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Common DNA methylation alterations in multiple brain regions in autism

Molecular Psychiatry volume 19, pages 862–871 (2014)Cite this article

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Abstract

Autism spectrum disorders (ASD) are increasingly common neurodevelopmental disorders defined clinically by a triad of features including impairment in social interaction, impairment in communication in social situations and restricted and repetitive patterns of behavior and interests, with considerable phenotypic heterogeneity among individuals. Although heritability estimates for ASD are high, conventional genetic-based efforts to identify genes involved in ASD have yielded only few reproducible candidate genes that account for only a small proportion of ASDs. There is mounting evidence to suggest environmental and epigenetic factors play a stronger role in the etiology of ASD than previously thought. To begin to understand the contribution of epigenetics to ASD, we have examined DNA methylation (DNAm) in a pilot study of postmortem brain tissue from 19 autism cases and 21 unrelated controls, among three brain regions including dorsolateral prefrontal cortex, temporal cortex and cerebellum. We measured over 485 000 CpG loci across a diverse set of functionally relevant genomic regions using the Infinium HumanMethylation450 BeadChip and identified four genome-wide significant differentially methylated regions (DMRs) using a bump hunting approach and a permutation-based multiple testing correction method. We replicated 3/4 DMRs identified in our genome-wide screen in a different set of samples and across different brain regions. The DMRs identified in this study represent suggestive evidence for commonly altered methylation sites in ASD and provide several promising new candidate genes.

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Acknowledgements

We thank Daniel Geschwind and Neelroop Parikshak for sharing the PFC and TC samples, obtained from the Autism Tissue Program (ATP) of Autism Speaks, for these analyses. In addition, we would also like to thank the NICHD Brain and Tissue Bank for Neurodevelopmental Disorders at The University of Maryland for providing brain samples from the CBL brain region. This work was supported by the US National Institutes of Health Centers of Excellence in Genomic Science, 5P50HG003233 to APF and Department of Defense (CDMRP) AR080125 to APF and WEK.

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  1. W E Kaufmann

    Present address: 6Current address: Department of Neurology, Children’s Hospital, Boston, MA, USA.,

Authors and Affiliations

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

    C Ladd-Acosta & M D Fallin

  2. Center for Epigenetics, Institute for Basic Biomedical Science, Johns Hopkins School of Medicine, Baltimore, MD, USA

    C Ladd-Acosta, K D Hansen, E Briem, M D Fallin & A P Feinberg

  3. Department of Biostatistics and Institute for Genetic Medicine, Johns Hopkins School of Public Health, Baltimore, MD, USA

    K D Hansen

  4. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    E Briem & A P Feinberg

  5. Kennedy-Krieger Institute, Baltimore, MD, USA

    W E Kaufmann

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Ladd-Acosta, C., Hansen, K., Briem, E. et al. Common DNA methylation alterations in multiple brain regions in autism. Mol Psychiatry 19, 862–871 (2014). https://doi.org/10.1038/mp.2013.114

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