Brain Transcriptional and Epigenetic Associations with Autism Matthew R. Ginsberg1, Robert A. Rubin2, Tatiana Falcone3, Angela H. Ting 4 , Marvin R. Natowicz1,3,4,5* 1 Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, United States of America, 2 Department of Mathematics, Whittier College, Whittier, California, United States of America, 3 Neurological Institute, Cleveland Clinic, Cleveland, Ohio, United States of America, 4 Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America, 5 Pathology and Laboratory Medicine and Pediatrics Institutes, Cleveland Clinic, Cleveland, Ohio, United States of America Abstract Background: Autism is a common neurodevelopmental syndrome. Numerous rare genetic etiologies are reported; most cases are idiopathic. Methodology/Principal Findings: To uncover important gene dysregulation in autism we analyzed carefully selected idiopathic autistic and control cerebellar and BA19 (occipital) brain tissues using high resolution whole genome gene expression and whole genome DNA methylation microarrays. No changes in DNA methylation were identified in autistic brain but gene expression abnormalities in two areas of metabolism were apparent: down-regulation of genes of mitochondrial oxidative phosphorylation and of protein translation. We also found associations between specific behavioral domains of autism and specific brain gene expression modules related to myelin/myelination, inflammation/immune response and purinergic signaling. Conclusions/Significance: This work highlights two largely unrecognized molecular pathophysiological themes in autism and suggests differing molecular bases for autism behavioral endophenotypes. Citation: Ginsberg MR, Rubin RA, Falcone T, Ting AH, Natowicz MR (2012) Brain Transcriptional and Epigenetic Associations with Autism. PLoS ONE 7(9): e44736. doi:10.1371/journal.pone.0044736 Editor: Nicoletta Landsberger, University of Insubria, Italy Received May 29, 2012; Accepted August 7, 2012; Published September 12, 2012 Copyright: 2012 Ginsberg et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by grants from the Cleveland Clinic Research Program Committee and the Autism Research Institute (www.autism.com/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: natowim@ccf.org Introduction Autism comprises a spectrum of neurodevelopmental disorders characterized by social impairments, language or communication difficulties, and restricted, stereotyped and repetitive behaviors. It is highly prevalent, has an approximately 4:1 male:female predominance, and there is highly variable phenotypic involve- ment in each of the core symptom domains in both genders [1]. Autism has high heritability, with numerous uncommon or rare genetic etiologies noted in about 10% of affected individuals; most cases are idiopathic [2–4]. Recent whole-exome sequencing studies have had limited success in identifying strong effect mutations in many persons with autism [5–9]. The clinical and genetic heterogeneity of autism have complicated attempts to understand its pathophysiology, especially in the majority of cases where autism is considered idiopathic. As non-syndromic autism is largely a disorder of the brain with specificity for particular brain regions and because there is no consensus animal model, studies on carefully selected postmortem human brains are needed and this, in turn, adds to the challenge of uncovering the pathophys- iologic mechanisms of autism. Despite these challenges, recent literature suggests that the initial genetic and/or environmental insults that cause autism converge on a small number of cellular pathways and processes, with data supporting multiple, non-mutually exclusive hypotheses [10–12]. A recent whole genome transcriptomic analysis of autism brain suggested candidate pathways in immune regulation and alternative splicing regulation in the temporal cortex, frontal cortex, and cerebellar vermis [13]. We chose to evaluate potentially disrupted pathways in autistic brain both at the gene expression and DNA methylation levels on a genome-wide scale and selected two other brain regions, cerebellar hemisphere cortex and Brodmann area 19 cortex (BA19, occipital cortex), which have been associated with autism pathogenesis based on histopathologic and neuroradiological analyses [14–16]. Additionally, to maximize the likelihood of determining common pathophysiologic mecha- nisms we chose to study brains from a subset of persons affected with autism – males with idiopathic autism - and explored how molecular heterogeneity within this group related to pathways associated with particular symptom domains. Materials and Methods Subjects and Samples Brain tissue samples from Brodmann area 19 (BA19) occipital cortex and cerebellar hemispheric cortex were procured from subjects and controls through the Autism Tissue Program (ATP, www.atpportal.org) from the Harvard Brain Tissue Resource Center (www.brainbank.mclean.org) and the National Institute for Child Health and Human Development (NICHD) Brain and Tissue Bank (www.btbank.org). Variables selected as candidate PLOS ONE | www.plosone.org 1 September 2012 | Volume 7 | Issue 9 | e44736