Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort

Molecular Psychiatry volume 29, pages 43–53 (2024)Cite this article

Subjects

Abstract

There is a need to consider paternal contributions to autism spectrum disorder (ASD) more strongly. Autism etiology is complex, and heritability is not explained by genetics alone. Understanding paternal gametic epigenetic contributions to autism could help fill this knowledge gap. In the present study, we explored whether paternal autistic traits, and the sperm epigenome, were associated with autistic traits in children at 36 months enrolled in the Early Autism Risk Longitudinal Investigation (EARLI) cohort. EARLI is a pregnancy cohort that recruited and enrolled pregnant women in the first half of pregnancy who already had a child with ASD. After maternal enrollment, EARLI fathers were approached and asked to provide a semen specimen. Participants were included in the present study if they had genotyping, sperm methylation data, and Social Responsiveness Scale (SRS) score data available. Using the CHARM array, we performed genome-scale methylation analyses on DNA from semen samples contributed by EARLI fathers. The SRS—a 65-item questionnaire measuring social communication deficits on a quantitative scale—was used to evaluate autistic traits in EARLI fathers (n = 45) and children (n = 31). We identified 94 significant child SRS-associated differentially methylated regions (DMRs), and 14 significant paternal SRS-associated DMRs (fwer p < 0.05). Many child SRS-associated DMRs were annotated to genes implicated in ASD and neurodevelopment. Six DMRs overlapped across the two outcomes (fwer p < 0.1), and, 16 DMRs overlapped with previous child autistic trait findings at 12 months of age (fwer p < 0.05). Child SRS-associated DMRs contained CpG sites independently found to be differentially methylated in postmortem brains of individuals with and without autism. These findings suggest paternal germline methylation is associated with autistic traits in 3-year-old offspring. These prospective results for autism-associated traits, in a cohort with a family history of ASD, highlight the potential importance of sperm epigenetic mechanisms in autism.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Volcano plots for child and paternal DMRs.
Fig. 2: Methylation plots for the top four statistical DMRs (P < 1.0 × 10−4) identified using CHARM and 36-month child SRS score.
Fig. 3: Methylation plots for the top four statistical DMRs (P < 1.0 × 10-4) identified using CHARM and Paternal SRS score.

Similar content being viewed by others

Data availability

The raw methylation data analyzed in the current study was previously uploaded to the National Database for Autism Research (NDAR) study 377 and is available at the following link: https://nda.nih.gov/study.html?id=377. Additional data is available from the corresponding author upon reasonable request.

Code availability

Code for performing the above analyses is available from the authors upon request.

References

  1. Hertz-Picciotto I, Schmidt RJ, Krakowiak P. Understanding environmental contributions to autism: Causal concepts and the state of science. Autism Res. 2018;11:554–86.

    Article  PubMed  Google Scholar 

  2. Havdahl A, Niarchou M, Starnawska A, Uddin M, van der Merwe C, Warrier V. Genetic contributions to autism spectrum disorder. Psychol Med. 2021;51:2260–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lyall K, Constantino JN, Weisskopf MG, Roberts AL, Ascherio A, Santangelo SL. Parental social responsiveness and risk of autism spectrum disorder in offspring. JAMA Psychiatry. 2014;71:936–42.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Bhandari R, Paliwal JK, Kuhad A. Neuropsychopathology of Autism Spectrum Disorder: Complex Interplay of Genetic, Epigenetic, and Environmental Factors. Adv Neurobiol. 2020;24:97–141.

    Article  PubMed  Google Scholar 

  5. Donkin I, Barres R. Sperm epigenetics and influence of environmental factors. Mol Metab. 2018;14:1–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Waye MMY, Cheng HY. Genetics and epigenetics of autism: A Review. Psychiatry Clin Neurosci. 2018;72:228–44.

    Article  PubMed  Google Scholar 

  7. Greenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019;20:590–607.

    Article  CAS  PubMed  Google Scholar 

  8. Feinberg JI, Bakulski KM, Jaffe AE, Tryggvadottir R, Brown SC, Goldman LR, et al. Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort. Int J Epidemiol. 2015;44:1199–210.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Garrido N, Cruz F, Egea RR, Simon C, Sadler-Riggleman I, Beck D, et al. Sperm DNA methylation epimutation biomarker for paternal offspring autism susceptibility. Clin Epigenet. 2021;13:6.

    Article  CAS  Google Scholar 

  10. McSwiggin HM, O’Doherty AM. Epigenetic reprogramming during spermatogenesis and male factor infertility. Reproduction 2018;156:R9–R21.

    Article  CAS  PubMed  Google Scholar 

  11. Stewart KR, Veselovska L, Kelsey G. Establishment and functions of DNA methylation in the germline. Epigenomics 2016;8:1399–413.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Trasler JM. Epigenetics in spermatogenesis. Mol Cell Endocrinol. 2009;306:33–6.

    Article  CAS  PubMed  Google Scholar 

  13. Uysal F, Akkoyunlu G, Ozturk S. DNA methyltransferases exhibit dynamic expression during spermatogenesis. Reprod Biomed Online. 2016;33:690–702.

    Article  CAS  PubMed  Google Scholar 

  14. Wu H, Hauser R, Krawetz SA, Pilsner JR. Environmental Susceptibility of the Sperm Epigenome During Windows of Male Germ Cell Development. Curr Environ Health Rep. 2015;2:356–66.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Zhang W, Yang J, Lv Y, Li S, Qiang M. Paternal benzo[a]pyrene exposure alters the sperm DNA methylation levels of imprinting genes in F0 generation mice and their unexposed F1-2 male offspring. Chemosphere 2019;228:586–94.

    Article  CAS  PubMed  Google Scholar 

  16. Murphy SK, Itchon-Ramos N, Visco Z, Huang Z, Grenier C, Schrott R, et al. Cannabinoid exposure and altered DNA methylation in rat and human sperm. Epigenetics 2018;13:1208–21.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, et al. Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology. 2017;5:1089–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Morkve Knudsen GT, Rezwan FI, Johannessen A, Skulstad SM, Bertelsen RJ, Real FG, et al. Epigenome-wide association of father’s smoking with offspring DNA methylation: a hypothesis-generating study. Environ Epigenet. 2019;5:dvz023.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Consales C, Toft G, Leter G, Bonde JP, Uccelli R, Pacchierotti F, et al. Exposure to persistent organic pollutants and sperm DNA methylation changes in Arctic and European populations. Environ Mol Mutagen. 2016;57:200–9.

    Article  CAS  PubMed  Google Scholar 

  20. Donkin I, Versteyhe S, Ingerslev LR, Qian K, Mechta M, Nordkap L, et al. Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans. Cell Metab. 2016;23:369–78.

    Article  CAS  PubMed  Google Scholar 

  21. Virkud YV, Todd RD, Abbacchi AM, Zhang Y, Constantino JN. Familial aggregation of quantitative autistic traits in multiplex versus simplex autism. Am J Med Genet B Neuropsychiatr Genet. 2009;150B:328–34.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Sandin S, Lichtenstein P, Kuja-Halkola R, Larsson H, Hultman CM, Reichenberg A. The familial risk of autism. JAMA 2014;311:1770–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Maenner MJ, Shaw KA, Bakian AV, Bilder DA, Durkin MS, Esler A, et al. Prevalence and Characteristics of Autism Spectrum Disorder Among Children Aged 8 Years - Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States. MMWR Surveill Summ. 2021;2018:1–16.

    Article  Google Scholar 

  24. Constantino JN, Davis SA, Todd RD, Schindler MK, Gross MM, Brophy SL, et al. Validation of a brief quantitative measure of autistic traits: comparison of the social responsiveness scale with the autism diagnostic interview-revised. J Autism Dev Disord. 2003;33:427–33.

    Article  PubMed  Google Scholar 

  25. Newschaffer CJ, Croen LA, Fallin MD, Hertz-Picciotto I, Nguyen DV, Lee NL, et al. Infant siblings and the investigation of autism risk factors. J Neurodev Disord. 2012;4:7.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Wigham S, McConachie H, Tandos J, Le Couteur AS. Gateshead Millennium Study core t. The reliability and validity of the Social Responsiveness Scale in a UK general child population. Res Dev Disabil. 2012;33:944–50.

    Article  PubMed  Google Scholar 

  27. Chan W, Smith LE, Hong J, Greenberg JS, Mailick MR. Validating the social responsiveness scale for adults with autism. Autism Res. 2017;10:1663–71.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Ladd-Acosta C, Aryee MJ, Ordway JM, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Curr Protoc Hum Genet. 2010;Chapter 20:Unit 20 1 1–19.

    PubMed  Google Scholar 

  29. Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 2015;4:7.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2:e190.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904–9.

    Article  CAS  PubMed  Google Scholar 

  32. Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, et al. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics 2011;12:197–210.

    Article  PubMed  Google Scholar 

  33. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3:1724–35.

    Article  CAS  PubMed  Google Scholar 

  34. Buja A, Eyuboglu N. Remarks on Parallel Analysis. Multivar Behav Res. 1992;27:509–40.

    Article  CAS  Google Scholar 

  35. Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012;41:200–9.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Ladd-Acosta C, Hansen KD, Briem E, Fallin MD, Kaufmann WE, Feinberg AP. Common DNA methylation alterations in multiple brain regions in autism. Mol Psychiatry. 2014;19:862–71.

    Article  CAS  PubMed  Google Scholar 

  37. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, et al. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014;2014:bau086.

    Article  PubMed  Google Scholar 

  38. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007;23:257–8.

    Article  CAS  PubMed  Google Scholar 

  39. Yao P, Lin P, Gokoolparsadh A, Assareh A, Thang MW, Voineagu I. Coexpression networks identify brain region-specific enhancer RNAs in the human brain. Nat Neurosci. 2015;18:1168–74.

    Article  CAS  PubMed  Google Scholar 

  40. Wilkinson B, Grepo N, Thompson BL, Kim J, Wang K, Evgrafov OV, et al. The autism-associated gene chromodomain helicase DNA-binding protein 8 (CHD8) regulates noncoding RNAs and autism-related genes. Transl Psychiatry. 2015;5:e568.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ozonoff S, Young GS, Landa RJ, Brian J, Bryson S, Charman T, et al. Diagnostic stability in young children at risk for autism spectrum disorder: a baby siblings research consortium study. J Child Psychol Psychiatry. 2015;56:988–98.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Hussain T, Liu B, Shrock MS, Williams T, Aldaz CM. WWOX, the FRA16D gene: A target of and a contributor to genomic instability. Genes Chromosom Cancer. 2019;58:324–38.

    Article  CAS  PubMed  Google Scholar 

  43. Banne E, Abudiab B, Abu-Swai S, Repudi SR, Steinberg DJ, Shatleh D, et al. Neurological Disorders Associated with WWOX Germline Mutations-A Comprehensive Overview. Cells. 2021;10:824.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Aldaz CM, Hussain T. WWOX Loss of Function in Neurodevelopmental and Neurodegenerative Disorders. Int J Mol Sci. 2020;21:8922.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Eyler LT, Pierce K, Courchesne E. A failure of left temporal cortex to specialize for language is an early emerging and fundamental property of autism. Brain 2012;135:949–60.

    Article  PubMed  PubMed Central  Google Scholar 

  46. Donovan AP, Basson MA. The neuroanatomy of autism - a developmental perspective. J Anat. 2017;230:4–15.

    Article  PubMed  Google Scholar 

  47. Courchesne E, Mouton PR, Calhoun ME, Semendeferi K, Ahrens-Barbeau C, Hallet MJ, et al. Neuron number and size in prefrontal cortex of children with autism. JAMA 2011;306:2001–10.

    Article  CAS  PubMed  Google Scholar 

  48. Gkountela S, Zhang KX, Shafiq TA, Liao WW, Hargan-Calvopina J, Chen PY, et al. DNA Demethylation Dynamics in the Human Prenatal Germline. Cell 2015;161:1425–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Tang WW, Dietmann S, Irie N, Leitch HG, Floros VI, Bradshaw CR, et al. A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development. Cell 2015;161:1453–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet. 2012;8:e1002440.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 2012;484:339–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Keyhan S, Burke E, Schrott R, Huang Z, Grenier C, Price T, et al. Male obesity impacts DNA methylation reprogramming in sperm. Clin Epigenet. 2021;13:17.

    Article  CAS  Google Scholar 

  53. Schrott R, Murphy SK, Modliszewski JL, King DE, Hill B, Itchon-Ramos N, et al. Refraining from use diminishes cannabis-associated epigenetic changes in human sperm. Environ Epigenet. 2021;7:dvab009.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Greeson KW, Fowler KL, Estave PM, Kate Thompson S, Wagner C, Clayton Edenfield R, et al. Detrimental effects of flame retardant, PBB153, exposure on sperm and future generations. Sci Rep. 2020;10:8567.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Maggio AG, Shu HT, Laufer BI, Bi C, Lai Y, LaSalle JM, et al. Elevated exposures to persistent endocrine disrupting compounds impact the sperm methylome in regions associated with autism spectrum disorder. Front Genet. 2022;13:929471.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, et al. Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. Nat Commun. 2017;8:1011.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Rizzardi LF, Hickey PF, Rodriguez DiBlasi V, Tryggvadottir R, Callahan CM, Idrizi A, et al. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nat Neurosci. 2019;22:307–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We would like to thank Rakel Tryggvadottir, Birna Berndsen, Roxann Ashworth, and the Johns Hopkins SNP Center at the Genome Resource Core Facility (GRCF) for processing the lab samples. This work was supported by R01ES017646 (Feinberg/Fallin), R01ES016443 (Newschaffer), R24ES030893 (Fallin), R01ES023780 (Volk), R01ES023780-04S01 (Volk), Autism Speaks grant no. 7785 (Volk).

Author information

Author notes

  1. These authors contributed equally: Jason I. Feinberg, Rose Schrott.

  2. These authors jointly supervised this work: Andrew P. Feinberg, Heather E. Volk.

Authors and Affiliations

  1. Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    Jason I. Feinberg, Christine Ladd-Acosta & Heather E. Volk

  2. Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    Jason I. Feinberg, Rose Schrott, Andrew P. Feinberg & Heather E. Volk

  3. Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    Christine Ladd-Acosta

  4. Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, State College, PA, USA

    Craig J. Newschaffer

  5. Department of Public Health Sciences, MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California, Davis, CA, USA

    Irva Hertz-Picciotto

  6. Autism Research Program, Division of Research, Kaiser Permanente, Oakland, CA, USA

    Lisa A. Croen

  7. Rollins School of Public Health, Emory University, Atlanta, GA, USA

    M. Daniele Fallin

  8. Center for Epigenetics, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Andrew P. Feinberg

Authors
  1. Jason I. Feinberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rose Schrott
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Christine Ladd-Acosta
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Craig J. Newschaffer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Irva Hertz-Picciotto
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lisa A. Croen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. Daniele Fallin
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Andrew P. Feinberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Heather E. Volk
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Laboratory studies were performed by JIF. Statistical analyses were performed by JIF and RS with assistance from APF, HEV, CLA, and MDF. EARLI cohort P.I.s were CJN, IHP, LAC, and MDF. The paper was written by JIF, RS, APF, and HEV. The overall design of the study was done by APF and HEV with assistance from MDF and CLA. JIF and RS are considered co-equal first authors, and APF and HV are considered co-equal corresponding authors.

Corresponding authors

Correspondence to Andrew P. Feinberg or Heather E. Volk.

Ethics declarations

Competing interests

Dr CL-A reports receiving consulting fees from the University of Iowa for providing expertize on autism spectrum disorder epigenetics outside of this work. The work described here is the subject of U.S. patent application 63/315,000 from Johns Hopkins University.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Feinberg, J.I., Schrott, R., Ladd-Acosta, C. et al. Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort. Mol Psychiatry 29, 43–53 (2024). https://doi.org/10.1038/s41380-023-02046-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41380-023-02046-7

This article is cited by

Search

Advanced search

Quick links