Functional annotation of the human PTSD methylome identifies tissue-specific epigenetic variation across subcortical brain regions

Post-traumatic stress disorder is a mental disorder that may occur in the aftermath of severe psychological trauma. We examined 1,065,750 DNA methylation (DNAm) sites from 171 donors including neurotypicals, PTSD, and major depressive disorder cases across six areas implicated in the fear circuitry of the brain. We found significant differential methylation for PTSD near 195 genes and utilizing cross-region modeling, identified 6,641 candidate genes. Approximately 26% of differentially methylated CpGs were present near risk loci for PTSD. To identify potential therapeutic intersections for PTSD, we found significant methylation changes in the MAD1L1, ELFN1, and WNT5A genes in ketamine responders. Finally, to better understand the unique biology of PTSD, we analyzed matching methylation data for a cohort of MDD donors with no known history of trauma or PTSD. Our results implicate DNAm as an epigenetic mechanism underlying the molecular changes associated with the subcortical fear circuitry of the PTSD brain. ### Competing Interest Statement Dr. John Krystal Financial Disclosure: Consultant (Note: The Individual Consultant Agreements listed below are less than $5000 per year): Aptinyx Inc.; Atai Life Sciences; AstraZeneca Pharmaceuticals; Biogen Idec ; MA; Biomedisyn Corporation; Bionomics Limited (Australia); Boehringer Ingelheim International; Cadent Therapeutics Inc.; Clexio Bioscience Ltd.; COMPASS Pathways Limited UK; Concert Pharmaceuticals Inc.; Epiodyne Inc.; EpiVario Inc.; Greenwich Biosciences Inc.; Heptares Therapeutics Limited (UK); Janssen Research & Development; Jazz Pharmaceuticals Inc.; Otsuka America Pharmaceutical Inc.; Perception Neuroscience Holdings Inc.; Spring Care Inc.; Sunovion Pharmaceuticals Inc.; Takeda Industries; Taisho Pharmaceutical Co. Ltd. Board of Directors: Freedom Biosciences Inc. Scientific Advisory Board: Biohaven Pharmaceuticals; BioXcel Therapeutics Inc. (Clinical Advisory Board); Cadent Therapeutics Inc. (Clinical Advisory Board); Cerevel; Therapeutics LLC; EpiVario Inc.; Eisai Inc.; Jazz Pharmaceuticals Inc.; Lohocla Research Corporation; Novartis Pharmaceuticals Corporation; PsychoGenics Inc.; RBNC Therapeutics Inc.; Tempero Bio Inc.; Terran Biosciences Inc. Stock: Biohaven Pharmaceuticals; Sage Pharmaceuticals; Spring Care Inc. Stock Options: Biohaven Pharmaceuticals Medical Sciences; EpiVario Inc.; RBNC Therapeutics Inc.; Terran Biosciences Inc.; Tempero Bio Inc. Income Greater than $10 000. Editorial Board: Editor Biological Psychiatry. Patents and Inventions: 1. Seibyl JP Krystal JH Charney DS. Dopamine and noradrenergic reuptake inhibitors in treatment of schizophrenia. US Patent #:5 447 948. 5 September 1995; 2. Vladimir Coric Krystal John H Sanacora Gerard Glutamate Modulating Agents in the Treatment of Mental Disorders. US Patent No. 8 778 979 B2 Patent Issue Date: 15 July 2014. US Patent Application No. 15/695 164: Filing Date: 09/05/2017; 3. Charney D Krystal JH Manji H Matthew S Zarate C. Intranasal Administration of Ketamine to Treat Depression United States Patent Number: 9592207 Issue date: 3/14/2017. Licensed to Janssen Research & Development; 4. Zarate C Charney DS Manji HK Mathew Sanjay J Krystal JH Yale University Methods for Treating Suicidal Ideation Patent Application No. 15/379 013 filed on 14 December 2016 by Yale University Office of Cooperative Research; 5. Arias A Petrakis I Krystal JH. Composition and methods to treat addiction. Provisional Use Patent Application no.61/973/961. 2 April 2014. Filed by Yale University Office of Cooperative Research.; 6. Chekroud A. Gueorguieva R. & Krystal JH. Treatment Selection for Major Depressive Disorder [filing date 3 June 2016 USPTO docket number Y0087.70116US00]. Provisional patent submission by Yale University; 7. Gihyun Yoon Petrakis I Krystal JH Compounds Compositions and Methods for Treating or Preventing Depression and Other Diseases. U. S. Provisional Patent Application No. 62/444 552 filed on 10 January 2017 by Yale University Office of Cooperative Research OCR 7088 US01; 8. Abdallah C Krystal JH Duman R Sanacora G. Combination Therapy for Treating or Preventing Depression or Other Mood Diseases. US Provisional Patent Application No. 62/719 935 filed on 20 August 2018 by Yale University Office of Cooperative Research OCR 7451 US01; 9. John Krystal Godfrey Pearlson Stephanie O Malley Marc Potenza Fabrizio Gasparini Baltazar Gomez Mancilla Vincent Malaterre. Mavoglurant in treating gambling and gaming disorders. US Provisional Patent Application No. 63/125 181filed on 14 December 2020 by Yale University Office of Cooperative Research OCR 8065 US00; NON Federal Research Support: AstraZeneca Pharmaceuticals provides the drug Saracatinib for research related to NIAAA grant Center for Translational Neuroscience of Alcoholism [CTNA 4]; Novartis provides the drug Mavoglurant for research related to NIAAA grant Center for Translational Neuroscience of Alcoholism [CTNA 4]; Cerevel provides the drug PF 06412562 for A Translational and Neurocomputational Evaluation of a D1R Partial Agonist for Schizophrenia (1 U01 MH121766 01). ### Funding Statement The research reported here was supported by the Department of Veterans Affairs, Veteran Health Administration, VISN1 Career Development Award, National Center for PTSD, a Brain and Behavior Research Foundation Young Investigator Award, and an American Foundation for Suicide Prevention Young Investigator Award to M.J.G. This work was funded in part by the State of Connecticut, Department of Mental Health and Addiction Services. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of Yale University waived ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors