Transcriptomic and Epigenetic Findings in Autism Figure 1. Autistic brain shows transcriptional heterogeneity and differential expression of genes of mitochondrial oxidative phosphorylation and protein translation. (A) Unsupervised correspondence analysis of whole-genome transcriptome expression data demonstrates that brain region is associated with the greatest source of variability in the data. The second principal component is associated with variability mostly among autistic samples. The first two principal components are listed on the x- and y-axis respectively, with percent of variance explained in parentheses. Bubbles represent individual samples, with area proportional to age, outline to brain region, and color to phenotype. (B) Heatmap of the top 50 differentially expressed probes between autistic and control brain, accounting for brain region, separates most autistic brains from controls (FDR #5%). Rows correspond to probes and columns to samples. The dendrogram represents sample similarity on the basis of the top 50 differentially expressed probes. Probes with log2-fold change .0.7 are listed in table S3. (C) The top 300 differentially expressed probes are enriched for gene ontology annotation clusters corresponding to mitochondrial oxidative phosphorylation and protein translation. ADI-R, Autism Diagnostic Interview-Revised; BA19, Brodmann area 19; CER, cerebellum; PMI, postmortem interval. doi:10.1371/journal.pone.0044736.g001 heterogeneity together with the use of different criteria for sample selection in each study. Because of the known etiological heterogeneity of autism, we designed our study to reduce variability in the data and increase statistical power through stringent subject selection criteria (see Methods). A more heterogeneous sample in other studies could limit the ability to identify differences in the expression of mitochondrial oxidative phosphorylation-related transcripts if the findings that we observed apply only to a subset of autistic persons (eg, males with idiopathic autism). The differences in the results of our study and other transcriptomic analyses of autistic brain might also be due to differences in the regions of brain that were analyzed. It is possible that the differences in metabolic demands or brain region specific pathophysiology could account for differences in expression of mitochondrial genes. The finding of down-regulation of genes of oxidative phosphorylation, if independently confirmed, will be important in future studies of pathophysiology of autistic brain. We also noted significant down-regulation of genes of protein synthesis. This finding suggests a generalized and non-targeted process and may be a result of dysregulation of other pathways. Alterations of neuronal protein synthesis involving selected pathways are increasingly understood to be key aspects of the pathogenesis of some forms of syndromic autism [29] and may be generalizable to many forms of cognitive and behavioral disease [30]. Our data do not inform whether the down-regulation of genes of mitochondrial oxidative phosphorylation or of protein synthesis mainly relates to glia and/or neurons. Of note, the differentially expressed genes of both mitochondrial oxidative phosphorylation and protein translation observed in this study are highly enriched for regulation by HNF4A in transcription factor analysis (p = 1.4E- 8; Fisher’s exact test) (Figure S1). HNF4A is involved in tissue- specific cell differentiation and energy metabolism and has been recently identified as a cerebellar-specific marker of the hypoxia response in mouse brain [31]. To our knowledge, an involvement of HNF4A in the pathophysiology of autism has not been previously noted. Differential Expression of Genes of Synapse and Other Brain Functions Numerous genes of brain development and function have been associated with the pathophysiology of autism with varying levels PLOS ONE | www.plosone.org 4 September 2012 | Volume 7 | Issue 9 | e44736