Social Epigenomics: Are we at an Impasse?

References

• Aristizabal MJ , AnreiterI , HalldorsdottirTet al. Biological embedding of experience: a primer on epigenetics. Proc. Natl Acad. Sci. USA117(38), 23261–23269 (2019).
   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
• Turecki G , MeaneyMJ. 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
• Naumova OY , RychkovSY , KornilovSAet al. Effects of early social deprivation on epigenetic statuses and adaptive behavior of young children: a study based on a cohort of institutionalized infants and toddlers. PLoS ONE14(3), e0214285 (2019).
   PubMed Web of Science ®Google Scholar
• Kertes DA , KaminHS , HughesDA , RodneyNC , BhattS , MulliganCJ. 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
• Cecil CA , SmithRG , WaltonE , MillJ , MccroryEJ , 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
• Marzi SJ , 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. Psych.175(6), 517–529 (2018).
   PubMed Web of Science ®Google Scholar
• Serpeloni F , RadtkeKM , HeckerTet al. Does prenatal stress shape postnatal resilience? – An epigenome-wide study on violence and mental health in humans. Front. Genet.10, 269 (2019).
   PubMed Web of Science ®Google Scholar
• Non AL , BinderAM , KubzanskyLD , MichelsKB. Genome-wide DNA methylation in neonates exposed to maternal depression, anxiety, or SSRI medication during pregnancy. Epigenetics9(7), 964–972 (2014).
   PubMed Web of Science ®Google Scholar
• McDade TW , RyanCP , JonesMJet 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
• Laubach ZM , PerngW , CardenasAet al. Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva. Epigenomics11(12), 1413–1427 (2019).
   PubMed Web of Science ®Google Scholar
• Mulder RH , WaltonE , NeumannAet al. Epigenomics of being bullied: changes in DNA methylation following bullying exposure. Epigenetics15(6–7), 750–764 (2020).
   PubMed Web of Science ®Google Scholar
• Houtepen LC , HardyR , MaddockJet al. Childhood adversity and DNA methylation in two population-based cohorts. Translat. Psych.8(1), 266 (2018).
   PubMedGoogle 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
• Clausing ES , BinderAM , NonAL. Epigenetic age associates with psychosocial stress and resilience in children of Latinx immigrants. Epigenomics doi: 10.2217/epi-2019-0343 (2020) ( Epub ahead of print).
   Web of Science ®Google Scholar
• Cao-Lei L , DancauseKN , ElgbeiliGet al. DNA methylation mediates the impact of exposure to prenatal maternal stress on BMI and central adiposity in children at age 13(1/2) years: Project Ice Storm. Epigenetics10(8), 749–761 (2015).
   PubMed Web of Science ®Google Scholar
• Provencal N , ArlothJ , CattaneoAet al. Glucocorticoid exposure during hippocampal neurogenesis primes future stress response by inducing changes in DNA methylation. Proc. Natl Acad. Sci. USA117(38), 23280–23285 (2019).
   PubMed Web of Science ®Google Scholar
• Sugden K , HannonEJ , ArseneaultLet al. Establishing a generalized polyepigenetic biomarker for tobacco smoking. Transl. Psychiatry9(1), 92 (2019).
   PubMedGoogle Scholar
• Horvath S . DNA methylation age of human tissues and cell types. Genome Biol.14(10), R115 (2013).
   PubMed Web of Science ®Google Scholar
• McEwen LM , O’DonnellKJ , McGillMGet al. The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc. Natl Acad. Sci. USA117(38), 23329–23335 (2019).
   PubMed Web of Science ®Google Scholar
• Hannum G , GuinneyJ , ZhaoLet al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol. Cell49(2), 359–367 (2013).
   PubMed Web of Science ®Google Scholar
• Brody GH , MillerGE , YuT , BeachSR , ChenE. Supportive family environments ameliorate the link between racial discrimination and epigenetic aging: a replication across two longitudinal cohorts. Psychol. Sci.27(4), 530–541 (2016).
   PubMed Web of Science ®Google Scholar
• Simons RL , LeiMK , BeachSRet al. Economic hardship and biological weathering: the epigenetics of aging in a U.S. sample of black women. Soc. Sci. Med.150, 192–200 (2016).
   PubMed Web of Science ®Google Scholar
• Ward-Caviness CK , PuS , MartinCLet al. Epigenetic predictors of all-cause mortality are associated with objective measures of neighborhood disadvantage in an urban population. Clin. Epigenetics12(1), 44 (2020).
   PubMed Web of Science ®Google Scholar
• Pedersen JS , ValenE , VelazquezAMet al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res.24(3), 454–466 (2014).
   PubMed Web of Science ®Google Scholar
• Gokhman D , LaviE , PruferKet al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science344(6183), 523–527 (2014).
   PubMed Web of Science ®Google Scholar
• Orlando L Hanghøj K . Ancient Epigenomics. In: Paleogenomics: genome-scale analysis of ancient DNALindqvistCRajoraOP ( Eds.). Springer Science & Business Media, New York, NY, 75–111 (2019).
   Google Scholar
• Wright ML , DozmorovMG , WolenARet al. Establishing an analytic pipeline for genome-wide DNA methylation. Clin. Epigenet.8, 45 (2016).
   PubMed Web of Science ®Google Scholar
• Edgar RD , JonesMJ , MeaneyMJ , TureckiG , KoborMS. BECon: a tool for interpreting DNA methylation findings from blood in the context of brain. Transl. Psychiatry7(8), e1187 (2017).
   PubMed Web of Science ®Google Scholar
• Philpott M , CribbsAP , BrownTJr , BrownTSr , OppermannU. Advances and challenges in epigenomic single-cell sequencing applications. Curr. Opin. Chem. Biol.57, 17–26 (2020).
   PubMed Web of Science ®Google Scholar
• Amiri A , CoppolaG , ScuderiSet al. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science362(6420), (2018).
   PubMed Web of Science ®Google Scholar
• Horvath S , OshimaJ , MartinGMet al. Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria syndrome and ex vivo studies. Aging (Albany NY)10(7), 1758–1775 (2018).
   PubMedGoogle Scholar
• Social Epidemiology.(2nd Edition)BerkmanLF , KawachiI , GlymourMM. ( Eds.). Oxford University Press, Oxford, UK (2014).
   Google Scholar
• Adler NE , BoyceT , ChesneyMAet al. Socioeconomic status and health. The challenge of the gradient. Am. Psychol.49(1), 15–24 (1994).
   PubMed Web of Science ®Google Scholar
• Arcaya MC , ArcayaAL , SubramanianSV. Inequalities in health: definitions, concepts, and theories. Glob. Health Action8, 27106 (2015).
   PubMed Web of Science ®Google Scholar
• Rivenbark J , ArseneaultL , CaspiAet al. Adolescents’ perceptions of family social status correlate with health and life chances: a twin difference longitudinal cohort study. Proc. Natl Acad. Sci. USA117(38), 23323–23328 (2020).
   PubMed Web of Science ®Google Scholar
• Williams DR , LawrenceJA , DavisBA. Racism and health: evidence and needed research. Annu. Rev. Public Health40, 105–125 (2019).
   PubMed Web of Science ®Google Scholar
• Chae DH , CloustonS , HatzenbuehlerMLet al. Association between an Internet-based measure of area racism and black mortality. PLoS ONE10(4), e0122963 (2015).
   PubMed Web of Science ®Google Scholar
• Manrai AK , CuiY , BushelPRet al. Informatics and data analytics to support exposome-based discovery for public health. Annu. Rev. Public Health38, 279–294 (2017).
   PubMed Web of Science ®Google Scholar
• Heijmans BT , MillJ. Commentary: the seven plagues of epigenetic epidemiology. Int. J. Epidemiol.41(1), 74–78 (2012).
   PubMed Web of Science ®Google Scholar
• Nebbioso A , TambaroFP , Dell’aversanaC , AltucciL. Cancer epigenetics: moving forward. PLoS Genet14(6), e1007362 (2018).
   PubMed Web of Science ®Google Scholar
• Phillips NLH , RothTL. Animal models and their contribution to our understanding of the relationship between environments, epigenetic modifications, and behavior. Genes (Basel)10(1), (2019).
   PubMed Web of Science ®Google Scholar
• Bakulski KM , HalladayA , HuVW , MillJ , FallinMD. Epigenetic research in neuropsychiatric disorders: the “tissue issue”. Curr. Behav. Neurosci. Reports3(3), 264–274 (2016).
   PubMedGoogle 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
• Jones MJ , MooreSR , KoborMS. Principles and challenges of applying epigenetic epidemiology to psychology. Annu. Rev. Psychol.69, 459–485 (2018).
   PubMed Web of Science ®Google Scholar
• Plomin R . Commentary: missing heritability, polygenic scores, and gene-environment correlation. J. Child Psychol. Psychiatry54(10), 1147–1149 (2013).
   PubMed Web of Science ®Google Scholar
• Lohmueller KE , PearceCL , PikeM , LanderES , HirschhornJN. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet.33(2), 177–182 (2003).
   PubMed Web of Science ®Google Scholar
• Baker M . 1,500 scientists lift the lid on reproducibility. Nature News533(7604), 452–454 (2016).
   PubMed Web of Science ®Google Scholar
• Choi SW , MakTSH , O’ReillyPF. A guide to performing plygenic risk score analyses. BioRxiv15, 2759–2772 (2018).
   Google Scholar
• Boyle EA , LiYI , PritchardJK. An expanded view of complex traits: from polygenic to omnigenic. Cell169(7), 1177–1186 (2017).
   PubMed Web of Science ®Google Scholar
• Melas PA , WeiY , WongCCet 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
• Tyrka AR , PriceLH , MarsitC , WaltersOC , CarpenterLL. Childhood adversity and epigenetic modulation of the leukocyte glucocorticoid receptor: preliminary findings in healthy adults. PLoS ONE7(1), e30148–e30148 (2012).
   PubMed Web of Science ®Google Scholar
• Mcgowan H . Bridging the gap between DNA methylation, dna methylation readers, and neurodevelopmental disorders. J. Neurosci.36(26), 6851–6853 (2016).
   PubMed Web of Science ®Google Scholar
• Leek JT , ScharpfRB , BravoHCet al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet.11(10), 733–739 (2010).
   PubMed Web of Science ®Google Scholar
• Michels KB , BinderAM , DedeurwaerderSet al. Recommendations for the design and analysis of epigenome-wide association studies. Nat. Methods10(10), 949–955 (2013).
   PubMed Web of Science ®Google Scholar
• Johnson WE , LiC , RabinovicA. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics8(1), 118–127 (2007).
   PubMed Web of Science ®Google Scholar
• Buhule OD , MinsterRL , HawleyNLet al. Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale. Front. Genet.5, 354 (2014).
   PubMed Web of Science ®Google Scholar
• Price EM , RobinsonWP. Adjusting for batch effects in DNA methylation microarray data, a lesson learned. Front. Genet9, 83 (2018).
   PubMed Web of Science ®Google Scholar
• Mansell G , Gorrie-StoneTJ , BaoYet al. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genom.20(1), 366 (2019).
   PubMedGoogle Scholar
• Krieger N . Methods for the scientific study of discrimination and health: an ecosocial approach. Am. J. Public Health102(5), 936–944 (2012).
   PubMed Web of Science ®Google Scholar
• Krieger N , CarneyD , LancasterK , WatermanPD , KoshelevaA , BanajiM. Combining explicit and implicit measures of racial discrimination in health research. Am. J. Public Health100(8), 1485–1492 (2010).
   PubMed Web of Science ®Google Scholar
• Chae DH , CloustonS , MartzCDet al. Area racism and birth outcomes among Blacks in the United States. Soc. Sci. Med.199, 49–55 (2018).
   PubMed Web of Science ®Google Scholar
• Kagawa Singer M , DresslerW , GeorgeS , PanelNIHE. Culture: the missing link in health research. Soc Sci Med170, 237–246 (2016).
   PubMed Web of Science ®Google Scholar
• Kaufman JS , CooperRS. Commentary: considerations for use of racial/ethnic classification in etiologic research. Am. J. Epidemiol.154(4), 291–298 (2001).
   PubMed Web of Science ®Google Scholar
• Vanderweele TJ , RobinsonWR. On the causal interpretation of race in regressions adjusting for confounding and mediating variables. Epidemiology25(4), 473–484 (2014).
   PubMed Web of Science ®Google Scholar
• Cheng TL , GoodmanE, Committee on Pediatric R. Race, ethnicity, and socioeconomic status in research on child health. Pediatrics135(1), e225–237 (2015).
   PubMed Web of Science ®Google Scholar
• Chitrala KN , HernandezDG , NallsMAet al. Race-specific alterations in DNA methylation among middle-aged African Americans and Whites with metabolic syndrome. Epigenetics15(5), 462–482 (2020).
   PubMed Web of Science ®Google Scholar
• Henrich J , HeineSJ , NorenzayanA. The weirdest people in the world?Behav. Brain Sci.33(2–3), 61–83 (2010).
   PubMed Web of Science ®Google Scholar
• Sirugo G , WilliamsSM , TishkoffSA. The missing diversity in human genetic studies. Cell177(4), 1080 (2019).
   PubMed Web of Science ®Google Scholar
• Pai MC , KuoYM , WangIF , ChiangPM , TsaiKJ. The role of methylated circulating nucleic acids as a potential biomarker in Alzheimer’s disease. Mol. Neurobiol.56(4), 2440–2449 (2019).
   PubMed Web of Science ®Google Scholar
• Brennand KJ , MarchettoMC , BenvenistyNet al. Creating patient-specific neural cells for the in vitro study of brain disorders. Stem Cell Reports5(6), 933–945 (2015).
   PubMed Web of Science ®Google Scholar
• Geronimus AT . Deep integration: letting the epigenome out of the bottle without losing sight of the structural origins of population health. Am. J. Public Health103(Suppl. 1), S56–S63 (2013).
   PubMedGoogle Scholar
• Thayer ZM , NonAL. Anthropology meets epigenetics: current and future directions. Am. Anthropologist117(4), 722–735 (2015).
   Web of Science ®Google Scholar
• Heijmans BT , TobiEW , SteinADet al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc. Natl Acad. Sci. USA105(44), 17046–17049 (2008).
   PubMed Web of Science ®Google Scholar
• Wiechmann T , RohS , SauerSet al. Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus. Clin. Epigenetics11(1), 83 (2019).
   PubMedGoogle Scholar
• Kubota T , MochizukiK. Epigenetic effect of environmental factors on autism spectrum disorders. Int. J. Environ. Res. Public Health13(5), (2016).
   PubMed Web of Science ®Google Scholar
• Boskovic A , RandoOJ. Transgenerational epigenetic inheritance. Annu. Rev. Genet.52, 21–41 (2018).
   PubMed Web of Science ®Google Scholar
• Kaufman JS , CooperRS. Seeking causal explanations in social epidemiology. Am. J. Epidemiol.150(2), 113–120 (1999).
   PubMed Web of Science ®Google Scholar
• Lowe R , BartonC , JenkinsCAet al. Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species. Genome Biol.19(1), 22 (2018).
   PubMedGoogle Scholar
• Hannon E , LunnonK , SchalkwykL , MillJ. Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics10(11), 1024–1032 (2015).
   PubMed Web of Science ®Google Scholar
• Non AL , ThayerZM. Epigenetics for anthropologists: an introduction to methods. Am. J. Hum. Biol.27(3), 295–303 (2015).
   PubMed Web of Science ®Google Scholar
• Summerfield D . How scientifically valid is the knowledge base of global mental health?BMJ336(7651), 992–994 (2008).
   PubMed Web of Science ®Google Scholar
• Global Mental Health: Anthropological Perspectives. (1st Edition) KohrtB , MendenhallE (Eds). Left Coast Press, Inc, Walnut Creek, CA, USA (2015).
   Google Scholar
• Operario D , AdlerNE , WilliamsDR. Subjective social status: reliability and predictive utility for global health. Psychol. Health19(2), 237–246 (2004).
   Web of Science ®Google Scholar
• Adler NE , EpelES , CastellazzoG , IckovicsJR. Relationship of subjective and objective social status with psychological and physiological functioning: preliminary data in healthy white women. Health Psychol.19(6), 586–592 (2000).
   PubMed Web of Science ®Google Scholar
• Yehuda R , FloryJD , BiererLMet al. Lower methylation of glucocorticoid receptor gene promoter 1F in peripheral blood of veterans with posttraumatic stress disorder. Biol. Psychiatry77(4), 356–364 (2015).
   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
• Barker ED , RobertsS , WaltonE. Hidden hypotheses in ‘hypothesis-free’ genome-wide epigenetic associations. Curr. Opin. Psychol.27, 13–17 (2019).
   PubMed Web of Science ®Google Scholar
• Valdez N . The redistribution of reproductive responsibility: on the epigenetics of “environment” in prenatal interventions. Med. Anthropol. Q.32(3), 425–442 (2018).
   PubMed Web of Science ®Google Scholar
• Chadwick LH , SawaA , YangIVet al. New insights and updated guidelines for epigenome-wide association studies. Neuroepigenetics1, 14–19 (2015).
   Google Scholar
• Birney E , SmithGD , GreallyJM. Epigenome-wide association studies and the interpretation of disease -omics. PLoS Genet.12(6), e1006105 (2016).
   PubMed Web of Science ®Google Scholar
• Teschendorff AE , ZhengSC. Cell-type deconvolution in epigenome-wide association studies: a review and recommendations. Epigenomics9(5), 757–768 (2017).
   PubMed Web of Science ®Google Scholar
• Ng JW , BarrettLM , WongA , KuhD , SmithGD , ReltonCL. The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol.13(6), 246 (2012).
   PubMed Web of Science ®Google Scholar
• Saulnier KM , DuprasC. Race in the postgenomic era: social epigenetics calling for interdisciplinary ethical safeguards. Am. J. Bioeth.17(9), 58–60 (2017).
   PubMed Web of Science ®Google Scholar