352Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, Utrecht Netherlands
| | - Elbert Geuze
- grid.7692.a0000000090126352Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, Utrecht Netherlands ,Brain Research and Innovation Centre, Netherlands Ministry of Defence, Utrecht, Utrecht Netherlands
| | - Gerald A. Grant
- grid.240952.80000000087342732Department of Neurosurgery, Stanford University Medical Center, Stanford, CA USA
| | - Michael A. Hauser
- grid.189509.c0000000100241216Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC USA
| | - Ronald C. Kessler
- grid.38142.3c000000041936754XDepartment of Health Care Policy, Harvard Medical School, Boston, MA USA
| | - Nathan A. Kimbrel
- grid.410332.70000 0004 0419 9846Research, Durham VA Medical Center, Durham, NC USA ,grid.281208.10000 0004 0419 3073Genetics Research Laboratory, VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center (MIRECC), Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University, Durham, NC USA
| | - Adam X. Maihofer
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA USA ,grid.410371.00000 0004 0419 2708Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Christine E. Marx
- grid.21925.3d0000 0004 1936 9000Department of Critical Care Medicine, Neurology, and Neurosurgery, University of Pittsburgh, Pittsburgh, PA USA ,grid.189509.c0000000100241216Department of Psychiatry & Behavioral Sciences, Duke University Medical Center, Durham, NC USA
| | - Xue-Jun Qin
- grid.189509.c0000000100241216Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC USA
| | - Victoria B. Risbrough
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA USA ,grid.410371.00000 0004 0419 2708Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Bart P. F. Rutten
- grid.412966.e0000 0004 0480 1382School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, Maastricht, Limburg Netherlands
| | - Murray B. Stein
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.410371.00000 0004 0419 2708Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA USA ,grid.410371.00000 0004 0419 2708Million Veteran Program, Veterans Affairs San Diego Healthcare System, San Diego, CA USA
| | - Robert J. Ursano
- grid.265436.00000 0001 0421 5525Department of Psychiatry, Uniformed Services University, Bethesda, MD USA
| | - Eric Vermetten
- Arq, Psychotrauma Reseach Expert Group, Diemen, NH Netherlands ,grid.10419.3d0000000089452978Department of Psychiatry, Leiden University Medical Center, Leiden, ZH Netherlands ,Netherlands Defense Department, Research Center, Utrecht, UT Netherlands ,grid.137628.90000 0004 1936 8753Department of Psychiatry, New York University School of Medicine, New York, NY USA
| | - Christiaan H. Vinkers
- Department of Anatomy and Neurosciences, Amsterdam UMC (location VUmc), Amsterdam, Holland Netherlands ,Department of Psychiatry, Amsterdam UMC (location VUmc), Amsterdam, Holland Netherlands
| | - Erin B. Ware
- grid.214458.e0000000086837370Institute for Social Research, Survey Research Center, University of Michigan, Michigan, MI USA
| | - Annjanette Stone
- grid.413916.80000 0004 0419 1545Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR USA
| | - Steven A. Schichman
- grid.413916.80000 0004 0419 1545Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR USA
| | - Regina E. McGlinchey
- grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.410370.10000 0004 4657 1992Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Health Care System, Boston, MA USA
| | - William P. Milberg
- grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.410370.10000 0004 4657 1992Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Health Care System, Boston, MA USA
| | - Jasmeet P. Hayes
- grid.410370.10000 0004 4657 1992National Center for PTSD, VA Boston Healthcare System, Boston, MA USA ,grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA ,grid.261331.40000 0001 2285 7943Department of Psychology and Chronic Brain Injury Program, The Ohio State University, Columbus, OH USA
| | - Mieke Verfaellie
- grid.475010.70000 0004 0367 5222Department of Psychiatry, Boston University School of Medicine, Boston, MA USA ,grid.475010.70000 0004 0367 5222Memory Disorders Research Center, VA Boston Healthcare System and Boston University School of Medicine, Boston, MA USA
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Ward-Caviness CK, Pu S, Martin CL, Galea S, Uddin M, Wildman DE, Koenen K, Aiello AE. Epigenetic predictors of all-cause mortality are associated with objective measures of neighborhood disadvantage in an urban population. Clin Epigenetics 2020; 12:44. [PMID: 32160902 PMCID: PMC7065313 DOI: 10.1186/s13148-020-00830-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/17/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Neighborhood characteristics are robust predictors of overall health and mortality risk for residents. Though there has been some investigation of the role that molecular indicators may play in mediating neighborhood exposures, there has been little effort to incorporate newly developed epigenetic biomarkers into our understanding of neighborhood characteristics and health outcomes. METHODS Using 157 participants of the Detroit Neighborhood Health Study with detailed assessments of neighborhood characteristics and genome-wide DNA methylation profiling via the Illumina 450K methylation array, we assessed the relationship between objective neighborhood characteristics and a validated DNA methylation-based epigenetic mortality risk score (eMRS). Associations were adjusted for age, race, sex, ever smoking, ever alcohol usage, education, years spent in neighborhood, and employment. A secondary model additionally adjusted for personal neighborhood perception. We summarized 19 neighborhood quality indicators assessed for participants into 9 principal components which explained over 90% of the variance in the data and served as metrics of objective neighborhood quality exposures. RESULTS Of the nine principal components utilized for this study, one was strongly associated with the eMRS (β = 0.15; 95% confidence interval = 0.06-0.24; P = 0.002). This principal component (PC7) was most strongly driven by the presence of abandoned cars, poor streets, and non-art graffiti. Models including both PC7 and individual indicators of neighborhood perception indicated that only PC7 and not neighborhood perception impacted the eMRS. When stratified on neighborhood indicators of greenspace, we observed a potentially protective effect of large mature trees as this feature substantially attenuated the observed association. CONCLUSION Objective measures of neighborhood disadvantage are significantly associated with an epigenetic predictor of mortality risk, presenting a potential novel avenue by which neighborhood-level exposures may impact health. Associations were independent of an individual's perception of their neighborhood and attenuated by neighborhood greenspace features. More work should be done to determine molecular risk factors associated with neighborhoods, and potentially protective neighborhood features against adverse molecular effects.
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Affiliation(s)
- Cavin K Ward-Caviness
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, 104 Mason Farm Rd, Chapel Hill, NC, 27514, USA.
| | - Shirley Pu
- University of North Carolina-Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Chantel L Martin
- Carolina Population Center, Univeristy of North Carolina-Chapel Hill, Chapel Hill, NC, 27514, USA
- Department of Epidemiology, Gillings School of Global Public Health, Univerity of North Carolina-Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Sandro Galea
- School of Public Health, Boston University, Boston, MA, 02118, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Karestan Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Allison E Aiello
- Carolina Population Center, Univeristy of North Carolina-Chapel Hill, Chapel Hill, NC, 27514, USA
- Department of Epidemiology, Gillings School of Global Public Health, Univerity of North Carolina-Chapel Hill, Chapel Hill, NC, 27514, USA
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35
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Snijders C, Maihofer AX, Ratanatharathorn A, Baker DG, Boks MP, Geuze E, Jain S, Kessler RC, Pishva E, Risbrough VB, Stein MB, Ursano RJ, Vermetten E, Vinkers CH, Smith AK, Uddin M, Rutten BPF, Nievergelt CM. Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder. Clin Epigenetics 2020; 12:11. [PMID: 31931860 PMCID: PMC6958602 DOI: 10.1186/s13148-019-0798-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/19/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Epigenetic mechanisms have been suggested to play a role in the development of post-traumatic stress disorder (PTSD). Here, blood-derived DNA methylation data (HumanMethylation450 BeadChip) collected prior to and following combat exposure in three cohorts of male military members were analyzed to assess whether DNA methylation profiles are associated with the development of PTSD. A total of 123 PTSD cases and 143 trauma-exposed controls were included in the analyses. The Psychiatric Genomics Consortium (PGC) PTSD EWAS QC pipeline was used on all cohorts, and results were combined using a sample size weighted meta-analysis in a two-stage design. In stage one, we jointly analyzed data of two new cohorts (N = 126 and 78) for gene discovery, and sought to replicate significant findings in a third, previously published cohort (N = 62) to assess the robustness of our results. In stage 2, we aimed at maximizing power for gene discovery by combining all three cohorts in a meta-analysis. RESULTS Stage 1 analyses identified four CpG sites in which, conditional on pre-deployment DNA methylation, post-deployment DNA methylation was significantly associated with PTSD status after epigenome-wide adjustment for multiple comparisons. The most significant (intergenic) CpG cg05656210 (p = 1.0 × 10-08) was located on 5q31 and significantly replicated in the third cohort. In addition, 19 differentially methylated regions (DMRs) were identified, but failed replication. Stage 2 analyses identified three epigenome-wide significant CpGs, the intergenic CpG cg05656210 and two additional CpGs located in MAD1L1 (cg12169700) and HEXDC (cg20756026). Interestingly, cg12169700 had an underlying single nucleotide polymorphism (SNP) which was located within the same LD block as a recently identified PTSD-associated SNP in MAD1L1. Stage 2 analyses further identified 12 significant differential methylated regions (DMRs), 1 of which was located in MAD1L1 and 4 were situated in the human leukocyte antigen (HLA) region. CONCLUSIONS This study suggests that the development of combat-related PTSD is associated with distinct methylation patterns in several genomic positions and regions. Our most prominent findings suggest the involvement of the immune system through the HLA region and HEXDC, and MAD1L1 which was previously associated with PTSD.
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Affiliation(s)
- Clara Snijders
- Department of Psychiatry and Neuropsychology, School for Mental health and Neuroscience, Maastricht University, Maastricht, Limburg, Netherlands
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | | | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Marco P Boks
- Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, Utrecht, Netherlands
| | - Elbert Geuze
- Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, Utrecht, Netherlands
- Brain Research & Innovation Centre, Netherlands Ministry of Defense, Utrecht, Utrecht, Netherlands
| | - Sonia Jain
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental health and Neuroscience, Maastricht University, Maastricht, Limburg, Netherlands
- College of Medicine and Health, University of Exeter Medical School, Exeter, UK
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Million Veteran Program, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Eric Vermetten
- Arq, Psychotrauma Research Expert Group, Diemen, North Holland, Netherlands
- Department of Psychiatry, Leiden University Medical Center, Leiden, South Holland, Netherlands
- Military Mental Healthcare, Netherlands Ministry of Defense, Utrecht, Utrecht, Netherlands
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Christiaan H Vinkers
- Department of Anatomy and Neurosciences, Amsterdam UMC (location VUmc), Amsterdam, Holland, Netherlands
- Department of Psychiatry, Amsterdam UMC (location VUmc), Amsterdam, Holland, Netherlands
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Monica Uddin
- Genomics Program, University of South Florida College of Public Health, Tampa, FL, USA
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental health and Neuroscience, Maastricht University, Maastricht, Limburg, Netherlands
| | - Caroline M Nievergelt
- Department of Psychiatry and Neuropsychology, School for Mental health and Neuroscience, Maastricht University, Maastricht, Limburg, Netherlands.
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
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Forero DA. Available Software for Meta-analyses of Genome-wide Expression Studies. Curr Genomics 2019; 20:325-331. [PMID: 32476989 PMCID: PMC7235394 DOI: 10.2174/1389202920666190822113912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 01/24/2023] Open
Abstract
Advances in transcriptomic methods have led to a large number of published Genome-Wide Expression Studies (GWES), in humans and model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, the main features of available software for carrying out meta-analysis of GWES have been reviewed and seven packages from the Bioconductor platform and five packages from the CRAN platform have been described. In addition, nine previously described programs and four online programs are reviewed. Finally, advantages and disadvantages of these available programs and proposed key points for future developments have been discussed.
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Affiliation(s)
- Diego A Forero
- PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
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Howie H, Rijal CM, Ressler KJ. A review of epigenetic contributions
to post-traumatic stress disorder
. DIALOGUES IN CLINICAL NEUROSCIENCE 2019; 21:417-428. [PMID: 31949409 PMCID: PMC6952751 DOI: 10.31887/dcns.2019.21.4/kressler] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Post-traumatic stress disorder (PTSD) is a syndrome which serves as a classic example of psychiatric disorders that result from the intersection of nature and nurture, or gene and environment. By definition, PTSD requires the experience of a traumatic exposure, and yet data suggest that the risk for PTSD in the aftermath of trauma also has a heritable (genetic) component. Thus, PTSD appears to require both a biological (genetic) predisposition that differentially alters how the individual responds to or recovers from trauma exposure. Epigenetics is defined as the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself, and more recently it has come to refer to direct alteration of DNA regulation, but without altering the primary sequence of DNA, or the genetic code. With regards to PTSD, epigenetics provides one way for environmental exposure to be "written" upon the genome, as a direct result of gene and environment (trauma) interactions. This review provides an overview of the main currently understood types of epigenetic regulation, including DNA methylation, histone regulation of chromatin, and noncoding RNA regulation of gene expression. Furthermore, we examine recent literature related to how these methods of epigenetic regulation may be involved in differential risk and resilience for PTSD in the aftermath of trauma.
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Affiliation(s)
- Hunter Howie
- Aartners Healthcare, Boston, Massachusetts, US; McLean Hospital, Belmont, Massachusetts, US
| | - Chuda M Rijal
- Partners Healthcare, Boston, Massachusetts, US; McLean Hospital, Belmont, Massachusetts, US
| | - Kerry J Ressler
- Partners Healthcare, Boston, Massachusetts, US; McLean Hospital, Belmont, Massachusetts, US; Harvard Medical School, Boston, Massachusetts, US
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Kim GS, Smith AK, Xue F, Michopoulos V, Lori A, Armstrong DL, Aiello AE, Koenen KC, Galea S, Wildman DE, Uddin M. Methylomic profiles reveal sex-specific differences in leukocyte composition associated with post-traumatic stress disorder. Brain Behav Immun 2019; 81:280-291. [PMID: 31228611 PMCID: PMC6754791 DOI: 10.1016/j.bbi.2019.06.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating mental disorder precipitated by trauma exposure. However, only some persons exposed to trauma develop PTSD. There are sex differences in risk; twice as many women as men develop a lifetime diagnosis of PTSD. Methylomic profiles derived from peripheral blood are well-suited for investigating PTSD because DNA methylation (DNAm) encodes individual response to trauma and may play a key role in the immune dysregulation characteristic of PTSD pathophysiology. In the current study, we leveraged recent methodological advances to investigate sex-specific differences in DNAm-based leukocyte composition that are associated with lifetime PTSD. We estimated leukocyte composition on a combined methylation array dataset (483 participants, ∼450 k CpG sites) consisting of two civilian cohorts, the Detroit Neighborhood Health Study and Grady Trauma Project. Sex-stratified Mann-Whitney U test and two-way ANCOVA revealed that lifetime PTSD was associated with significantly higher monocyte proportions in males, but not in females (Holm-adjusted p-val < 0.05). No difference in monocyte proportions was observed between current and remitted PTSD cases in males, suggesting that this sex-specific difference may reflect a long-standing trait of lifetime history of PTSD, rather than current state of PTSD. Associations with lifetime PTSD or PTSD status were not observed in any other leukocyte subtype and our finding in monocytes was confirmed using cell estimates based on a different deconvolution algorithm, suggesting that our sex-specific findings are robust across cell estimation approaches. Overall, our main finding of elevated monocyte proportions in males, but not in females with lifetime history of PTSD provides evidence for a sex-specific difference in peripheral blood leukocyte composition that is detectable in methylomic profiles and that may reflect long-standing changes associated with PTSD diagnosis.
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Affiliation(s)
- Grace S Kim
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Medical Scholars Program, University of Illinois College of Medicine, Urbana, IL, USA
| | - Alicia K Smith
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA; Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Fei Xue
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Vasiliki Michopoulos
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Adriana Lori
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Don L Armstrong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Allison E Aiello
- Gillings School of Global Public Health, University of North Carolina - Chapel Hill, Chapel Hill, NC, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sandro Galea
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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DePierro J, Lepow L, Feder A, Yehuda R. Translating Molecular and Neuroendocrine Findings in Posttraumatic Stress Disorder and Resilience to Novel Therapies. Biol Psychiatry 2019; 86:454-463. [PMID: 31466562 PMCID: PMC6907400 DOI: 10.1016/j.biopsych.2019.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Many biological systems are altered in association with posttraumatic stress disorder (PTSD) and resilience. However, there are only few approved pharmacological treatments for PTSD, and no approved medications to enhance resilience. This article provides a critical review of select neurobiological findings in PTSD and resilience, and also of pharmacologic approaches that have emerged from this work. The medications summarized involve engagement with targets in the adrenergic, hypothalamic-pituitary-adrenal axis, and neuropeptide Y systems. Other highlighted approaches involve the use of ketamine and 3,4-methylenedioxymethamphetamine-assisted psychotherapy, which recently surfaced as promising strategies for PTSD, though the neurobiological mechanisms underlying their actions, including for promoting resilience, are not yet fully understood. The former approaches fall within the broad concept of "rational pharmacotherapy," in that they attempt to directly target dysregulated systems known to be associated with posttraumatic symptoms. To the extent that use of ketamine and 3,4-methylenedioxymethamphetamine promotes symptom improvement and resilience in PTSD, this provides an opportunity for reverse translation and identification of relevant targets and mechanisms of action through careful study of biological changes resulting from these interventions. Promoting resilience in trauma-exposed individuals may involve more than pharmacologically manipulating dysregulated molecules and pathways associated with developing and sustaining PTSD symptom severity, but also producing a substantial change in mental state that increases the ability to engage with traumatic material in psychotherapy. Neurobiological examination in the context of treatment studies may yield novel targets and promote a greater understanding of mechanisms of recovery from trauma.
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Affiliation(s)
- Jonathan DePierro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lauren Lepow
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adriana Feder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rachel Yehuda
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, James J. Peters Veterans Affairs Medical Center, Bronx, New York.
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40
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Han LKM, Verhoeven JE, Tyrka AR, Penninx BWJH, Wolkowitz OM, Månsson KNT, Lindqvist D, Boks MP, Révész D, Mellon SH, Picard M. Accelerating research on biological aging and mental health: Current challenges and future directions. Psychoneuroendocrinology 2019; 106:293-311. [PMID: 31154264 PMCID: PMC6589133 DOI: 10.1016/j.psyneuen.2019.04.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/22/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Aging is associated with complex biological changes that can be accelerated, slowed, or even temporarily reversed by biological and non-biological factors. This article focuses on the link between biological aging, psychological stressors, and mental illness. Rather than comprehensively reviewing this rapidly expanding field, we highlight challenges in this area of research and propose potential strategies to accelerate progress in this field. This effort requires the interaction of scientists across disciplines - including biology, psychiatry, psychology, and epidemiology; and across levels of analysis that emphasize different outcome measures - functional capacity, physiological, cellular, and molecular. Dialogues across disciplines and levels of analysis naturally lead to new opportunities for discovery but also to stimulating challenges. Some important challenges consist of 1) establishing the best objective and predictive biological age indicators or combinations of indicators, 2) identifying the basis for inter-individual differences in the rate of biological aging, and 3) examining to what extent interventions can delay, halt or temporarily reverse aging trajectories. Discovering how psychological states influence biological aging, and vice versa, has the potential to create novel and exciting opportunities for healthcare and possibly yield insights into the fundamental mechanisms that drive human aging.
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Affiliation(s)
- Laura K M Han
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Josine E Verhoeven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands
| | - Audrey R Tyrka
- Butler Hospital and the Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Brenda W J H Penninx
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Owen M Wolkowitz
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Kristoffer N T Månsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Psychology, Stockholm University, Stockholm, Sweden; Department of Psychology, Uppsala University, Uppsala, Sweden
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Department of Psychiatry, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; Psychiatric Clinic, Lund, Division of Psychiatry, Lund, Sweden
| | - Marco P Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, the Netherlands
| | - Dóra Révész
- Center of Research on Psychology in Somatic diseases (CoRPS), Department of Medical and Clinical Psychology, Tilburg University, Tilburg, the Netherlands
| | - Synthia H Mellon
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY, USA; Columbia Aging Center, Columbia University, New York, NY, USA.
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Zhou Z, Lunetta KL, Smith AK, Wolf EJ, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW, Logue MW. Correction for multiple testing in candidate-gene methylation studies. Epigenomics 2019; 11:1089-1105. [PMID: 31240951 PMCID: PMC7132638 DOI: 10.2217/epi-2018-0204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/15/2019] [Indexed: 01/02/2023] Open
Abstract
Aim: We compared the performance of multiple testing corrections for candidate gene methylation studies, namely Sidak (accurate Bonferroni), false-discovery rate and three adjustments that incorporate the correlation between CpGs: extreme tail theory (ETT), Gao et al. (GEA), and Li and Ji methods. Materials & methods: The experiment-wide type 1 error rate was examined in simulations based on Illumina EPIC and 450K data. Results: For high-correlation genes, Sidak and false-discovery rate corrections were conservative while the Li and Ji method was liberal. The GEA method tended to be conservative unless a threshold parameter was adjusted. The ETT yielded an appropriate type 1 error rate. Conclusion: For genes with substantial correlation across measured CpGs, GEA and ETT can appropriately correct for multiple testing in candidate gene methylation studies.
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Affiliation(s)
- Zhenwei Zhou
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Alicia K Smith
- Department of Gynecology & Obstetrics, Emory University, Atlanta, GA 30322, USA
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA 30329, USA
| | - Erika J Wolf
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Steven A Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Regina E McGlinchey
- Geriatric Research Educational & Clinical Center & Translational Research Center for TBI & Stress Disorders, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - William P Milberg
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
| | - Mark W Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
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Morrison FG, Logue MW, Guetta R, Maniates H, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW, Wolf EJ. Investigation of bidirectional longitudinal associations between advanced epigenetic age and peripheral biomarkers of inflammation and metabolic syndrome. Aging (Albany NY) 2019; 11:3487-3504. [PMID: 31173577 PMCID: PMC6594822 DOI: 10.18632/aging.101992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
Epigenetic age estimations based on DNA methylation (DNAm) can predict human chronological age with a high level of accuracy. These DNAm age algorithms can also be used to index advanced cellular age, when estimated DNAm age exceeds chronological age. Advanced DNAm age has been associated with several diseases and metabolic and inflammatory pathology, but the causal direction of this association is unclear. The goal of this study was to examine potential bidirectional associations between advanced epigenetic age and metabolic and inflammatory markers over time in a longitudinal cohort of 179 veterans with a high prevalence of posttraumatic stress disorder (PTSD) who were assessed over the course of two years. Analyses focused on two commonly investigated metrics of advanced DNAm age derived from the Horvath (developed across multiple tissue types) and Hannum (developed in whole blood) DNAm age algorithms. Results of cross-lagged panel models revealed that advanced Hannum DNAm age at Time 1 (T1) was associated with increased (i.e., accounting for T1 levels) metabolic syndrome (MetS) severity at Time 2 (T2; p = < 0.001). This association was specific to worsening lipid panels and indicators of abdominal obesity (p = 0.001). In contrast, no baseline measures of inflammation or metabolic pathology were associated with changes in advanced epigenetic age over time. No associations emerged between advanced Horvath DNAm age and any of the examined biological parameters. Results suggest that advanced epigenetic age, when measured using an algorithm developed in whole blood, may be a prognostic marker of pathological metabolic processes. This carries implications for understanding pathways linking advanced epigenetic age to morbidity and mortality.
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Affiliation(s)
- Filomene G. Morrison
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rachel Guetta
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
| | - Hannah Maniates
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
| | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Regina E. McGlinchey
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - William P. Milberg
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
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Wolf EJ, Logue MW, Morrison FG, Wilcox ES, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW. Posttraumatic psychopathology and the pace of the epigenetic clock: a longitudinal investigation. Psychol Med 2019; 49:791-800. [PMID: 29897034 PMCID: PMC6292741 DOI: 10.1017/s0033291718001411] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Posttraumatic stress disorder (PTSD) and stress/trauma exposure are cross-sectionally associated with advanced DNA methylation age relative to chronological age. However, longitudinal inquiry and examination of associations between advanced DNA methylation age and a broader range of psychiatric disorders is lacking. The aim of this study was to examine if PTSD, depression, generalized anxiety, and alcohol-use disorders predicted acceleration of DNA methylation age over time (i.e. an increasing pace, or rate of advancement, of the epigenetic clock). METHODS Genome-wide DNA methylation and a comprehensive set of psychiatric symptoms and diagnoses were assessed in 179 Iraq/Afghanistan war veterans who completed two assessments over the course of approximately 2 years. Two DNA methylation age indices (Horvath and Hannum), each a weighted index of an array of genome-wide DNA methylation probes, were quantified. The pace of the epigenetic clock was operationalized as change in DNA methylation age as a function of time between assessments. RESULTS Analyses revealed that alcohol-use disorders (p = 0.001) and PTSD avoidance and numbing symptoms (p = 0.02) at Time 1 were associated with an increasing pace of the epigenetic clock over time, per the Horvath (but not the Hannum) index of cellular aging. CONCLUSIONS This is the first study to suggest that posttraumatic psychopathology is longitudinally associated with a quickened pace of the epigenetic clock. Results raise the possibility that accelerated cellular aging is a common biological consequence of stress-related psychopathology, which carries implications for identifying mechanisms of stress-related cellular aging and developing interventions to slow its pace.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
- Biomedical Genetics, Boston University School of Medicine
| | - Filomene G. Morrison
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | | | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Regina E. McGlinchey
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - William P. Milberg
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
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Abstract
Resilience is defined as the dynamic ability to adapt successfully in the face of adversity, trauma, or significant threat. Some of the key early studies of resilience were observational studies in children. They were followed by research in adults, studies testing interventions to promote resilience in different populations, and a recent upsurge of studies on the underlying genomic and neurobiological mechanisms. Neural and molecular studies in preclinical models of resilience are also increasingly identifying active stress adaptations in resilient animals. Knowledge gained from animal and human studies of resilience can be harnessed to develop new preventive interventions to enhance resilience in at-risk populations. Further, treatment interventions focused on enhancing potentially modifiable protective factors that are consistently linked to psychological resilience can enrich currently available treatment interventions for individuals with posttraumatic stress disorder (PTSD). Translating our expanding knowledge of the neurobiology of resilience additionally promises to yield novel therapeutic strategies for treating this disabling condition. This review summarizes the vast field of resilience research spanning genomic, psychosocial, and neurobiological levels, and discusses how findings have led and can lead to new preventive and treatment interventions for PTSD.
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Morrison FG, Miller MW, Logue MW, Assef M, Wolf EJ. DNA methylation correlates of PTSD: Recent findings and technical challenges. Prog Neuropsychopharmacol Biol Psychiatry 2019; 90:223-234. [PMID: 30503303 PMCID: PMC6314898 DOI: 10.1016/j.pnpbp.2018.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
There is increasing evidence that epigenetic factors play a critical role in posttraumatic stress disorder (PTSD), by mediating the impact of environmental exposures to trauma on the regulation of gene expression. DNA methylation is one epigenetic process that has been highly studied in PTSD. This review will begin by providing an overview of DNA methylation (DNAm) methods, and will then highlight two major biological systems that have been identified in the epigenetic regulation in PTSD: (a) the immune system and (b) the stress response system. In addition to candidate gene approaches, we will review novel strategies to study epigenome-wide PTSD-related effects, including epigenome-wide algorithms that distill information from many loci into a single summary score (e.g., measures of "epigenetic age" which have been associated with PTSD). This review will also cover recent epigenome wide association studies (EWAS) of PTSD, and biological pathway models used to identify gene sets enriched in PTSD. Finally, we address technical and methodological advances and challenges to the field, and highlight exciting directions for future research.
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Affiliation(s)
- Filomene G Morrison
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA.
| | - Mark W Miller
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA; Biomedical Genetics, Boston University School of Medicine, USA; Department of Biostatistics, Boston University School of Public Health, USA
| | - Michele Assef
- Boston University, College of Health & Rehabilitation Sciences: Sargent College, USA
| | - Erika J Wolf
- National Center for PTSD, VA Boston Healthcare System, USA; Department of Psychiatry, Boston University School of Medicine, USA
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46
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Snijders C, Pries LK, Sgammeglia N, Al Jowf G, Youssef NA, de Nijs L, Guloksuz S, Rutten BPF. Resilience Against Traumatic Stress: Current Developments and Future Directions. Front Psychiatry 2018; 9:676. [PMID: 30631285 PMCID: PMC6315131 DOI: 10.3389/fpsyt.2018.00676] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 11/23/2018] [Indexed: 12/22/2022] Open
Abstract
Given the high prevalence of stress-related mental disorders, their impact on person, family, and society and the paucity of treatment options for most of these disorders, there is currently a pressing need for innovative approaches to deal with these issues and enhance well-being. One approach which has received increasing attention over the last decade is to shift our scientific and clinical focus from risk factors for psychopathology to factors promoting resilience and mental well-being. In order to summarize and evaluate the current state of scientific affairs on the biological basis of resilience, we provide an overview of the literature on animal and human studies of resilience. Because resilience can only truly be operationalized through longitudinal data collection and analyses, we focus primarily on longitudinal studies. This review shows that the concept of resilience is currently being operationalized, measured and even defined in widely variable manners, both within animal and human studies. We further provide an overview of existing and new strategies that could help promote resilience and which are proposed to be implemented more often in clinical situations. Finally, we summarize the challenges the field is facing and provide recommendations for future research.
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Affiliation(s)
- Clara Snijders
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Lotta-Katrin Pries
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Noemi Sgammeglia
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Ghazi Al Jowf
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
- College of Applied Medical Sciences, Department of Public Health, King Faisal University, Al-Ahsa, Saudi Arabia
- European Graduate School of Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Nagy A. Youssef
- Department of Psychiatry and Health Behavior, Medical College of Georgia, Augusta University, Augusta, GA, United States
- Office of Academic Affairs, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Laurence de Nijs
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Sinan Guloksuz
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Bart P. F. Rutten
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
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47
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Uddin M, Ratanatharathorn A, Armstrong D, Kuan PF, Aiello AE, Bromet EJ, Galea S, Koenen KC, Luft B, Ressler KJ, Wildman DE, Nievergelt CM, Smith A. Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder. Epigenomics 2018; 10:1585-1601. [PMID: 30456986 DOI: 10.2217/epi-2018-0049] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIM Trauma exposure is a necessary, but not deterministic, contributor to post-traumatic stress disorder (PTSD). Epigenetic factors may distinguish between trauma-exposed individuals with versus without PTSD. MATERIALS & METHODS We conducted a meta-analysis of PTSD epigenome-wide association studies in trauma-exposed cohorts drawn from civilian contexts. Whole blood-derived DNA methylation levels were analyzed in 545 study participants, drawn from the three civilian cohorts participating in the PTSD working group of the Psychiatric Genomics Consortium. RESULTS Two CpG sites significantly associated with current PTSD in NRG1 (cg23637605) and in HGS (cg19577098). CONCLUSION PTSD is associated with differential methylation, measured in blood, within HGS and NRG1 across three civilian cohorts.
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Affiliation(s)
- Monica Uddin
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.,Department of Psychology, University of Illinois Urbana-Champaign, 603 East Daniel St, Champaign, IL 61820, USA
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th St, NY 10032, USA
| | - Don Armstrong
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics & Statistics, Stony Brook University, John S Toll Drive, Stony Brook, NY 11794, USA
| | - Allison E Aiello
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, 135 Dauer Drive, Chapel Hill, NC 27599, USA
| | - Evelyn J Bromet
- Department of Psychiatry, Stony Brook University School of Medicine, 101 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Sandro Galea
- Boston University School of Public Health, 715 Albany St, Boston, MA 02118, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.,Psychiatic & Neurodevelopmental Genetics Unit & Department of Psychiatry, Massachusetts General Hospital, Simches Research Building, 185 Cambridge Street, Boston, MA 02114, USA.,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02142, USA
| | - Benjamin Luft
- Department of Medicine, Stony Brook University School of Medicine, 101 Nicolls Road, Stony Brook, NY 11794, USA
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, 115 Mill Street, Belmont, MA 02478, USA
| | - Derek E Wildman
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.,Department of Molecular & Integrative Physiology, University of Illinois at Urbana-Champaign, 407 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego School of Medicine, 9500 Gilman Dr, La Jolla, CA 92093, USA.,VA Center of Excellence for Stress & Mental Health, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92161, USA
| | - Alicia Smith
- Department of Psychiatry & Behavioral Sciences & Department of Obstetrics & Gynecology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA 30322, USA
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48
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Shinozaki G, Braun PR, Hing BWQ, Ratanatharathorn A, Klisares MJ, Duncan GN, Jellison SS, Heinzman JT, Nagahama Y, Close L, Sabbagh S, Dlouhy BJ, Howard MA, Kawasaki H, Cho HR. Epigenetics of Delirium and Aging: Potential Role of DNA Methylation Change on Cytokine Genes in Glia and Blood Along With Aging. Front Aging Neurosci 2018; 10:311. [PMID: 30405391 PMCID: PMC6206747 DOI: 10.3389/fnagi.2018.00311] [Citation(s) in RCA: 20] [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: 07/18/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Delirium in elderly patients is common and dangerous. Major risk factors include aging and exogenous insults, such as infection or surgery. In animal models, aging enhances pro-inflammatory cytokine release from microglia in response to exogenous insults. The epigenetic mechanism DNA methylation (DNAm) regulates gene expression and changes with age. Older individuals may have methylation changes that influence the increased cytokine upon insult, but the degree to which aging affects DNAm of cytokine genes is not fully understood. Methods: The relationship between DNAm and aging of pro-inflammatory cytokine genes (TNF-alpha, IL1-beta, IL-6) was investigated using methylation array data in two cohorts. Brain and blood samples were collected from a neurosurgery cohort (NSG) of 21 subjects who underwent brain resection. A second cohort, the Grady Trauma Project (GTP), included blood samples from 265 subjects. Results: In the NSG cohort, a significant negative correlation between age and DNAm in brain was found at a CpG in IL-6. With the GTP dataset, significant negative correlations between age and DNAm were seen at most of the CpGs in TNF-alpha. Also, TNF-Alpha expression increases with age. These GTP DNAm correlations were also nominally significant in NSG blood samples. In neuronal negative NSG brain tissue, a similar negative trend was observed. Conclusions: With aging, a decrease in DNAm of cytokines gene CpGs in glia and blood was seen. As this can affect their expression, additional research is needed to fully elucidate the role of DNAm in aging and how it may influence the pathogenesis of delirium.
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Affiliation(s)
- Gen Shinozaki
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Patricia R. Braun
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Benjamin W. Q. Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Andrew Ratanatharathorn
- Department of Epidemiology, School of Public Health, Columbia University Medical Center, Columbia University, New York, NY, United States
| | - Mason J. Klisares
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gabrielle N. Duncan
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Sydney S. Jellison
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Jonathan T. Heinzman
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Yasunori Nagahama
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Liesl Close
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Sayeh Sabbagh
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Brian J. Dlouhy
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Matthew A. Howard
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Hyunkeun R. Cho
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
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49
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Abstract
PURPOSE OF REVIEW The purpose of this review is to contextualize findings from the first 25 years of PTSD genetics research, focusing on the most robust findings and interpreting results in light of principles that have emerged from modern genetics studies. RECENT FINDINGS Genome-wide association studies (GWAS) encompassing tens of thousands of participants enabled the first molecular genetic heritability and genetic correlation estimates for PTSD in 2017. In 2018, highly promising loci for PTSD were reported, including variants in and near the CAMKV, KANSL1, and TCF4 genes. Twin studies from 25 years ago established that PTSD is genetically influenced and foreshadowed the molecular genetic findings of today. Discoveries that were impossible with smaller studies have been achieved via collaborative/team-science efforts. Most promisingly, individual genomic loci offer entirely novel clues about PTSD etiology, providing the raw material for transformative discoveries, and the future of PTSD research is bright.
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Affiliation(s)
- Laramie E Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Road, Room 3320, Stanford, CA, 94305, USA.
| | | | - Hanyang Shen
- Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Road, Room 3320, Stanford, CA, 94305, USA
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50
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Wolf EJ, Maniates H, Nugent N, Maihofer AX, Armstrong D, Ratanatharathorn A, Ashley-Koch AE, Garrett M, Kimbrel NA, Lori A, Aiello AE, Baker DG, Beckham JC, Boks MP, Galea S, Geuze E, Hauser MA, Kessler RC, Koenen KC, Miller MW, Ressler KJ, Risbrough V, Rutten BP, Stein MB, Ursano RJ, Vermetten E, Vinkers CH, Uddin M, Smith AK, Nievergelt CM, Logue MW. Traumatic stress and accelerated DNA methylation age: A meta-analysis. Psychoneuroendocrinology 2018; 92:123-134. [PMID: 29452766 PMCID: PMC5924645 DOI: 10.1016/j.psyneuen.2017.12.007] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/12/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Recent studies examining the association between posttraumatic stress disorder (PTSD) and accelerated aging, as defined by DNA methylation-based estimates of cellular age that exceed chronological age, have yielded mixed results. METHODS We conducted a meta-analysis of trauma exposure and PTSD diagnosis and symptom severity in association with accelerated DNA methylation age using data from 9 cohorts contributing to the Psychiatric Genomics Consortium PTSD Epigenetics Workgroup (combined N = 2186). Associations between demographic and cellular variables and accelerated DNA methylation age were also examined, as was the moderating influence of demographic variables. RESULTS Meta-analysis of regression coefficients from contributing cohorts revealed that childhood trauma exposure (when measured with the Childhood Trauma Questionnaire) and lifetime PTSD severity evidenced significant, albeit small, meta-analytic associations with accelerated DNA methylation age (ps = 0.028 and 0.016, respectively). Sex, CD4T cell proportions, and natural killer cell proportions were also significantly associated with accelerated DNA methylation age (all ps < 0.02). PTSD diagnosis and lifetime trauma exposure were not associated with advanced DNA methylation age. There was no evidence of moderation of the trauma or PTSD variables by demographic factors. CONCLUSIONS Results suggest that traumatic stress is associated with advanced epigenetic age and raise the possibility that cells integral to immune system maintenance and responsivity play a role in this. This study highlights the need for additional research into the biological mechanisms linking traumatic stress to accelerated DNA methylation age and the importance of furthering our understanding of the neurobiological and health consequences of PTSD.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
| | | | - Nicole Nugent
- Bradley Hasbro Children’s Research Center, Rhode Island Hospital,Departments of Psychiatry and Human Behavior and Pediatrics, Brown Medical School
| | | | - Don Armstrong
- University of Illinois Urbana-Champaign, Carl R. Woese Institute for Genomic Biology
| | | | | | - Melanie Garrett
- Department of Psychiatry & Behavioral Sciences, Duke University Medical Center
| | - Nathan A. Kimbrel
- Department of Psychiatry & Behavioral Sciences, Duke University Medical Center,VA Mid-Atlantic, Mental Illness Research, Education, and Clinical Center,Durham VA Medical Center
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University
| | | | - Allison E. Aiello
- Department of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health
| | - Dewleen G. Baker
- University of California San Diego, Department of Psychiatry,Veterans Affairs San Diego Healthcare System,Veterans Affairs Center of Excellence for Stress and Mental Health
| | - Jean C. Beckham
- Department of Psychiatry & Behavioral Sciences, Duke University Medical Center,VA Mid-Atlantic, Mental Illness Research, Education, and Clinical Center,Durham VA Medical Center
| | - Marco P. Boks
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Department of Psychiatry, Utrecht the Netherlands
| | | | - Elbert Geuze
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Department of Psychiatry, Utrecht the Netherlands,Ministry of Defence, Military Mental Healthcare, Utrecht the Netherlands
| | - Michael A. Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine
| | | | - Karestan C. Koenen
- Harvard T.H. Chan School of Public Health, Department of Epidemiology,Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Department of Psychiatry
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine
| | - Kerry J. Ressler
- Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Victoria Risbrough
- University of California San Diego, Department of Psychiatry,Veterans Affairs San Diego Healthcare System,Veterans Affairs Center of Excellence for Stress and Mental Health
| | - Bart P.F. Rutten
- School for Mental Health and Neuroscience and the European Graduate School of Neuroscience (EURON), Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Murray B. Stein
- University of California San Diego, Department of Psychiatry,Veterans Affairs San Diego Healthcare System,University of California San Diego, Department of Family Medicine and Public Health
| | - Robert J. Ursano
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University of the Health Sciences
| | - Eric Vermetten
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Department of Psychiatry, Utrecht the Netherlands,Ministry of Defence, Military Mental Healthcare, Utrecht the Netherlands,Arq Psychotrauma Expert Group
| | - Christiaan H. Vinkers
- University Medical Center Utrecht, Brain Center Rudolf Magnus, Department of Psychiatry, Utrecht the Netherlands
| | - Monica Uddin
- University of Illinois Urbana-Champaign, Carl R. Woese Institute for Genomic Biology,University of Illinois Urbana-Champaign, Department of Psychology
| | - Alicia K. Smith
- Department of Psychiatry and Behavioral Sciences, Emory University,Department of Gynecology and Obstetrics, Emory University
| | - Caroline M. Nievergelt
- University of California San Diego, Department of Psychiatry,Veterans Affairs San Diego Healthcare System,Veterans Affairs Center of Excellence for Stress and Mental Health
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System,Department of Psychiatry, Boston University School of Medicine,Biomedical Genetics, Boston University School of Medicine
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