Things often show up where you least expect. Whether it’s finding your keys in the freezer, your phone in the couch, English kings underneath a car park, or the secrets of brain development in spit. Sometimes all you have to do is look.
Previously, the lab of Shiva Singh from the University of Western Ontario developed extensive mouse models of prenatal alcohol exposure that showed that moderate alcohol exposure causes long lasting and brain-specific changes in DNA methylation and ncRNA. In this report, the team examined Buccal swabs from young children with fetal alcohol spectrum disorders (FASD) and found some identical changes to what they had seen in adult mouse brains.
Here’s what they found using human methylation 450K arrays:
- The swabs of FASD children clustered separately from those of carefully matched controls to reveal hundreds of informative CpGs.
- Strangely, the alterations to DNA methylation occurred in genes, functions (ontologies), and pathways related to the brain’s synaptic signaling (glutamatergic synapses) as well as developmental (hippo signaling) and calcium signaling pathways.
- Taking inspiration from the skyscrapers of Dubai, the clustered protocadherins gave a strong signal in the Manhattan plot. This complex locus relies on DNA methylation and CTCF to create alternative transcripts with diversity paralleling that of the immune system and generates individual neuronal identity.
- These findings were replicated via pyrosequencing for select CpGs and verified at the omic level in a separate and more diverse replication cohort.
- Interestingly, buccal epithelial cells and neurons of the adult brain are derived from a common precursor whose potency shifts between epithelial and neuronal state during development. Lead author Ben Laufer says that “these findings highlight the informative nature of buccal swabs for neuroepigenomics and also provide an example of mouse models being efficiently translated to human discovery.”
Laufer also shares that EpigenDx performed the gene-specific DNA methylation pyrosequencing. When examining methylation on the 450K array, many probes are often discarded for containing SNPs, which can alter their performance.
However, pyrosequencing enabled the team to maximize the value of the 450K array by not having to discard these probes because they were now able to examine for the presence of SNPs. “This was critical as some of the most informative probes were known to have CpG SNPs or SNPs in them/nearby” adds Laufer. EpigenDx has a rapidly growing database of over 4000 validated assays for human, mouse, and rat gene loci and extensive custom design experience.
They also have the track record to prove it, with a library of 60 publications using their DNA methylation services that also contains many familiar names.