Aberrant Genome-Wide DNA Methylation Identified in Disorders Associated with 7q11.23 Copy Number Variation

Background: Autism spectrum disorders (ASD) arise from many different genetic alterations. By understanding all forms of ASD we will be able to piece together a picture of key, common changes that occur in the developing brain, as well as those that are unique and lead to specific phenotypic features. The complex neurodevelopmental disorders that arise from either deletion (Williams syndrome, WS) or duplication (7q11.23 duplication syndrome, Dup7) of 26 genes on chromosome 7q11.23 result in phenotypic spectra that include both core and associated features of ASD and so provide a unique window into genes and pathways that contribute to symptoms. Dup7 has recently been identified as an ASD-associated CNV, with four de novo cases identified during screening of a large autism cohort, and features common to ASD, such as speech disorder and repetitive behaviors, have been reported in other individuals with Dup7. We, and others, have reported socio-communicative difficulties in children with WS that overlap significantly with ASD and >20% of children with WS are classified as “ASD” on the ADOS-2.

Objectives: Since five genes within 7q11.23 have been implicated in epigenetic regulation, we hypothesized that deletion or duplication of this region would disrupt the epigenetic profile of individuals with WS or Dup7, and that this disruption could play an integral role in the ASD phenotypes. Our objective was to investigate epigenetic regulation, specifically DNA methylation, in these disorders.

Methods: We measured genome-wide DNA methylation in whole blood from 20 children with WS, 10 with Dup7 and 15 age- and sex-matched typically developing controls, using the Infinium HumanMethylation450 array from Illumina. Differential methylation was assessed using a stringent cut off of 17% gain or loss of methylation (adjusted p≤0.05). The functional impact was assessed using real time PCR of differentially methylated (DM) genes from whole blood RNA.

Results: We identified over 1,000 DM probes across the WS and Dup7 cohorts that correspond to approximately 500 unique genes. Many of the DM probes span genes involved in neurodevelopment. Hierarchical clustering of the methylation profiles of participants with WS or Dup7 correctly grouped each individual with his/her respective syndrome, and distinct from controls, suggesting the methylation differences may contribute to the phenotypic differences between these disorders. Moreover, of the 46 DM probes that overlapped between WS and Dup7, the majority showed opposite levels of methylation, suggesting a dose-dependent change in DNA methylation at these sites. For the few DM genes that were expressed in blood we showed corresponding changes in expression level.

Conclusions: We have identified aberrant genome-wide DNA methylation in these deletion and reciprocal duplication syndromes with features of ASD. This study identified striking differences in methylation profiles, with corresponding changes in gene expression, suggesting that epigenetic pathways may be involved in pathogenesis and confirming that one or more genes within 7q11.23 is important for proper DNA methylation at specific sites. Future studies will involve correlative epigenotype-phenotype analyses to understand the impact of dysregulated genes and pathways on ASD features in children with WS or Dup7.