HERVs and ADHD

HERVs. Human endogenous retroviruses. The remnants of our evolutionary struggle with the viruses of the times of our distant ancestors, now part and parcel of our modern-day genome. Yes, genetically, we are all part virus to various extents [so embrace your viral self].

HMS Beagle @ Wikipedia

I've talked HERVs on a few occasions on this blog, in relation both to the autism spectrum conditions (see here) and myalgic encephalomyelitis (ME) (see here).

Without getting too technical, the crux of those posts was to suggest that although those bits of virus in our genomes are not necessarily 'active viruses' (i.e. not able to produce infectious virus or replicate) they may have implications for things like autoimmunity given that HERV proteins are supposedly recognised as 'self' by the almighty MHC [1] and seem to be able to provoke autoimmunity (in mice) [2]. That and the fact that the expression of HERVs may be kept in check by epigenetic means (methylation) [3] and 'hypomethylation [of DNA] = more genomic instability' [4] so, theoretically under certain circumstances could mean HERVs get a chance to start expressing (something). Or that's the theory (I think)...

With all that in mind, I move to the paper by Balestrieri and colleagues [5] (yes, the same group who completed the HERV paper with autism in mind) who discussed some very preliminary data on the expression of certain families of HERVs. Indeed, they reported: "The expression levels of HERV-H are significantly higher in patients with ADHD [attention-deficit hyperactivity disorder] compared to healthy controls".

I can't pretend to know all the ins-and-outs of how one goes about assaying for the expression of HERVs - "expression of retroviral mRNAs from the three HERV families was evaluated in peripheral blood mononuclear cells (PBMCs)" apparently. It was however interesting to see that HERV-H 'over-expression' was "significantly higher in patients with ADHD compared to healthy controls". HERV-H was also the same family reported to be 'more abundantly expressed' in cases of autism.

A search of some of the literature covering HERV-H reveals that it is a gamma-retrovirus (yes, similar to those letters X-M-R-V and that de-discovery issue). In terms of associations and roles, it "contributes to pluripotency in human cells" according to the paper by Santoni and colleagues [6] and their finding of high levels of HERV-H RNA in human embryonic stem cells. The HERV-H family have also been suggested to have immunosuppressive properties [7].

HERV-H has been linked to conditions such as multiple sclerosis as per papers like this one by Christensen [8] which also hinted at how other viruses may 'interact' with HERVs; in that paper concluding that: "retroviruses and herpes viruses have complex interactions". That being said, not all results have arrived at the same conclusion.

I was also particularly interested to read the paper by Shuvarikov and colleagues [9] who seemed to suggest "HERV-H elements as a mechanism of deletion formation", as in genetic deletions. I might be making mountains out of molehills but their case report that HERV-H elements seemed to flank "recurrent, 3.4-Mb, de novo deletions of 3q13.2-q13.31" could potentially lead down some very important paths as intimated in a previous post. The fact that they mention autism as being part and parcel of some of their participant group description is likewise intriguing.  As I've indicated in other posts on this blog where the term 'de novo' has been used, the uncertainty or chance finding of de novo now, might not be so in X numbers of years time. And the future may already be here [10] with schizophrenia in mind.

I'm going to stop there with this quite heavy going post and the chatter about HERVs and ADHD (or autism or anything else). Science is to quite a large extent still feeling it's way around the HERVs and their role - if any - in health and wellbeing. The reported link between the expression of HERVs and a condition as complicated as ADHD needs a lot more work on it before anyone can arrive at any firm conclusions. That being said, I find this to be a fascinating area of science which really does add a new layer of complexity to the whole genetics-environment relationship.

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[1] Lavie L. et al. CpG Methylation Directly Regulates Transcriptional Activity of the Human Endogenous Retrovirus Family HERV-K(HML-2). J. Virol. 2005; 79: 876-883

[2] Perron H. et al. Human Endogenous Retrovirus Protein Activates Innate Immunity and Promotes Experimental Allergic Encephalomyelitis in Mice. PLoS ONE 8(12): e80128. doi:10.1371/journal.pone.0080128

[3] Wilson AS. et al. DNA hypomethylation and human diseases. Biochimica et Biophysica Acta. 2007; 1775: 138–162.

[4] Tugnet N. et al. Human Endogenous Retroviruses (HERVs) and Autoimmune Rheumatic Disease: Is There a Link? Open Rheumatol J. 2013; 7: 13–21.

[5] Balestrieri E. et al. Human endogenous retroviruses and ADHD. World J Biol Psychiatry. 2013 Nov 28. [Epub ahead of print]

[6] Santoni FA. et al. HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology. 2012; 9: 111.

[7] Mangeney M. et al. The full-length envelope of an HERV-H human endogenous retrovirus has immunosuppressive properties. J General Virology. 2001; 82: 2515-2518.

[8] Christensen T. Association of human endogenous retroviruses with multiple sclerosis and possible interactions with herpes viruses. Rev Med Virol. 2005 May-Jun;15(3):179-211.

[9] Shuvarikov A. et al. Recurrent HERV-H-Mediated 3q13.2-q13.31 Deletions Cause a Syndrome of Hypotonia and Motor, Language, and Cognitive Delays. Hum Mutat. 2013 Oct;34(10):1415-23.

[10] Bundo M. et al. Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia. Neuron. 2014. 2 Jan.

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Balestrieri E, Pitzianti M, Matteucci C, D'Agati E, Sorrentino R, Baratta A, Caterina R, Zenobi R, Curatolo P, Garaci E, Sinibaldi-Vallebona P, & Pasini A (2013). Human endogenous retroviruses and ADHD. The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry PMID: 24286278

The gut microbiota and ME/CFS

Continuing a common theme of gut bacteria on this blog, most recently with autism in mind, my attention today turns to a paper by Frémont and colleagues* looking at the gut microbiota in cases of myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS).

Cross my palm @ Wikipedia 

This is not the first time that those trillions of bacterial masters of ours have cropped up on this blog with CFS/ME in mind as per my recent post on yuck factor 10 and the fecal microbiota transplant (FMT) with CFS/ME in mind (see here).

Frémont et al utilised the most commonly used tool of the bacteriologists trade, high-throughput 16S rRNA gene sequencing (see here for an overview** and here for some issues with the method), to classify bacteria derived from a lovely sample medium - stool samples - provided by 43 participants diagnosed with ME/CFS compared with 36 asymptomatic controls.

They reported a few interesting things.

• Because samples were provided by both Belgian and Norwegian participants (both ME/CFS and control groups), the authors reported differences in the type of bacteria between the different country samples. I'm guessing that quite a lot of this variation has to do with environmental factors such as food preferences and the like as per what other studies have shown. We also know for example that what you eat can have a fairly important effect on what bacteria you have in your gut (see here).
• "Norwegians showed higher percentages of specific Firmicutes populations" when looked at as a whole in comparison to the Belgian samples.
• When comparing Norwegian CFS/ME participants with their fellow asymptomatic country-people "patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations". Readers who clicked on the link for more information about Alistipes might recognise the name carried by a particular species, A. finegoldii named in honour of one Sydney Finegold, a regular on the autism-gut bacteria research scene. 
• "In Belgian subjects the patient/control separation was less pronounced, however some abnormalities observed in Norwegian patients were also found in Belgian patients". Not too much more to add there aside from the suggestion that searching for diagnosis-wide biomarkers for a heterogeneous condition like CFS/ME perhaps suffers from the same methodological ills as has been talked about with the autisms in mind (see here). That and the whole brain CFS/ME vs gut CFS/ME subgroup discussions that I've had on this blog. 

Appreciating that this was a relatively small scale study in terms of participant numbers, I'm intrigued by this study and its results. Heterogeneity in presentation and all the myriad of other factors which can and do affect gut bacteria are important interfering factors in any kind of research in this area. Indeed if one compares the gut microbiome with some of the other -omes such as the genome or epigenome, one starts to appreciate the similar issues involved in building up a picture of the underlying pathology behind a condition like CFS/ME in terms of no one gene or epigenetic factor probably working in isolation covering all cases. So it is probably true for the gut microbiome too.

That being said, unlike genes and to a lesser extent the epigenome, where differences are identified in the various phylum/class/order/family/genus/species of bacteria present potentially even in just subgroups of the condition, one would assume that some corrective intervention could be put in place which might, just might, affect the presentation of symptoms. Indeed the authors speculate on "treatments based on gut microbiota modulation (antibiotics, pre and probiotics supplementation)" which brings me to the paper by Groeger and colleagues**** and back to the original paper by Borody and colleagues***** and indeed outside of CFS/ME, that interesting case study on antibiotics and autism which I discussed recently (see here) [no medical advice is given or intended].

To close, Muscial Youth and a blast from the 80s past.

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* Frémont M. et al. High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients. Anaerobe. 2013 Jun 19. pii: S1075-9964(13)00092-9. doi: 10.1016/j.anaerobe.2013.06.002.

** Trichopoulou A. et al. Disparities in food habits across Europe. Proceedings of the Nutrition Society. 2002; 61, 553–558.

*** Větrovský T. & Baldrian P. The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses. PLoS ONE. 2013; 8(2): e57923. doi:10.1371/journal.pone.0057923

**** Groeger D. et al. Bifidobacterium infantis 35624 modulates host inflammatory processes beyond the gut. Gut Microbes. 2013 Jun 21;4(4).

***** Borody TJ. et al. The GI microbiome and its role in Chronic Fatigue Syndrome: A summary of bacteriotherapy. Journal of the Australasian College of Nutritional and Environmental Medicine. 2012; 31: 3-8.

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Frémont M, Coomans D, Massart S, & De Meirleir K (2013). High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients. Anaerobe PMID: 23791918

Autism and the methylome

Q: When is an identical twin not an identical twin? A: Pretty much all the time (at least according to some people) as our increasing understanding of the complexity of genetics stretches and modifies long-held beliefs about the building blocks of life and their role in our health and wellbeing.

DNA methylation differences? @ Wikipedia  

Today I'm talking about identical (monozygotic) twins - siblings derived from one fertilised egg - and how the science of epigenetics might have some interesting implications for autism research as per the study by Chloe Wong and colleagues* (open-access). I should perhaps also direct you to some other interesting research recently discussed in this area too (see here) which might be relevant.

Regular readers will probably already know about my amateur interest in epigenetics (see here and here) and how the area of the epigenome - those chemical marks which have the ability to influence the expression of the genome - has started to yield some potentially important observations. At times I'll admit to being slightly too over-excited at the possibilities of epigenetics. Subsequently brought back down to earth by more sobering accounts (see here**) but not yet ready to poo-poo the whole science just yet***.

I don't want to rehash the whole epigenetic story in this one post, so instead am going to concentrate on the particular area covered by Wong et al and their analysis of the methylome (yes, another -ome for you) which is concerned with the addition of methyl groups to various regions of the genome and how that subsequently alters the expression of genes. DNA methylation has been a sort of peripheral topic in relation to cases of autism for quite some time now; brought to the forefront by all that folic acid (see here) and MTHFR research (see here) and the availability of those lovely methyl groups. Suffice to say that we are still very much at the beginning when it comes to looking at the relationship between all these elements and very complicated conditions like autism.

Anyhow, after that very long introduction (I am only an amateur science blogger after all), a few details from the Wong paper might be in order, bearing in mind it is open-access:

• Part of the UK TEDS initiative and partly sponsored by Autism Speaks who were involved in that recent environmental epigenetics symposium (see here), researchers looked at 50 monozygotic (MZ) twin pairs. It wasn't just a case of 25 twin pairs where one twin was diagnosed with an autism spectrum disorder (ASD) compared with 25 twin pairs where both were concordant for ASD. No, instead the authors looked at a variety of phenotypic combinations based on concordance/discordance for ASD and various core traits based on the Childhood Autism Symptom Test (CAST) schedule. Supplementary table 1 shows the combinations (see here).
• A genome-wide analysis of DNA methylation was undertaken on blood samples provided by participants. I can't pretend to intimately know all the techniques that were employed so won't profess to do so. What I can glean from the paper is that both DNA methylation differences between MZ twin pairs discordant for ASD and analyses between groups scoring high and low on the various core symptom areas were completed with "the aim of identifying real, biologically relevant within-twin and between group DNA methylation differences".
• Results: "ASD is not associated with systemic differences in global DNA methylation". In other words, within the twins, there is quite a high degree of similarity when it comes to patterns of DNA methylation. This might tie in with other work looking at methylation in cases of autism and other family members (see here). 
• When looking at DNA methylation patterns between twin pairs discordant for ASD, specific sites of the genome however seemed to show some variability as a function of ASD diagnosis or not. The authors list the top 50 "differentially methylated CpG sites" (see here) showing gene and position, with a combination of hyper- and hypo-methylated regions identified. Top of the methylation differences pops was the NFYC promoter which was "consistently hypermethylated in affected individuals" (see here for some additional papers on this gene). Hypermethylation by the way, generally means gene silencing as per its function when it comes to transposons (think HERVs). 
• Various other data are presented based on either syndrome or trait specific differences across the twins. I'm not going to go through all of these because, well because that's called plagiarism. I will draw your attention to one particular finding which might be important as they identified "one MZ twin pair, concordant for a very severe autistic phenotype, that appear to represent epigenetic outliers at multiple CpG sites across the genome". I'm immediately drawn back to my autism or autisms post and that all-important phenotypic variability as potentially being relevant here too. That and the tie-up with more structural changes to the genome as per the mention of CNVs and hotspots.

I know I've gone on a bit in the post but this is potentially a very important paper. Not only does it put the epigenome, or at least one part of the epigenome, firmly on the autism research map, but it offers something of a partial explanation for [some of] that 'missing heritability' which was talked about not so many years ago (see here).

The fact also that methylation patterns might be variable both intra-twins and intra-ASD is also important; suggesting that as with more traditional genomic findings in relation to autism, there isn't going to be just one epigenomic factor affecting risk or presentation, but rather a plethora of sites which are hyper- or hypo-methylated, potentially also linked to (affecting?) more structural changes to the genome in cases of ASD.

Don't get me wrong, the same questions remain as are seen in other areas of biological functioning with autism in mind: the heterogeneity, the reliance on diagnosis by observation and note-taking, the (elevated) risk of comorbidities, etc. All of which cloud the waters of association. Distinct however from the question of whether there is anything that can be done when structural changes to the genome are observed (outside of gene therapy for example), when talking about methylation, one speculates that this might be something that lends itself to pharmacotherapy as per the already use of DNA methyltransferase inhibitors for example. Yes, going back to that folic acid-autism link work, the possibility also that environment might help shape gene function and some new light on other external factors (noting that I am not advocating anything at the current time).

So endth the lesson for today.

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* Wong CC. et al. Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits. Molecular Psychiatry. April 2013.

** Ptashne M. Epigenetics: core misconcept. PNAS. April 2013.

*** Fraga MF. et al. Epigenetic differences arise during the lifetime of monozygotic twins. PNAS. 2005; 102: 10604-10609.

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Wong, C., Meaburn, E., Ronald, A., Price, T., Jeffries, A., Schalkwyk, L., Plomin, R., & Mill, J. (2013). Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits Molecular Psychiatry DOI: 10.1038/mp.2013.41

CNV duplication load, hotspots and autism

Viewers here in the UK might remember the catchphrase of one Michael Barrymore on the show 'Strike It Lucky': "What is a hotspot not? A good spot". It is with a rather different kind of hotspot in mind, that I'm posting about today: genomic hotspots and autism with a specific focus on copy number variants.

An intriguing paper by Santhosh Girirajan and colleagues* (open-access) popped up on my Twitter radar recently discussing copy number variant (CNV) load in relation to autism spectrum disorders. Whilst only being an amateur enthusiast when it comes to all things genes and genomic, I can't offer an expert opinion on what CNVs are, just that fairly similar to single-nucleotide polymorphisms (SNPs), we're talking physical alterations to the genome and in particular gains/losses to segments of DNA (I think!)

A hotspot indeed... @ Wikipedia  

I'll start by saying that this is not the first time that CNVs have cropped up on this blog either with autism in mind (see here) or with other conditions such as ADHD (see here) and intellectual disability (ID) in mind (see here).

Indeed readers who looked at that ID link will see that we are talking about another paper from Girirajan following the previous suggestion that ID might be particularly prone to a high CNV load. Keep that in mind for now.

Thankfully the latest paper has been very nicely covered by a ScienceDaily entry (see here with a sigh of relief) so as to patch over my considerable non-expertise in this area. Without plagiarising the paper or SD entry, the general gist of the work was to initially look at CNV data from over 500 people with autism (n=274) or asymptomatic controls (n=242) derived from the CHARGE initiative (see here), to ascertain exactly what the CNV load was and how it might link into some of the signs and symptoms of autism. There was also a further testing group to confirm "the increased duplication load" based on a further cohort of autism and control cases but I'm not going to bore you with all the details.

If I'm reading this right, there were some interesting findings to take from this study:

• Children with autism "exhibited a significantly elevated copy number load, represented principally as an increase in duplicated base pairs found in large CNVs". Importantly, this copy number load seemed to include quite a bit of de novo, so not passed from parents to offspring.
• Duplication over deletion seemed to be the important variable for autism cases, which as the authors note "is associated with genomic variants with more modest functional impact". As per that previous CNV work with ID in mind, I think the authors seemed to be suggesting a sort of sliding scale of phenotypes based on CNV profiles: ID at the more severe end of the spectrum (with more deletions also), autism somewhere in the middle and dyslexia at the less severe end of the spectrum in terms of functioning. I could be wrong and I could be over-simplifying the whole thing so accept my apologies if so.
• Copy number load in autism cases also seemed to show some relationship with certain aspects of behaviour. Significant negative correlations for example, were observed between CNV load and VABS scores in core areas of communication and socialisation. That being said, the correlations were not exactly all that great (p=0.048 and p=0.022 respectively) and should be compared with other gold-standard schedules such as the ADOS that did not turn up anything significant. 
• The notion of genomic 'hotspots' is also raised as a consequence of the results, suggesting that parts of the autistic genome already under the spotlight might be more susceptible to such CNVs. Those words-of-the-hour DNA methylation get a mention alongside the folate story (see here). Personally and with my non-expertise caveat in full working order, I'm also wondering about those archived portions of viruses called HERVs - human endogenous retroviruses - (see this post and this post) which dot the genome and whether they might be contributory in any way, shape or form to any genomic instability in target areas.

Putting aside the complexity of the genome when it comes to autism and the suggestion that we might want to be rethinking how we view the condition** (I've a post coming up on this paper fairly soon), there are some interesting themes emerging from the Girirajan paper. That for example CNV load and the type of CNV (duplication or deletion) might roughly fit into phenotypic differences between inter-related conditions including autism and ID is definitely something worth pursuing in future work. That also such CNVs might tie into genomic hotspot areas is also an important point particularly when it comes to things like systems biology. Lest we also forget the potential importance of any genomic instability and how, with the DNA methylation point in mind, this *might* be attenuated via changes to the environment (remember SAMe)?

To close Chuck Berry and a song about Johnny B Goode and his guitar-playing skills.

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* Girirajan S. et al. Global increases in both common and rare copy number load associated with autism. Hum. Mol. Genet. March 2013.

** Moreno-De-Luca A. et al. Developmental brain dysfunction: revival and expansion of old concepts based on new genetic evidence. The Lancet Neurology. 2013; 12: 406-414.

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Girirajan S, Johnson RL, Tassone F, Balciuniene J, Katiyar N, Fox K, Baker C, Srikanth A, Yeoh KH, Khoo SJ, Nauth TB, Hansen R, Ritchie M, Hertz-Picciotto I, Eichler EE, Pessah IN, & Selleck SB (2013). Global increases in both common and rare copy number load associated with autism. Human molecular genetics PMID: 23535821