Autism is a developmental disorder that’s shrouded in mystery. Its causes are unknown and hotly debated, but some recent detective work hints that through changes in miRNA expression and DNA methylation (DNAm) patterns, there is an epigenetic link.
Autism often brings to mind Dustin Hoffman’s character in Rain Man, who was deeply focused on only a few things (Like watching People’s Court, or counting cards) but in reality, the symptoms and their severity can vary widely. Sometimes, autistic children develop normally, and then suddenly regress while others have problems from the get-go. Those with autism may also have limited language skills, difficulty with social interactions, or develop issues with sleep, digestion, and muscles.
To get at the molecular basis of autism, Valerie Hu’s group at George Washington University Medical Center formed two collaborations to figure out if miRNA expression and DNAm are different in people with autism.
Autism Isn’t All in the Family
A few years ago, Hu and others at The Institute for Genomic Research and Dana-Farber found gene expression differences in identical twins in which one twin had autism and the other didn’t ( called “discordant twins”) (BMC Genomics, 2006). Identical twins have the exact same genes, though, so what gives? The researchers had a hunch that epigenetic mods might explain the results.
Putting the Epigenetic Puzzle Pieces Together
So, Hu followed up on this hunch and joined forces with researchers at NIH to analyze miRNAs (Genome Medicine, April 2010) and collaborated with researchers at City of Hope to study DNAm (FASEB Journal, April 2010). In both studies, they derived lymphoblastoid cell lines from discordant twins and compared these samples with each other, as well as with samples from non-autistic siblings and controls.
Using custom-printed miRNA microarrays, the scientists found 43 miRNAs that were differentially expressed, and identified their possible targets with miRBase Target software. In the Genome Medicine paper, they report:
- Most targets were genes involved in neurological function, but they also got targets involved in conditions associated with autism, such as muscular, circadian, steroid, and gastrointestinal disorders.
- ~1400 (36%) of the differentially expressed genes in the 2006 paper were predicted targets. Most of these had the expected inverse relationship between miRNA and mRNA levels.
- Two of the miRNAs were validated by qRT-PCR. Knockdown and overexpression experiments suggested that ID3 and PLK2 were the in vivo targets of these miRNAs.
In the FASEB Journal article, the researchers used CpG island arrays to profile DNAm globally. Autistic and nonautistic subjects had different patterns. Many of these modified genes were differentially expressed in the 2006 work, and DNAm was inversely related to the gene expression level. Again, genes involved in neurological, digestive, and steroid function were differentially modified. The researchers focused on two of these genes: BCL-2 and RORA.
- Bisulfite sequencing showed that BCL-2 promoters were more highly methylated in autistic subjects than in controls.
- MSP on RORA showed that only RORA promoters in autistic subjects were methylated.
With both studies, some of the differential epigenetic mods were found in both lymphoblastoid cells and in actual autopsy brain samples. The researchers say that this shows that the blood-derived lymphoblasts are good substitutes for brain cells (which is a good thing, since it’s really tough to get living people to donate theirs!).
Research like this makes us think that we’ve only scratched the surface of what epigenetics could be doing in autism, and we’ll be following closely as this mystery unravels.