Sex differences are pervasive in schizophrenia (SCZ), but the extent and magnitude of DNA methylation (DNAm) changes underlying these differences remain uncharacterized. In this study, sex-stratified differential DNAm analysis was performed in postmortem brain samples from 117 SCZ and 137 controls, partitioned into discovery and replication datasets. Three differentially methylated positions (DMPs) were identified (adj.p < 0.05) in females and 29 DMPs in males without overlap between them. Over 81% of these sex-stratified DMPs were directionally consistent between sexes but with different effect sizes. Females experienced larger magnitude of DNAm changes and more DMPs (based on data of equal sample size) than males, contributing to a higher dysregulation burden of DNAm in females SCZ. Additionally, despite similar proportions of female-related DMPs (fDMPs, 8%) being under genetic control compared with males (10%), significant enrichment of DMP-related single nucleotide polymorphisms (SNPs) in signals of genome-wide association studies was identified only in fDMPs. One DMP in each sex connected the SNPs and gene expression of CALHM1 in females and CCDC149 in males. PPI subnetworks revealed that both female- and male-related differential DNAm interacted with synapse-related dysregulation. Immune-related pathways were unique for females and neuron-related pathways were associated with males. This study reveals remarkable quantitative differences in DNAm-related sexual dimorphism in SCZ and that females have a higher dysregulation burden of SCZ-associated DNAm than males.
This is a preview of subscription content, access via your institution
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
All data are available in the main text or the supplementary materials. Published DNAm datasets analyzed in this study are available on Gene Expression Omnibus (accession No. GSE74193, GSE61431 and GSE61380).
The code of this work can be found at https://github.com/zhoujiaqi704/Sex-stratified-differential-DNAm-in-schizophrenia.
Castle DJ, Murray RM. The neurodevelopmental basis of sex differences in schizophrenia. Psychol Med. 1991;21:565–75.
Leung A, Chue P. Sex differences in schizophrenia, a review of the literature. Acta Psychiatr Scand Suppl. 2000;401:3–38.
Abel KM, Drake R, Goldstein JM. Sex differences in schizophrenia. Int Rev Psychiatry. 2010;22:417–28.
Aleman A, Kahn RS, Selten JP. Sex differences in the risk of schizophrenia: evidence from meta-analysis. Arch Gen Psychiatry. 2003;60:565–71.
Bergen SE, O’Dushlaine CT, Lee PH, Fanous AH, Ruderfer DM, Ripke S, et al. Genetic modifiers and subtypes in schizophrenia: investigations of age at onset, severity, sex and family history. Schizophr Res. 2014;154:48–53.
Walder DJ, Seidman LJ, Cullen N, Su J, Tsuang MT, Goldstein JM. Sex differences in language dysfunction in schizophrenia. Am J Psychiatry. 2006;163:470–7.
Morgan VA, Castle DJ, Jablensky AV. Do women express and experience psychosis differently from men? Epidemiological evidence from the Australian National Study of Low Prevalence (Psychotic) disorders. Aust N. Z J Psychiatry. 2008;42:74–82.
Seeman MV. Gender differences in the prescribing of antipsychotic drugs. Am J Psychiatry. 2004;161:1324–33.
Smith S. Gender differences in antipsychotic prescribing. Int Rev Psychiatry. 2010;22:472–84.
Jacquemont S, Coe BP, Hersch M, Duyzend MH, Krumm N, Bergmann S, et al. A higher mutational burden in females supports a “female protective model” in neurodevelopmental disorders. Am J Hum Genet. 2014;94:415–25.
Goldstein JM, Cherkerzian S, Tsuang MT, Petryshen TL. Sex differences in the genetic risk for schizophrenia: history of the evidence for sex-specific and sex-dependent effects. Am J Med Genet B Neuropsychiatr Genet. 2013;162b:698–710.
Sham PC, MacLean CJ, Kendler KS. A typological model of schizophrenia based on age at onset, sex and familial morbidity. Acta Psychiatr Scand. 1994;89:135–41.
Kubota T, Miyake K, Hirasawa T. Epigenetic understanding of gene-environment interactions in psychiatric disorders: a new concept of clinical genetics. Clin Epigenet. 2012;4:1.
Qureshi IA, Mehler MF. Genetic and epigenetic underpinnings of sex differences in the brain and in neurological and psychiatric disease susceptibility. Prog Brain Res. 2010;186:77–95.
Xia Y, Dai R, Wang K, Jiao C, Zhang C, Xu Y et al. Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders. Mol Psychiatry. 2019.
Maschietto M, Bastos LC, Tahira AC, Bastos EP, Euclydes VL, Brentani A, et al. Sex differences in DNA methylation of the cord blood are related to sex-bias psychiatric diseases. Sci Rep. 2017;7:44547.
Singmann P, Shem-Tov D, Wahl S, Grallert H, Fiorito G, Shin SY, et al. Characterization of whole-genome autosomal differences of DNA methylation between men and women. Epigenet Chromatin. 2015;8:43.
Yousefi P, Huen K, Davé V, Barcellos L, Eskenazi B, Holland N. Sex differences in DNA methylation assessed by 450 K BeadChip in newborns. BMC Genom. 2015;16:911.
Xu H, Wang F, Liu Y, Yu Y, Gelernter J, Zhang H. Sex-biased methylome and transcriptome in human prefrontal cortex. Hum Mol Genet. 2014;23:1260–70.
McCarthy NS, Melton PE, Cadby G, Yazar S, Franchina M, Moses EK, et al. Meta-analysis of human methylation data for evidence of sex-specific autosomal patterns. BMC Genom. 2014;15:981.
Spiers H, Hannon E, Schalkwyk LC, Smith R, Wong CC, O’Donovan MC, et al. Methylomic trajectories across human fetal brain development. Genome Res. 2015;25:338–52.
Khramtsova EA, Davis LK, Stranger BE. The role of sex in the genomics of human complex traits. Nat Rev Genet. 2019;20:173–90.
McCarthy MM, Nugent BM, Lenz KM. Neuroimmunology and neuroepigenetics in the establishment of sex differences in the brain. Nat Rev Neurosci. 2017;18:471–84.
Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, et al. Association of DNA Methylation differences with schizophrenia in an epigenome-wide association study. JAMA Psychiatry. 2016;73:506–14.
Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet. 2008;82:696–711.
Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207–10.
Athar A, Fullgrabe A, George N, Iqbal H, Huerta L, Ali A, et al. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019;47:D711–D715.
Jaffe AE, Gao Y, Deep-Soboslay A, Tao R, Hyde TM, Weinberger DR, et al. Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. Nat Neurosci. 2016;19:40–47.
Pidsley R, Viana J, Hannon E, Spiers H, Troakes C, Al-Saraj S, et al. Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. Genome Biol. 2014;15:483.
Tian Y, Morris TJ, Webster AP, Yang Z, Beck S, Feber A, et al. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics. 2017;33:3982–4.
Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017;45:e22.
Nordlund J, Bäcklin CL, Wahlberg P, Busche S, Berglund EC, Eloranta ML, et al. Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol. 2013;14:r105.
Pidsley R, Y Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genom. 2013;14:293.
Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics. 2013;29:189–96.
Naeem H, Wong NC, Chatterton Z, Hong MK, Pedersen JS, Corcoran NM, et al. Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array. BMC Genom. 2014;15:51.
Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinform. 2012;13:86.
Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics. 2013;8:290–302.
Jiao C, Zhang C, Dai R, Xia Y, Wang K, Giase G, et al. Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics. 2018;10:643–59.
Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L, et al. Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One. 2011;6:e17238.
Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3:1724–35.
Plaisier SB, Taschereau R, Wong JA, Graeber TG. Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res. 2010;38:e169.
Ng B, White CC, Klein HU, Sieberts SK, McCabe C, Patrick E, et al. An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome. Nat Neurosci. 2017;20:1418–26.
Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet. 2015;47:1228–35.
Wang K, Dai R, Xia Y, Tian J, Jiao C, Mikhailova T et al. Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development. Epigenetics. 2021:1-18.
Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science. 2018;362:eaat8127.
Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics. 2014;30:2360–6.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, et al. Pathway commons, a web resource for biological pathway data. Nucleic Acids Res. 2011;39:D685–690.
West J, Beck S, Wang X, Teschendorff AE. An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci Rep. 2013;3:1630.
Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16:284–7.
Seney ML, Huo Z, Cahill K, French L, Puralewski R, Zhang J, et al. Opposite molecular signatures of depression in men and women. Biol Psychiatry. 2018;84:18–27.
Zamanian JL, Xu L, Foo LC, Nouri N, Zhou L, Giffard RG, et al. Genomic analysis of reactive astrogliosis. J Neurosci. 2012;32:6391–410.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, et al. Landscape of X chromosome inactivation across human tissues. Nature. 2017;550:244–8.
Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, et al. IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients. Genet Med. 2019;21:837–49.
Decarpentrie F, Vernet N, Mahadevaiah SK, Longepied G, Streichemberger E, Aknin-Seifer I, et al. Human and mouse ZFY genes produce a conserved testis-specific transcript encoding a zinc finger protein with a short acidic domain and modified transactivation potential. Hum Mol Genet. 2012;21:2631–45.
Trubetskoy V, Pardinas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, et al. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature. 2022;604:502–8.
Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, et al. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. Sci Transl Med. 2018;10:eaat8178.
Ding C, Zhang C, Kopp R, Kuney L, Meng Q, Wang L, et al. Transcription factor POU3F2 regulates TRIM8 expression contributing to cellular functions implicated in schizophrenia. Mol Psychiatry. 2021;26:3444–60.
Tanis JE, Ma Z, Krajacic P, He L, Foskett JK, Lamitina T. CLHM-1 is a functionally conserved and conditionally toxic Ca2+-permeable ion channel in Caenorhabditis elegans. J Neurosci. 2013;33:12275–86.
Rusakov DA, Fine A. Extracellular Ca2+ depletion contributes to fast activity-dependent modulation of synaptic transmission in the brain. Neuron. 2003;37:287–97.
Ripke S, O’Dushlaine C, Chambert K, Moran JL, Kahler AK, Akterin S, et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet. 2013;45:1150–9.
Guan F, Zhang T, Li L, Fu D, Lin H, Chen G, et al. Two-stage replication of previous genome-wide association studies of AS3MT-CNNM2-NT5C2 gene cluster region in a large schizophrenia case-control sample from Han Chinese population. Schizophr Res. 2016;176:125–30.
Christoforou A, Le Hellard S, Thomson PA, Morris SW, Tenesa A, Pickard BS, et al. Association analysis of the chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia. Mol Psychiatry. 2007;12:1011–25.
Nugent BM, Wright CL, Shetty AC, Hodes GE, Lenz KM, Mahurkar A, et al. Brain feminization requires active repression of masculinization via DNA methylation. Nat Neurosci. 2015;18:690–7.
Markham JA. Sex steroids and schizophrenia. Rev Endocr Metab Disord. 2012;13:187–207.
Tang S, Han H, Bajic VB. ERGDB: estrogen responsive genes database. Nucleic Acids Res. 2004;32:D533–536.
Jiang M, Ma Y, Chen C, Fu X, Yang S, Li X, et al. Androgen-responsive gene database: integrated knowledge on androgen-responsive genes. Mol Endocrinol. 2009;23:1927–33.
Blokland GAM, Grove J, Chen CY, Cotsapas C, Tobet S, Handa R, et al. Sex-dependent shared and nonshared genetic architecture across mood and psychotic disorders. Biol Psychiatry. 2022;91:102–17.
Martin J, Khramtsova EA, Goleva SB, Blokland GAM, Traglia M, Walters RK, et al. Examining sex-differentiated genetic effects across neuropsychiatric and behavioral traits. Biol Psychiatry. 2021;89:1127–37.
Polderman TJ, Benyamin B, de Leeuw CA, Sullivan PF, van Bochoven A, Visscher PM, et al. Meta-analysis of the heritability of human traits based on fifty years of twin studies. Nat Genet. 2015;47:702–9.
Oliva M, Munoz-Aguirre M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, et al. The impact of sex on gene expression across human tissues. Science. 2020;369:eaba3066.
Hoffman GE, Ma Y, Montgomery KS, Bendl J, Jaiswal MK, Kozlenkov A, et al. Sex differences in the human brain transcriptome of cases with schizophrenia. Biol Psychiatry. 2022;91:92–101.
Wijchers PJ, Festenstein RJ. Epigenetic regulation of autosomal gene expression by sex chromosomes. Trends Genet. 2011;27:132–40.
Hannon E, Spiers H, Viana J, Pidsley R, Burrage J, Murphy TM, et al. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nat Neurosci. 2016;19:48–54.
Perzel Mandell KA, Eagles NJ, Wilton R, Price AJ, Semick SA, Collado-Torres L, et al. Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk. Nat Commun. 2021;12:5251.
Gamazon ER, Badner JA, Cheng L, Zhang C, Zhang D, Cox NJ, et al. Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. Mol Psychiatry. 2013;18:340–6.
Nelson LH, Saulsbery AI, Lenz KM. Small cells with big implications: Microglia and sex differences in brain development, plasticity and behavioral health. Prog Neurobiol. 2019;176:103–19.
Frye HE, Izumi Y, Harris AN, Williams SB, Trousdale CR, Sun MY, et al. Sex differences in the role of CNIH3 on spatial memory and synaptic plasticity. Biol Psychiatry. 2021;90:766–80.
Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, et al. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. Science. 2018;359:693–7.
Chen Y, Dai J, Tang L, Mikhailova T, Liang Q, Li M, et al. Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders. Mol Psychiatry. 2023;28:710–21.
Alonso-Nanclares L, Gonzalez-Soriano J, Rodriguez JR, DeFelipe J. Gender differences in human cortical synaptic density. Proc Natl Acad Sci USA. 2008;105:14615–9.
Cooke BM, Woolley CS. Sexually dimorphic synaptic organization of the medial amygdala. J Neurosci. 2005;25:10759–67.
Uhl M, Schmeisser MJ, Schumann S. The sexual dimorphic synapse: from spine density to molecular composition. Front Mol Neurosci. 2022;15:818390.
We thank Richard F. Kopp from SUNY Upstate Medical University, for his critical reading and language editing, which greatly improved the manuscript. We gratefully acknowledge the families of the brain donors, without whom this work would not have been possible. This work was supported in part by the High Performance Computing Center of Central South University.
FundingThis work was supported by the National Natural Science Foundation of China (Grants Nos. 82022024, 31970572, 31871276), the National Key R&D Project of China (Grants No. 2016YFC1306000), the science and technology innovation Program of Hunan Province, Innovation-driven Project of Central South University (Grant Nos. 2020CX003) (to C. Chen), and NIH grants U01MH122591, 1U01MH116489, 1R01MH110920 (to C. Liu).
The authors declare no cmpeting interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Zhou, J., Xia, Y., Li, M. et al. A higher dysregulation burden of brain DNA methylation in female patients implicated in the sex bias of Schizophrenia. Mol Psychiatry (2023). https://doi.org/10.1038/s41380-023-02243-4