Evaluating the Challenges and Reproducibility of Studies Investigating DNA Methylation Signatures of Psychological Stress

References

• Selye H . Stress and the general adaptation syndrome. Br. Med. J.1(4667), 1383–1392 (1950).
   PubMedGoogle Scholar
• Schneiderman N , IronsonG , SiegelSD. Stress and health: psychological, behavioral, and biological determinants. Annu. Rev. Clin. Psychol.1, 607–628 (2005).
   PubMed Web of Science ®Google Scholar
• McEwen B . Protective and damaging effects of stress mediators. N. Engl. J. Med.338(3), 171–179 (1998).
   PubMed Web of Science ®Google Scholar
• Cohen S , Janicki-DevertsD , MillerG. Psychological stress and disease. JAMA298(14), 1685–1687 (2007).
   PubMed Web of Science ®Google Scholar
• Segerstrom S , MillerG. Psychological stress and the human immune system: a meta-analytic study of 30 years of inquiry. Psychol. Bull.130(4), 601–630 (2004).
   PubMed Web of Science ®Google Scholar
• Widom C . Posttraumatic stress disorder in abused and neglected children grown up. Am. J. Psychiatry156(8), 1223–1229 (1999).
   PubMed Web of Science ®Google Scholar
• Bremner J , SouthwickS , JohnsonD , YehudaR , CharneyD. Childhood physical abuse and combat-related posttraumatic stress disorder in Vietnam veterans. Am. J. Psychiatry150(2), 235–239 (1993).
   PubMed Web of Science ®Google Scholar
• Heim C , NemeroffC. The role of childhood trauma in the neurobiology of mood and anxiety disorders: preclinical and clinical studies. Biol. Psychiatry49(12), 1023–1039 (2001).
   PubMed Web of Science ®Google Scholar
• Kendler K , KarkowskiL , PrescottC. Causal relationship between stressful life events and the onset of major depression. Am. J. Psychiatry156(6), 837–841 (1999).
   PubMed Web of Science ®Google Scholar
• Cohen B , EdmondsonD , KronishI. State of the art review: depression, stress, anxiety, and cardiovascular disease. Am. J. Hypertens.28(11), 1295–1302 (2015).
   PubMed Web of Science ®Google Scholar
• Van Winkel R , Van NieropM , Myin-GermeysI , Van OsJ. Childhood trauma as a cause of psychosis: linking genes, psychology, and biology. Can. J. Psychiatry58(1), 44–51 (2013).
   PubMed Web of Science ®Google Scholar
• Brady K , SinhaR. Co-occurring mental and substance use disorders: the neurobiological effects of chronic stress. Am. J. Psychiatry162(8), 1483–1493 (2005).
   PubMed Web of Science ®Google Scholar
• Sinha R , JastreboffA. Stress as a common risk factor for obesity and addiction. Biol. Psychiatry73(9), 827–835 (2013).
   PubMed Web of Science ®Google Scholar
• McGowan P , SzyfM. Environmental epigenomics: understanding the effects of parental care on the epigenome. Essays Biochem.48(1), 275–287 (2010).
   PubMedGoogle Scholar
• Murgatroyd C , PatchevA , WuYet al. Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat. Neurosci.12(12), 1559–1566 (2009).
   PubMed Web of Science ®Google Scholar
• Irwin RE , ThakurA , KmON , WalshCP. 5-hydroxymethylation marks a class of neuronal gene regulated by intragenic methylcytosine levels. Genomics104(5), 383–392 (2014).
   PubMed Web of Science ®Google Scholar
• Richa R , SinhaR. Hydroxymethylation of DNA: an epigenetic marker. EXCLI J.13, 592–610 (2014).
   PubMed Web of Science ®Google Scholar
• Mellén M , AyataP , DewellS , KriaucionisS , HeintzN. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell151(7), 1417–1430 (2012).
   PubMed Web of Science ®Google Scholar
• Laurent L , WongE , LiGet al. Dynamic changes in the human methylome during differentiation. Genome Res.20(3), 320–331 (2010).
   PubMed Web of Science ®Google Scholar
• Lister R , MukamelE , NeryJet al. Global epigenomic reconfiguration during mammalian brain development. Science341(6146), 1237905 (2013).
   PubMed Web of Science ®Google Scholar
• Anastasiadi D , Esteve-CodinaA , PiferrerF. Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics Chromatin11(1), 37 (2018).
   PubMed Web of Science ®Google Scholar
• Spainhour J , LimH , YiS , QiuP. Correlation patterns between DNA methylation and gene expression in The Cancer Genome Atlas. Cancer Inform.18, 1176935119828776 (2019).
   Web of Science ®Google Scholar
• Aran D , ToperoffG , RosenbergM , HellmanA. Replication timing-related and gene body-specific methylation of active human genes. Hum. Mol. Genet.20(4), 670–680 (2011).
   PubMed Web of Science ®Google Scholar
• Hellman A , ChessA. Gene body-specific methylation on the active X chromosome. Science315(5815), 1141–1143 (2007).
   PubMed Web of Science ®Google Scholar
• Wang K , DaiR , XiaYet al. Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development. Epigenetics (2022). (Epub ahead of print) doi:10.1080/15592294.2021.1993607
   Web of Science ®Google Scholar
• Zhang D , ChengL , BadnerJet al. Genetic control of individual differences in gene-specific methylation in human brain. Am. J. Hum. Genet.86(3), 411–419 (2010).
   PubMed Web of Science ®Google Scholar
• Kaplow I , MacIsaacJ , MahS , McEwenL , KoborM , FraserH. A pooling-based approach to mapping genetic variants associated with DNA methylation. Genome Res.25(6), 907–917 (2015).
   PubMed Web of Science ®Google Scholar
• Murgatroyd C , WuY , BockmühlY , SpenglerD. Genes learn from stress: how infantile trauma programs us for depression. Epigenetics5(3), 194–199 (2010).
   PubMed Web of Science ®Google Scholar
• Feil R , FragaM. Epigenetics and the environment: emerging patterns and implications. Nat. Rev. Genet.13(2), 97–109 (2012).
   PubMed Web of Science ®Google Scholar
• Klengel T , MehtaD , AnackerCet al. Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions. Nat. Neurosci.16(1), 33–41 (2013).
   PubMed Web of Science ®Google Scholar
• Zhi D , AslibekyanS , IrvinMet al. SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics8(8), 802–806 (2013).
   PubMed Web of Science ®Google Scholar
• Alexander N , WankerlM , HennigJet al. DNA methylation profiles within the serotonin transporter gene moderate the association of 5-HTTLPR and cortisol stress reactivity. Transl. Psychiatry4, e443 (2014).
   PubMed Web of Science ®Google Scholar
• McGowan P , SudermanM , SasakiAet al. Broad epigenetic signature of maternal care in the brain of adult rats. PLoS One6(2), e14739 (2011).
   PubMed Web of Science ®Google Scholar
• Weaver IC , CervoniN , ChampagneFAet al. Epigenetic programming by maternal behavior. Nat. Neurosci.7(8), 847–854 (2004).
   PubMed Web of Science ®Google Scholar
• Barker E , WaltonE , CecilC. Annual research review: DNA methylation as a mediator in the association between risk exposure and child and adolescent psychopathology. J. Child Psychol. Psychiatry59(4), 303–322 (2018).
   PubMed Web of Science ®Google Scholar
• Turecki G , MeaneyM. Effects of the social environment and stress on glucocorticoid receptor gene methylation: a systematic review. Biol. Psychiatry79(2), 87–96 (2016).
   PubMed Web of Science ®Google Scholar
• Palma-Gudiel H , Córdova-PalomeraA , EixarchE , DeuschleM , FañanásL. Maternal psychosocial stress during pregnancy alters the epigenetic signature of the glucocorticoid receptor gene promoter in their offspring: a meta-analysis. Epigenetics10(10), 893–902 (2015).
   PubMed Web of Science ®Google Scholar
• Devlin AM , BrainU , AustinJ , OberlanderTF. Prenatal exposure to maternal depressed mood and the MTHFR C677T variant affect SLC6A4 methylation in infants at birth. PLoS One5(8), e12201 (2010).
   PubMed Web of Science ®Google Scholar
• Mendonça M , MangiavacchiP , DeSousa Pet al. Epigenetic variation at the SLC6A4 gene promoter in mother-child pairs with major depressive disorder. J. Affect. Disord.245, 716–723 (2019).
   PubMed Web of Science ®Google Scholar
• Dukal H , FrankJ , LangMet al. New-born females show higher stress- and genotype-independent methylation of SLC6A4 than males. Borderline Personal. Disord. Emot. Dysregul.2, 8 (2015).
   PubMed Web of Science ®Google Scholar
• Duman E , CanliT. Influence of life stress, 5-HTTLPR genotype, and SLC6A4 methylation on gene expression and stress response in healthy Caucasian males. Biol. Mood Anxiety Disord.5, 2 (2015).
   PubMed Web of Science ®Google Scholar
• Sbarra D , CookC , HasselmoK , NoonM , MehlM. DNA methylation across the serotonin transporter gene following marital separation: a pilot study. Ann. Behav. Med.53(12), 1081–1087 (2019).
   PubMed Web of Science ®Google Scholar
• Alasaari J , LagusM , OllilaHet al. Environmental stress affects DNA methylation of a CpG rich promoter region of serotonin transporter gene in a nurse cohort. PLoS One7(9), e45813 (2012).
   PubMed Web of Science ®Google Scholar
• Needham B , SmithJ , ZhaoWet al. Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: the multi-ethnic study of atherosclerosis. Epigenetics10(10), 958–969 (2015).
   PubMed Web of Science ®Google Scholar
• Vijayendran M , BeachS , PlumeJ , BrodyG , PhilibertR. Effects of genotype and child abuse on DNA methylation and gene expression at the serotonin transporter. Front. Psychiatry3, 55 (2012).
   PubMedGoogle Scholar
• Beach S , BrodyG , LeiMet al. Impact of child sex abuse on adult psychopathology: a genetically and epigenetically informed investigation. J. Fam. Psychol.27(1), 3–11 (2013).
   PubMed Web of Science ®Google Scholar
• Booij L , SzyfM , CarballedoAet al. DNA methylation of the serotonin transporter gene in peripheral cells and stress-related changes in hippocampal volume: a study in depressed patients and healthy controls. PLoS One10(3), e0119061 (2015).
   PubMed Web of Science ®Google Scholar
• Kang H , KimJ , StewartRet al. Association of SLC6A4 methylation with early adversity, characteristics and outcomes in depression. Prog. Neuropsychopharmacol. Biol. Psychiatry44, 23–28 (2013).
   PubMed Web of Science ®Google Scholar
• Ouellet-Morin I , WongC , DaneseAet al. Increased serotonin transporter gene (SERT) DNA methylation is associated with bullying victimization and blunted cortisol response to stress in childhood: a longitudinal study of discordant monozygotic twins. Psychol. Med.43(9), 1813–1823 (2013).
   PubMed Web of Science ®Google Scholar
• Parade S , ParentJ , RabemananjaraKet al. Change in FK506 binding protein 5 (FKBP5) methylation over time among preschoolers with adversity. Dev. Psychopathol.29(5), 1627–1634 (2017).
   PubMed Web of Science ®Google Scholar
• Tyrka A , RidoutK , ParadeS , PaquetteA , MarsitC , SeiferR. Childhood maltreatment and methylation of FK506 binding protein 5 gene (FKBP5). Dev. Psychopathol.27, 1637–1645 (2015).
   PubMed Web of Science ®Google Scholar
• Saito T , ShinozakiG , KogaMet al. Effect of interaction between a specific subtype of child abuse and the FKBP5 rs1360780 SNP on DNA methylation among patients with bipolar disorder. J. Affect. Disord.272, 417–422 (2020).
   PubMed Web of Science ®Google Scholar
• Klinger-König J , HertelJ , VanDer Auwera Set al. Methylation of the FKBP5 gene in association with FKBP5 genotypes, childhood maltreatment and depression. Neuropsychopharmacology44(5), 930–938 (2019).
   PubMed Web of Science ®Google Scholar
• Bustamante A , AielloA , GuffantiG , GaleaS , WildmanD , UddinM. FKBP5 DNA methylation does not mediate the association between childhood maltreatment and depression symptom severity in the Detroit Neighborhood Health Study. J. Psychiatr. Res.96, 39–48 (2018).
   PubMed Web of Science ®Google Scholar
• Farrell C , DoolinK , O’LearyNet al. DNA methylation differences at the glucocorticoid receptor gene in depression are related to functional alterations in hypothalamic–pituitary–adrenal axis activity and to early life emotional abuse. Psychiatry Res.265, 341–348 (2018).
   PubMed Web of Science ®Google Scholar
• Alexander N , KirschbaumC , StalderT , MuehlhanM , VogelS. No association between FKBP5 gene methylation and acute and long-term cortisol output. Transl. Psychiatry10(1), 175 (2020).
   PubMed Web of Science ®Google Scholar
• Marzi S , SugdenK , ArseneaultLet al. Analysis of DNA methylation in young people: limited evidence for an association between victimization stress and epigenetic variation in blood. Am. J. Psychiatry175(6), 517–529 (2018).
   PubMed Web of Science ®Google Scholar
• Khulan B , ManningJ , DunbarDet al. Epigenomic profiling of men exposed to early-life stress reveals DNA methylation differences in association with current mental state. Transl. Psychiatry4, e448 (2014).
   PubMed Web of Science ®Google Scholar
• Rijlaarsdam J , PappaI , WaltonEet al. An epigenome-wide association meta-analysis of prenatal maternal stress in neonates: a model approach for replication. Epigenetics11(2), 140–149 (2016).
   PubMed Web of Science ®Google Scholar
• Yang B , ZhangH , GeWet al. Child abuse and epigenetic mechanisms of disease risk. Am. J. Prev. Med.44(2), 101–107 (2013).
   PubMed Web of Science ®Google Scholar
• Weder N , ZhangH , JensenKet al. Child abuse, depression, and methylation in genes involved with stress, neural plasticity, and brain circuitry. J. Am. Acad. Child Adolesc. Psychiatry53(4), 417–424.e415 (2014).
   PubMed Web of Science ®Google Scholar
• Houtepen L , VinkersC , Carrillo-RoaTet al. Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans. Nat. Commun.7, 10967 (2016).
   PubMed Web of Science ®Google Scholar
• Frach L , TierlingS , SchwaigerMet al. The mediating role of KITLG DNA methylation in the association between childhood adversity and cortisol stress reactivity does not replicate in monocytes. Psychoneuroendocrinology116, 104653 (2020).
   PubMed Web of Science ®Google Scholar
• Houtepen L , HardyR , MaddockJet al. Childhood adversity and DNA methylation in two population-based cohorts. Transl. Psychiatry8(1), 266 (2018).
   PubMedGoogle Scholar
• Suderman M , PappasJ , BorgholNet al. Lymphoblastoid cell lines reveal associations of adult DNA methylation with childhood and current adversity that are distinct from whole blood associations. Int. J. Epidemiol.44(4), 1331–1340 (2015).
   PubMed Web of Science ®Google Scholar
• Prados J , StenzL , CourtetPet al. Borderline personality disorder and childhood maltreatment: a genome-wide methylation analysis. Genes Brain Behav.14(2), 177–188 (2015).
   PubMed Web of Science ®Google Scholar
• Bush N , EdgarR , ParkMet al. The biological embedding of early-life socioeconomic status and family adversity in children’s genome-wide DNA methylation. Epigenomics10(11), 1445–1461 (2018).
   PubMed Web of Science ®Google Scholar
• Reuben A , SugdenK , ArseneaultLet al. Association of neighborhood disadvantage in childhood with DNA methylation in young adulthood. JAMA Netw. Open3(6), e206095 (2020).
   PubMed Web of Science ®Google Scholar
• Lam L , EmberlyE , FraserHet al. Factors underlying variable DNA methylation in a human community cohort. Proc. Natl Acad. Sci. U. S. A.109(Suppl. 2), 17253–17260 (2012).
   PubMed Web of Science ®Google Scholar
• McDade T , RyanC , JonesMet al. Genome-wide analysis of DNA methylation in relation to socioeconomic status during development and early adulthood. Am. J. Phys. Anthropol.169(1), 3–11 (2019).
   PubMed Web of Science ®Google Scholar
• McDade T , RyanC , JonesMet al. Social and physical environments early in development predict DNA methylation of inflammatory genes in young adulthood. Proc. Natl Acad. Sci. U. S. A.114(29), 7611–7616 (2017).
   PubMed Web of Science ®Google Scholar
• Cecil C , SmithR , WaltonE , MillJ , McCroryE , VidingE. Epigenetic signatures of childhood abuse and neglect: implications for psychiatric vulnerability. J. Psychiatr. Res.83, 184–194 (2016).
   PubMed Web of Science ®Google Scholar
• Labonté B , SudermanM , MaussionGet al. Genome-wide epigenetic regulation by early-life trauma. Arch. Gen. Psychiatry69(7), 722–731 (2012).
   PubMed Web of Science ®Google Scholar
• Mehta D , KlengelT , ConneelyKet al. Childhood maltreatment is associated with distinct genomic and epigenetic profiles in posttraumatic stress disorder. Proc. Natl Acad. Sci. U. S. A.110(20), 8302–8307 (2013).
   PubMed Web of Science ®Google Scholar
• Roberts A , GladishN , GatevEet al. Exposure to childhood abuse is associated with human sperm DNA methylation. Transl. Psychiatry8(1), 194 (2018).
   PubMedGoogle Scholar
• Lutz P , TantiA , GaseckaAet al. Association of a history of child abuse with impaired myelination in the anterior cingulate cortex: convergent epigenetic, transcriptional, and morphological evidence. Am. J. Psychiatry174(12), 1185–1194 (2017).
   PubMed Web of Science ®Google Scholar
• Suderman M , BorgholN , PappasJet al. Childhood abuse is associated with methylation of multiple loci in adult DNA. BMC Med. Genomics7, 13 (2014).
   PubMed Web of Science ®Google Scholar
• Robakis T , ZhangS , RasgonNet al. Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression. Transl. Psychiatry10(1), 48 (2020).
   PubMed Web of Science ®Google Scholar
• Kinnally E , FeinbergC , KimDet al. DNA methylation as a risk factor in the effects of early life stress. Brain Behav. Immun.25(8), 1548–1553 (2011).
   PubMed Web of Science ®Google Scholar
• Melas P , WeiY , WongCet al. Genetic and epigenetic associations of MAOA and NR3C1 with depression and childhood adversities. Int. J. Neuropsychopharmacol.16(7), 1513–1528 (2013).
   PubMed Web of Science ®Google Scholar
• Dunn E , SoareT , ZhuYet al. Sensitive periods for the effect of childhood adversity on DNA methylation: results from a prospective, longitudinal study. Biol. Psychiatry85(10), 838–849 (2019).
   PubMed Web of Science ®Google Scholar
• Sumner J , ColichN , UddinM , ArmstrongD , McLaughlinK. Early experiences of threat, but not deprivation, are associated with accelerated biological aging in children and adolescents. Biol. Psychiatry85(3), 268–278 (2019).
   PubMed Web of Science ®Google Scholar
• Fagiolini M , JensenC , ChampagneFA. Epigenetic influences on brain development and plasticity. Curr. Opin. Neurobiol.19(2), 207–212 (2009).
   PubMed Web of Science ®Google Scholar
• Kanherkar R , Bhatia-DeyN , CsokaA. Epigenetics across the human lifespan. Front. Cell Dev. Biol.2, 49 (2014).
   PubMed Web of Science ®Google Scholar
• McEwen B . Understanding the potency of stressful early life experiences on brain and body function. Metabolism57(Suppl. 2), S11–S15 (2008).
   PubMed Web of Science ®Google Scholar
• Cao-Lei L , MassartR , SudermanMet al. DNA methylation signatures triggered by prenatal maternal stress exposure to a natural disaster: Project Ice Storm. PLoS One9(9), e107653 (2014).
   PubMed Web of Science ®Google Scholar
• Cicchetti D , HetzelS , RogoschF , HandleyE , TothS. An investigation of child maltreatment and epigenetic mechanisms of mental and physical health risk. Dev. Psychopathol.28, 1305–1317 (2016).
   PubMed Web of Science ®Google Scholar
• Naumova O , LeeM , KoposovR , SzyfM , DozierM , GrigorenkoE. Differential patterns of whole-genome DNA methylation in institutionalized children and children raised by their biological parents. Dev. Psychopathol.24(1), 143–155 (2012).
   PubMed Web of Science ®Google Scholar
• McGuinness D , McGlynnL , JohnsonPet al. Socio-economic status is associated with epigenetic differences in the pSoBid cohort. Int. J. Epidemiol.41(1), 151–160 (2012).
   PubMed Web of Science ®Google Scholar
• Beach S , LeiM , BrodyGet al. Parenting, socioeconomic status risk, and later young adult health: exploration of opposing indirect effects via DNA methylation. Child Dev.87(1), 111–121 (2016).
   PubMed Web of Science ®Google Scholar
• Borghol N , SudermanM , McArdleWet al. Associations with early-life socio-economic position in adult DNA methylation. Int. J. Epidemiol.41(1), 62–74 (2012).
   PubMed Web of Science ®Google Scholar
• Marinova Z , MaerckerA , KüfferAet al. DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma. BMC Med. Genet.18(1), 21 (2017).
   PubMedGoogle Scholar
• Essex M , BoyceW , HertzmanCet al. Epigenetic vestiges of early developmental adversity: childhood stress exposure and DNA methylation in adolescence. Child Dev.84(1), 58–75 (2013).
   PubMed Web of Science ®Google Scholar
• Cao-Lei L , ElgbeiliG , MassartR , LaplanteD , SzyfM , KingS. Pregnant women’s cognitive appraisal of a natural disaster affects DNA methylation in their children 13 years later: Project Ice Storm. Transl. Psychiatry5, e515 (2015).
   PubMed Web of Science ®Google Scholar
• Tsai P , BellJ. Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation. Int. J. Epidemiol.44(4), 1429–1441 (2015).
   PubMed Web of Science ®Google Scholar
• Cardenas A , FaleschiniS , CortesHidalgo Aet al. Prenatal maternal antidepressants, anxiety, and depression and offspring DNA methylation: epigenome-wide associations at birth and persistence into early childhood. Clin. Epigenetics11(1), 56 (2019).
   PubMedGoogle Scholar
• Tay N , MacareC , LiuYet al. Allele-specific methylation of SPDEF: a novel moderator of psychosocial stress and substance abuse. Am. J. Psychiatry176(2), 146–155 (2019).
   PubMed Web of Science ®Google Scholar
• O’Donnell KJ , ChenL , MacIsaacJLet al. DNA methylome variation in a perinatal nurse-visitation program that reduces child maltreatment: a 27-year follow-up. Transl. Psychiatry8(1), 15 (2018).
   PubMedGoogle Scholar
• Burns S , SzyszkowiczJ , LuheshiG , LutzP , TureckiG. Plasticity of the epigenome during early-life stress. Semin. Cell Dev. Biol.77, 115–132 (2018).
   PubMed Web of Science ®Google Scholar
• Boyce W . Differential susceptibility of the developing brain to contextual adversity and stress. Neuropsychopharmacology41(1), 142–162 (2016).
   PubMed Web of Science ®Google Scholar
• Masten A . Ordinary magic. Resilience processes in development. Am. Psychol.56(3), 227–238 (2001).
   PubMed Web of Science ®Google Scholar
• Jiao C , ZhangC , DaiRet al. Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics10(5), 643–659 (2018).
   PubMed Web of Science ®Google Scholar
• Blaze J , RothT. Caregiver maltreatment causes altered neuronal DNA methylation in female rodents. Dev. Psychopathol.29(2), 477–489 (2017).
   PubMed Web of Science ®Google Scholar
• Lei L , WuX , GuH , JiM , YangJ. Differences in DNA methylation reprogramming underlie the sexual dimorphism of behavioral disorder caused by prenatal stress in rats. Front. Neurosci.14, 573107 (2020).
   PubMed Web of Science ®Google Scholar
• Singmann P , Shem-TovD , WahlSet al. Characterization of whole-genome autosomal differences of DNA methylation between men and women. Epigenetics Chromatin8, 43 (2015).
   PubMed Web of Science ®Google Scholar
• Van Dongen J , NivardM , WillemsenGet al. Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun.7, 11115 (2016).
   PubMed Web of Science ®Google Scholar
• Jahnke J , TeránE , MurgueitioF , CabreraH , ThompsonA. Maternal stress, placental 11β-hydroxysteroid dehydrogenase type 2, and infant HPA axis development in humans: psychosocial and physiological pathways. Placenta104, 179–187 (2021).
   PubMed Web of Science ®Google Scholar
• Gouin J , ZhouQ , BooijLet al. Associations among oxytocin receptor gene (OXTR) DNA methylation in adulthood, exposure to early life adversity, and childhood trajectories of anxiousness. Sci. Rep.7(1), 7446 (2017).
   PubMedGoogle Scholar
• Ostlund B , ConradtE , CrowellS , TyrkaA , MarsitC , LesterB. Prenatal stress, fearfulness, and the epigenome: exploratory analysis of sex differences in DNA methylation of the glucocorticoid receptor gene. Front. Behav. Neurosci.10, 147 (2016).
   PubMed Web of Science ®Google Scholar
• Braithwaite E , KundakovicM , RamchandaniP , MurphyS , ChampagneF. Maternal prenatal depressive symptoms predict infant NR3C1 1F and BDNF IV DNA methylation. Epigenetics10(5), 408–417 (2015).
   PubMed Web of Science ®Google Scholar
• Vukojevic V , KolassaI , FastenrathMet al. Epigenetic modification of the glucocorticoid receptor gene is linked to traumatic memory and post-traumatic stress disorder risk in genocide survivors. J. Neurosci.34(31), 10274–10284 (2014).
   PubMed Web of Science ®Google Scholar
• Hill J , PicklesA , WrightN , QuinnJ , MurgatroydC , SharpH. Mismatched prenatal and postnatal maternal depressive symptoms and child behaviours: a sex-dependent role for DNA methylation in the Wirral Child Health and Development Study. Cells8(9), 943 (2019).
   PubMed Web of Science ®Google Scholar
• Beach S , DoganM , BrodyG , PhilibertR. Differential impact of cumulative SES risk on methylation of protein–protein interaction pathways as a function of SLC6A4 genetic variation in African American young adults. Biol. Psychol.96, 28–34 (2014).
   PubMed Web of Science ®Google Scholar
• Liu Y , MurphyS , MurthaAet al. Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements. Epigenetics7(7), 735–746 (2012).
   PubMed Web of Science ®Google Scholar
• Checknita D , TiihonenJ , HodginsS , NilssonK. Associations of age, sex, sexual abuse, and genotype with monoamine oxidase A gene methylation. J. Neural Transm. (Vienna)128(11), 1721–1739 (2021).
   PubMed Web of Science ®Google Scholar
• Loucks E , HuangY , AghaGet al. Epigenetic mediators between childhood socioeconomic disadvantage and mid-life body mass index: the New England Family Study. Psychosom. Med.78(9), 1053–1065 (2016).
   PubMed Web of Science ®Google Scholar
• Santos H , BhattacharyaA , MartinEet al. Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status. Epigenetics14(8), 751–765 (2019).
   PubMed Web of Science ®Google Scholar
• Czamara D , EraslanG , PageCet al. Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns. Nat. Commun.10(1), 2548 (2019).
   PubMedGoogle Scholar
• Teh A , PanH , ChenLet al. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res.24(7), 1064–1074 (2014).
   PubMed Web of Science ®Google Scholar
• Gibbs J , VanDer Brug M , HernandezDet al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet.6(5), e1000952 (2010).
   PubMed Web of Science ®Google Scholar
• Van Der Knaap L , RieseH , HudziakJet al. Adverse life events and allele-specific methylation of the serotonin transporter gene (SLC6A4) in adolescents: the TRAILS study. Psychosom. Med.77(3), 246–255 (2015).
   PubMed Web of Science ®Google Scholar
• Tozzi L , FarrellC , BooijLet al. Epigenetic changes of FKBP5 as a link connecting genetic and environmental risk factors with structural and functional brain changes in major depression. Neuropsychopharmacology43(5), 1138–1145 (2018).
   PubMed Web of Science ®Google Scholar
• Parade S , NovickA , ParentJet al. Stress exposure and psychopathology alter methylation of the serotonin receptor 2A (HTR2A) gene in preschoolers. Dev. Psychopathol.29(5), 1619–1626 (2017).
   PubMed Web of Science ®Google Scholar
• Wankerl M , MillerR , KirschbaumC , HennigJ , StalderT , AlexanderN. Effects of genetic and early environmental risk factors for depression on serotonin transporter expression and methylation profiles. Transl. Psychiatry4, e402 (2014).
   PubMed Web of Science ®Google Scholar
• Kumsta R , MarziS , VianaJet al. Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1. Transl. Psychiatry6(6), e830 (2016).
   PubMedGoogle Scholar
• Papale L , SeltzerL , MadridA , PollakS , AlischR. Differentially methylated genes in saliva are linked to childhood stress. Sci. Rep.8(1), 10785 (2018).
   PubMedGoogle Scholar
• Subramanyam M , Diez-RouxA , PilsnerJet al. Social factors and leukocyte DNA methylation of repetitive sequences: the multi-ethnic study of atherosclerosis. PLoS One8(1), e54018 (2013).
   PubMed Web of Science ®Google Scholar
• Ewald E , WandG , SaifuddinFet al. Alterations in DNA methylation of Fkbp5 as a determinant of blood–brain correlation of glucocorticoid exposure. Psychoneuroendocrinology44, 112–122 (2014).
   PubMed Web of Science ®Google Scholar
• Witzmann S , TurnerJ , MériauxS , MeijerO , MullerC. Epigenetic regulation of the glucocorticoid receptor promoter 1(7) in adult rats. Epigenetics7(11), 1290–1301 (2012).
   PubMed Web of Science ®Google Scholar
• Riese H , VanDen Heuvel E , SniederHet al. Association between methylation of the SLC6A4 promoter region in peripheral blood leukocytes and methylation in amygdala tissue. Psychosom. Med.76(3), 244–246 (2014).
   PubMed Web of Science ®Google Scholar
• Kertes D , KaminH , HughesD , RodneyN , BhattS , MulliganC. Prenatal maternal stress predicts methylation of genes regulating the hypothalamic–pituitary–adrenocortical system in mothers and newborns in the Democratic Republic of Congo. Child Dev.87(1), 61–72 (2016).
   PubMed Web of Science ®Google Scholar
• Galbally M , WatsonS , Van IjzendoornMet al. The role of glucocorticoid and mineralocorticoid receptor DNA methylation in antenatal depression and infant stress regulation. Psychoneuroendocrinology115, 104611 (2020).
   PubMed Web of Science ®Google Scholar
• Leek J , StoreyJ. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet.3(9), 1724–1735 (2007).
   PubMed Web of Science ®Google Scholar
• Stegle O , PartsL , PiipariM , WinnJ , DurbinR. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc.7(3), 500–507 (2012).
   PubMed Web of Science ®Google Scholar
• Mostafavi S , BattleA , ZhuXet al. Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge. PLoS One8(7), e68141 (2013).
   PubMed Web of Science ®Google Scholar