DNA methylation patterns and autism: buccal up

"The results indicate the presence of a mosaic subpopulation of epigenetically-dysregulated, ectodermally-derived cells in subjects with ASD [autism spectrum disorder]". That was the very clinical primary conclusion reached in the study by Esther Berko and colleagues [1] (open-access here). They looked at DNA methylation patterns in cheek cell samples for a small sample of children diagnosed with an ASD (n=47) "born to mothers aged 35 and over" compared with samples from an asymptomatic control group (n=48) and found some potentially important differences.

Cheek of it.. @ Wikipedia 

Some of the accompanying press for this paper can be found here. As per the headline: "Study shows environmental influences may cause autism in some cases" the results have been suggested to further add to the notion that genetics may not be the be-all-and-end-all of autism, at least some cases of autism. We'll see about that. That alongside the body of research which seems to suggest that offspring of older mums might be at increased risk of being diagnosed with autism (see here) makes for some interesting reading.

Before going on, I should perhaps define a few terms which have or will crop up in this post. So, buccal swabs refers to a way of collecting cells and DNA [non-invasively] from the inside of a person's cheek. Ectoderm refers to the outer layer of germ cells which eventually give rise to hair, skin, the lens of the eye and importantly, the nervous system including neurons and glial cells, as well as the mucus membrane of the mouth. DNA methylation is something which has been covered a few times on this blog (see here and see here) and is part of that wonderful concept of epigenetics and one of the ways that genes are turned on or off depending on their methylation status.

The Berko paper is open-access but a few pointers might be useful:

• Buccal cells were examined as a sort of proxy for brain cells (which generally aren't harvested from live donors). As per the description previously, the ectodermal origins of buccal cells cross that proxy bridge. DNA was extracted from the buccal cells and subjected to various genetic and epigenetic analyses.
• Researchers used the Mosaic Alteration Detection (MAD) algorithm [2] to test "for abnormal chromosome numbers as well as other chromosomal defects". No evidence of chromosome aneuploidy was detected in either cases or controls which kinda ruled out more traditional genetic effects being related to advancing maternal age.
• Methylation was then the name of the game, and as I've talked about on a previous post (see here) various ways and means of looking at the methylation status of those little genetic islands: CpG sites. 
• Results:  "a first pass" approach looking at DNA methylation patterns between the groups identified "3560 differentially methylated GCs". Researchers then further refined their analysis by means of something called bump-hunting which took into account age and ancestry as potential effectors of DNA methylation and something called co-methylation network analysis. They were then left with 15 differentially methylated regions (DMRs) on 14 genes "distinguishing the ASD and TD [typically developing] samples". Even further refinement taking into account the overlapping presence of copy number variations (CNVs) (see here for an explanation) boiled the total down and looked at which genes might be associated with DMRs.
• "The candidate DMRs from the genome-wide analysis were associated with genes, of which many have already been implicated in previous studies with ASD" shown in Table 1 of the paper. Further: "The model that results is of mosaic epigenetic dysregulation affecting the same networks and pathways targeted by mutational mechanisms, creating comparable deleterious effects on neuronal function". In other words, the more traditional genetic mutations noted in other work on some genes in relation to autism might also be complemented by epigenetic changes affecting those gene functions too. 

I found the results of this paper to be absolutely fascinating. Not only that the emphasis was on cells which share some source commonality with those found in the grey-pink matter which has been a primary focus of autism research but also that genetic mutations and epigenetic changes may potentially work synergistically in cases of autism. The added detail that this tied into the seemingly enhanced risk of autism in older mothers [3] (at conception) adds further interest to this work. As the authors noted: "The epigenetic dysregulation observed in these ASD subjects born to older mothers may be associated with aging parental gametes, environmental influences during embryogenesis or could be the consequence of mutations of the chromatin regulatory genes increasingly implicated in ASD". Chromatin by the way, is something of an upcoming star in autism research [4] (open-access here).

Obviously there is quite a bit more work to do in this area not least to test whether the Berko findings are also applicable to children with autism born to younger mothers and any influence from the various overlapping conditions which can and do occur in cases of autism such as epilepsy (see here) or intellectual disability. I also hark back to some interesting work presented at IMFAR this year (2014) by Feinberg and colleagues who talked about age-related methylation changes found in semen as being something to watch when it comes to the older dads and autism risk work (see here) which might point to a cumulative effect. Combined with what is already being reported about methylation status and something like those HERVs in relation to autism (see here) and even ADHD (see here), epigenetics is certainly continuing its rise and rise in autism research [5].

Music then to close. Hey Ya!

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[1] Berko ER. et al. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet. 2014 May 29;10(5):e1004402.

[2] González JR. et al. A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data. BMC Bioinformatics 2011, 12:166

[3] Gillberg C. Maternal age and infantile autism. J Autism Dev Disord. 1980 Sep;10(3):293-7.

[4] Lasalle JM. Autism genes keep turning up chromatin. OA Autism. 2013 Jun 19;1(2):14.

[5] Siniscalco D. et al. Epigenetic Findings in Autism: New Perspectives for Therapy. Int. J. Environ. Res. Public Health. 2013; 10: 4261-4273.

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Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, & Greally JM (2014). Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS genetics, 10 (5) PMID: 24875834