Making Sense of Abnormal EEGs in Autism

There is no medical consensus about what to do with people who have subclinical epileptiform discharges (SEDs) on their EEG. That is people who do not have seizures but have an abnormal EEG. There is evidence to support the use of anti-epileptic drugs (AEDs) in such people.

About 5% of the general population have SEDs, but a far higher number of people with autism have SEDs.

You are more likely to detect epileptiform activity depending on which test you use. Magnetoencephalography (MEG) detects the most abnormalities, followed by a sleep EEG and then an EEG with a subject wide awake.

It had been thought that epileptiform activity (SEDs) was more common in regressive autism, but that is no longer thought to be the case. It even briefly had a name, Autistic Epileptiform Regression (AER). Subsequent studies indicate that regression is not relevant to subclinical epileptiform discharges (SEDs).

Estimates of prevalence still vary dramatically from Dr Chez at 60% to others believing it is 20-30%.

Epileptiform activity without seizures does also occur in about 5% of neurotypical people.

Dr Chez and some others believe in treating epileptiform activity with anti-epileptic drugs (AEDs), with valproate being the popular choice. Some neurologists believe in leaving SEDs untreated. 

Personally I would consider minor epileptiform activity in autism as pre-epilepsy. We know that about 30% of those with more severe autism will develop epilepsy and we know that in many cases when they start to receive AEDs their autism tends to moderate.

We know that an excitatory/inhibitory (E/I) imbalance is at the core of many types of autism and we should not be surprised that brains in an excitatory state produce odd electrical activity; rather we should be expecting it.

There are different types of possible E/I imbalance in the brain and there are very many different biological mechanisms that can trigger seizures. So nothing is simple and exceptions may be more likely than valid generalizations. So we should not be surprised that in one child valproate normalized their EEG, while in another it makes it worse.

In this post we review the far from conclusive literature.

I think that everything should be done to avoid the first seizure in a child with autism, for some people this may possible using bumetanide, but for others very likely entirely different therapy will be needed. The first seizure seems to lower the threshold at which further seizures may occur. 

Valproate appears to be the preferred AED, but in some people it can actually make epileptiform activity worse. In some people the Modified Atkins Diet (MAD) has normalized epileptiform activity, this is not a surprise given that this diet and the more complex ketogenic diet are successfully used to treat epilepsy.

If an AED can normalize the EEG result and at the same time improve behavior or cognition, it would seem a good choice.

It would be interesting if the Bumetanide researchers carried out a before and after sleep EEG in their autism clinical trials, along with the IQ test that I suggested to them a long time ago. 

EEG changes associated with autistic spectrum disorders 

Autism Spectrum Disorders (ASD) are an etiologically and clinically heterogeneous group of neurodevelopmental disorders. The pathophysiology of ASD remains largely unknown. One essential and well-documented observation is high comorbidity between ASD and epilepsy. Electroencephalography (EEG) is the most widely used tool to detect epileptic brain activity. The EEG signal is characterized by a high temporal resolution (on the order of milliseconds) allowing for precise temporal examination of cortical activity. This review addresses the main EEG findings derived from both the standard or qualitative (visually inspected) EEG and the quantitative (computer analyzed) EEG during resting state in individuals with ASD. The bulk of the evidence supports significant connectivity disturbances in ASD that are possibly widespread with two specific aspects: over-connectivity in the local networks and under-connectivity in the long-distance networks. Furthermore, the review suggested that disruptions appear more severe in later developing parts of the brain (e.g., prefrontal cortex). Based on available information, from both the qualitative and quantitative EEG literature, we postulate a preliminary hypothesis that increased cortical excitability may contribute to the significant overlap between ASD and epilepsy and may be contributing to the connectivity deviations noted. As the presence of a focal epileptic discharge is a clear indication of such hyperexcitability, we conclude that the presence of epileptic discharges is a potential biomarker at least for a subgroup of ASD.

Finally, it is not known whether currently available seizure medications are effective in normalizing hyperexcitable brain tissue that has not yet become capable of inducing seizures. Scattered reports suggest that a few of these medications may have some efficacy in this regards but further research is needed to examine these efficacies, particularly in newly diagnosed ASD patients.  

Predictive Value of Isolated Epileptiform Discharges for a Favorable Therapeutic Response to Antiepileptic Drugs in Nonepileptic Psychiatric Patients

Summary: The efficacy of antiepileptic drugs (AEDs) in treating behavioral symptoms in nonepileptic psychiatric patients with abnormal EEGs is currently unknown. Although isolated epileptiform discharges have been reported in many psychiatric conditions, they are most commonly observed in patients with aggression, panic, or autistic spectrum disorders. The literature search was guided by 3 criteria: (1) studies had patients who did not experience seizures, (2) patients had EEGs, and (3) an AED was administered. Most important finding is that the number of “controlled” studies was extremely small. Overall, most reports suggest that the use of an AED can be associated with clinical and, at times, improved EEG abnormalities. Additionally, six controlled studies were found for other psychiatric disorders, such as learning disabilities with similar results. Overall, the use of anticonvulsants to treat nonepileptic psychiatric patients needs further controlled studies to better define indications, adequate EEG work-up, best AED to be used, and optimal durations of treatment attempts.  

What does the Simons Foundation have to say? They are funding a clinical trial. 

Treating autism and epileptic discharges with valproic acid 

Spence and her collaborator, Greg Barnes at Vanderbilt Medical Center in Nashville, plan to test whether an anticonvulsant medication (valproic acid, also known as divalproex sodium or Depakote) can be used to treat children with autism and epileptiform EEGs. The researchers aim to recruit 30 participants between 4 and 8 years old who have been diagnosed with an autism spectrum disorder and who do not have epilepsy or metabolic disorders.

The views of the US National Institute of Mental Health:-  

The Role of Epilepsy and Epileptiform EEGs in Autism Spectrum Disorders

Autism is a neurodevelopmental disorder of unknown etiology characterized by social and communication deficits and the presence of restricted interests/repetitive behaviors. Higher rates of epilepsy have long been reported, but prevalence estimates vary from as little as 5% to as much as 46%. This variation is probably the result of sample characteristics that increase epilepsy risk such as sample ascertainment, lower IQ, the inclusion of patients with non-idiopathic autism, age, and gender. However, critical review of the literature reveals that the rate in idiopathic cases with normal IQ is still significantly above the population risk suggesting that autism itself is associated with an increased risk of epilepsy. Recently there has been interest in the occurrence of epileptiform electroencephalograms (EEGs) even in the absence of epilepsy. Rates as high as 60% have been reported and some investigators propose that these abnormalities may play a causal role in the autism phenotype. While this phenomenon is still not well understood and risk factors have yet to be determined, the treatment implications are increasingly important. We review the recent literature to elucidate possible risk factors for both epilepsy and epileptiform EEGs. We then review existing data and discuss controversies surrounding treatment of EEG abnormalities.

The now disputed AER subgroup:- 

Autistic epileptiform regression

Autistic regression is a well known condition that occurs in one third of children with pervasive developmental disorders, who, after normal development in the first year of life, undergo a global regression during the second year that encompasses language, social skills and play. In a portion of these subjects, epileptiform abnormalities are present with or without seizures, resembling, in some respects, other epileptiform regressions of language and behaviour such as Landau-Kleffner syndrome. In these cases, for a more accurate definition of the clinical entity, the term autistic epileptifom regression has been suggested.

As in other epileptic syndromes with regression, the relationships between EEG abnormalities, language and behaviour, in autism, are still unclear. We describe two cases of autistic epileptiform regression selected from a larger group of children with autistic spectrum disorders, with the aim of discussing the clinical features of the condition, the therapeutic approach and the outcome.

Dr Chez has a long involvement and his findings have evolved:-

In 1999:- 

Magnetoencephalographic patterns of epileptiform activity in children with regressive autism spectrum disorders. 

Background. One-third of children diagnosed with autism spectrum disorders (ASDs) are reported to have had normal early development followed by an autistic regression between the ages of 2 and 3 years. This clinical profile partly parallels that seen in Landau-Kleffner syndrome (LKS), an acquired language disorder (aphasia) believed to be caused by epileptiform activity. Given the additional observation that one-third of autistic children experience one or more seizures by adolescence, epileptiform activity may play a causal role in some cases of autism.

Objective. To compare and contrast patterns of epileptiform activity in children with autistic regressions versus classic LKS to determine if there is neurobiological overlap between these conditions. It was hypothesized that many children with regressive ASDs would show epileptiform activity in a multifocal pattern that includes the same brain regions implicated in LKS.

Design. Magnetoencephalography (MEG), a noninvasive method for identifying zones of abnormal brain electrophysiology, was used to evaluate patterns of epileptiform activity during stage III sleep in 6 children with classic LKS and 50 children with regressive ASDs with onset between 20 and 36 months of age (16 with autism and 34 with pervasive developmental disorder–not otherwise specified). Whereas 5 of the 6 children with LKS had been previously diagnosed with complex-partial seizures, a clinical seizure disorder had been diagnosed for only 15 of the 50 ASD children. However, all the children in this study had been reported to occasionally demonstrate unusual behaviors (eg, rapid blinking, holding of the hands to the ears, unprovoked crying episodes, and/or brief staring spells) which, if exhibited by a normal child, might be interpreted as indicative of a subclinical epileptiform condition. MEG data were compared with simultaneously recorded electroencephalography (EEG) data, and with data from previous 1-hour and/or 24-hour clinical EEG, when available. Multiple-dipole, spatiotemporal modeling was used to identify sites of origin and propagation for epileptiform transients.

Results. The MEG of all children with LKS showed primary or secondary epileptiform involvement of the left intra/perisylvian region, with all but 1 child showing additional involvement of the right sylvian region. In all cases of LKS, independent epileptiform activity beyond the sylvian region was absent, although propagation of activity to frontal or parietal regions was seen occasionally. MEG identified epileptiform activity in 41 of the 50 (82%) children with ASDs. In contrast, simultaneous EEG revealed epileptiform activity in only 68%. When epileptiform activity was present in the ASDs, the same intra/perisylvian regions seen to be epileptiform in LKS were active in 85% of the cases. Whereas primary activity outside of the sylvian regions was not seen for any of the children with LKS, 75% of the ASD children with epileptiform activity demonstrated additional nonsylvian zones of independent epileptiform activity. Despite the multifocal nature of the epileptiform activity in the ASDs, neurosurgical intervention aimed at control has lead to a reduction of autistic features and improvement in language skills in 12 of 18 cases.

Conclusions. This study demonstrates that there is a subset of children with ASDs who demonstrate clinically relevant epileptiform activity during slow-wave sleep, and that this activity may be present even in the absence of a clinical seizure disorder. MEG showed significantly greater sensitivity to this epileptiform activity than simultaneous EEG, 1-hour clinical EEG, and 24-hour clinical EEG. The multifocal epileptiform pattern identified by MEG in the ASDs typically includes the same perisylvian brain regions identified as abnormal in LKS. When epileptiform activity is present in the ASDs, therapeutic strategies (antiepileptic drugs, steroids, and even neurosurgery) aimed at its control can lead to a significant improvement in language and autistic features. autism, pervasive developmental disorder–not otherwise specified, epilepsy, magnetoencephalography, Landau-Kleffner syndrome.

2004

Frequency of EEG abnormalities in age-matched siblings of autistic children with abnormal sleep EEG patterns

Epileptiform activity in sleep has been described even in the absence of clinical seizures in 43–68% of patients with autistic spectrum disorders (ASDs). Genetic factors may play a significant role in the frequency of epilepsy, yet the frequency in normal age-matched controls is unknown. We studied overnight ambulatory electroencephalograms (EEGs) in 12 nonepileptic, nonautistic children with a sibling with both ASDs and an abnormal EEG. EEG studies were read and described independently by two pediatric epileptologists; 10 were normal studies and 2 were abnormal. The occurrence of abnormal EEGs in our sample (16.6%) was lower than the reported occurrence in children with ASDs. Further, the two abnormal EEGs were of types typically found in childhood and were different from those found in the ASD-affected siblings. The lack of similarity between sibling EEGs suggests that genetic factors alone do not explain the higher frequency of EEG abnormalities reported in ASDs.

2006:

Frequency of epileptiform EEG abnormalities in a sequential screening of autistic patients with no known clinical epilepsy from 1996 to2005. 

Abstract

Autism spectrum disorders (ASDs) affect 1 in 166 births. Although electroencephalogram (EEG) abnormalities and clinical seizures may play a role in ASDs, the exact frequency of EEG abnormalities in an ASD population that has not had clinical seizures or prior abnormal EEGs is unknown. There is no current consensus on whether treatment of EEG abnormalities may influence development. This retrospective review of 24-hour ambulatory digital EEG data collected from 889 ASD patients presenting between 1996 and 2005 (with no known genetic conditions, brain malformations, prior medications, or clinical seizures) shows that 540 of 889 (60.7%) subjects had abnormal EEG epileptiform activity in sleep with no difference based on clinical regression. The most frequent sites of epileptiform abnormalities were localized over the right temporal region. Of 176 patients treated with valproic acid, 80 normalized on EEG and 30 more showed EEG improvement compared with the first EEG (average of 10.1 months to repeat EEG).

  

An easy to read two page review paper: 

EEG Abnormalities in Autism: What is the Significance 

Many authors focused their research on the relationship between EEG abnormalities and autistic regression. Our analysis included only studies that involved autistic children with and without regression, i.e. clinically non-selected samples. We excluded studies involving only children with regression, or only children with EEG abnormalities. A summary of our findings is presented in Table 1.

A large majority of the studies (7 of 9 studies) did not find any significant relationship between EEG abnormalities and autistic regression. Only two studies were positive [10,11]. Of all the studies, Tuchman & Rapin [10] had the largest sample (585 children) but only part of the sample (392 children) had EEGs available (i.e. sleep EEGs; only sleep EEGs were performed in this study). Readers of the Tuchman & Rapin [10] study should note that the overall rate of epilepsy in the autistic sample was quite low (11%), as was the rate of epileptiform EEG abnormalities in non-epileptic autistic patients (15%). In comparison, other studies listed in our summary gave higher rates of epileptiform abnormalities in non-epileptic autistic children, 19% [12], 22% [13], and 24% [14]. The overall rate of epileptiform EEG abnormalities in the whole sample (21%) was also very low, where other comparable studies were in the range of 28 - 48% [5,11,14-17].  

What about Keppra (Levetiracetam) ? Here we have a clinical trial

Levetiracetam is associated with decrease in subclinical epileptiform discharges and improved cognitive functions in pediatric patients with autism spectrum disorder 

Subclinical epileptiform discharges (SEDs) are common in pediatric patients with autism spectrum disorder (ASD), but the effect of antiepileptic drugs on SEDs in ASD remains inconclusive. This physician-blinded, prospective, randomized controlled trial investigated an association between the anticonvulsant drug levetiracetam and SEDs in children with ASD.

Methods

A total of 70 children with ASD (4–6 years) and SEDs identified by electroencephalogram were randomly divided into two equal groups to receive either levetiracetam and educational training (treatment group) or educational training only (control). At baseline and after 6 months treatment, the following scales were used to assess each individual’s behavioral and cognitive functions: the Chinese version of the Psychoeducational Profile – third edition (PEP-3), Childhood Autism Rating Scale (CARS), and Autism Behavior Checklist (ABC). A 24-hour electroencephalogram was recorded on admission (baseline) and at follow-up. The degree of satisfaction of each patient was also evaluated.

Results

Relative to baseline, at the 6-month follow-up, the PEP-3, CARS, and ABC scores were significantly improved in both the treatment and control groups. At the 6-month follow-up, the PEP-3 scores of the treatment group were significantly higher than those of the control, whereas the CARS and ABC scores were significantly lower, and the rate of electroencephalographic normalization was significantly higher in the treatment group.

Conclusion

Levetiracetam appears to be effective for controlling SEDs in pediatric patients with ASD and was also associated with improved behavioral and cognitive functions. 

Levetiracetam as an alternative therapy for Tourette syndrome 

Levetiracetam

Levetiracetam (LEV) is a broad-spectrum antiepileptic agent that has been used effectively for a variety of seizure types in adults and children, and for different psychiatric disorders.39,40

LEV does not have a direct effect on GABA receptor-mediated responses. In vitro findings reveal that LEV behaves as a modulator of GABA type A and of the glycine receptors, suppressing the inhibitory effect of other negative modulators (beta-carbolines and zinc). LEV inhibits the ability of zinc and beta-carbolines to interrupt chloride influx, an effect that enhances chloride ion influx at the GABA type A receptor complex.

And Lamictal (Lamotrigine)? 

This study is in general autism, not autism with epileptiform activity:- 

Lamotrigine therapy for autistic disorder: a randomized, double-blind, placebo-controlled trial 

In autism, glutamate may be increased or its receptors up-regulated as part of an excitotoxic process that damages neural networks and subsequently contributes to behavioral and cognitive deficits seen in the disorder. This was a double-blind, placebo-controlled, parallel group study of lamotrigine, an agent that modulates glutamate release. Twenty-eight children (27 boys) ages 3 to 11 years (M = 5.8) with a primary diagnosis of autistic disorder received either placebo or lamotrigine twice daily. In children on lamotrigine, the drug was titrated upward over 8 weeks to reach a mean maintenance dose of 5.0 mg/kg per day. This dose was then maintained for 4 weeks. Following maintenance evaluations, the drug was tapered down over 2 weeks. The trial ended with a 4-week drug-free period. Outcome measures included improvements in severity and behavioral features of autistic disorder (stereotypies, lethargy, irritability, hyperactivity, emotional reciprocity, sharing pleasures) and improvements in language and communication, socialization, and daily living skills noted after 12 weeks (the end of a 4-week maintenance phase). We did not find any significant differences in improvements between lamotrigine or placebo groups on the Autism Behavior Checklist, the Aberrant Behavior Checklist, the Vineland Adaptive Behavior scales, the PL-ADOS, or the CARS. Parent rating scales showed marked improvements, presumably due to expectations of benefits

  

Conclusion

What would be nice to know is whether epileptiform activity is a precursor to seizures, in the way that atopic dermatitis is often a precursor to developing asthma. Perhaps by treating epileptiform activity, some people could avoid ever developing epilepsy.

As I have pointed out before, I think that treating the E/I imbalance in autism with Bumetanide may well reduce the likelihood of later developing epilepsy.

In people with epileptiform activity but no seizures, treatment with AEDs can often normalize this activity within a few years.  Does the possible autism benefit correlate with this normalization? Or do you need to maintain the AED treatment even after the epileptiform activity has gone?

Do some people with autism, but no epileptiform activity, also demonstrate behavioral improvement on AEDs? I suspect some might, but it will depend on the AED.

Since medicine does not fully understand how most AEDs work and there are very many types of epilepsy, we cannot really expect concrete answers.

AEDs help many people with seizures, but a substantial number of people have seizures that do not respond to standard AEDs. Matching the AED to the person with seizures is more art than science and I would call it trial and error.

I did write a post a long time ago on the benefit of low dose AEDs in people with autism, but without seizures.  Given the many and varied effects of AEDs, it is not surprising that some people benefit.

The side effects of AEDs vary widely and some look more suitable than others for people that do not actually have seizures.

You might think based on the currently understanding of how Keppra works, it would not be helpful in someone that responds to Bumetanide.  But anecdotally people do respond to both, so most likely Keppra’s mode of action is not quite what we think it is.

So just like a neurologist applies trial and error to find an effective therapy for his patients, the same method can be applied to those with autism.

Clearly some people with autism do benefit from Valproate, others from Keppra and others from Lamotrigine. In my autism Polypill there is a little Potassium Bromide, the original AED from the 19^th century.

If your neurologist does not want to treat your child's sub-clinical epileptiform activity, suggest he or she reads the literature and the very recent clinical trial using Keppra.  It is not guaranteed to improve autism, but you have a pretty good chance that one AED will help.

Therapeutic Epigenetics in Autism and Junk DNA

Epigenopathies were introduced in an earlier post

Today’s post takes another dip into the genetics of autism and currently existing therapies that could be re-purposed for autism.  We also see that many secrets remain beyond the 3% of your DNA that usually gets all the research attention.  The remaining 97% is not junk after all.

There was an earlier post on this blog that introduced Epigenetics.  It is not such a complicated subject, just think about it as little tags on your DNA that turn genes on/off usually when they should not be, but there remains the possibility to use epigenetics for good.  In people with under-expression of an important gene you could “tag it” and then increase its expression.

The exome is the part of your DNA that encodes the various proteins needed to build your body.  The remaining 97% of your DNA was once thought to be just junk; we saw in recent post that one part contains enhancers and silencers that control expression of the genes in the 3% that is the exome.

A recent study of gene expression in neurological conditions including autism showed just how broadly disturbed gene expression is.

Post-mortem transcriptomes from patients with Alzheimer'sdisease, Autism and Schizophrenia show distinctive cellular phenotypes.

(A) Consistent fold enrichments were found for each cell type across fourteen cortical and three subcortical brain regions of Alzheimer's patients. The box plots mark the distribution of cellular fold enrichments across all the brain regions examined. Asterisks mark that the fold enrichment for each cell type that was found to be significantly non-zero with p < 0.05. (B) Two independent autism studies show the same cellular phenotypes, including upregulation of glial cells and downregulation of neurons. Asterisks mark those cell types found to be significantly differential with p < 0.05 after BH correction over all groups.

Here I am making the point that even though only a handful of genes may have an identifiable dysfunction, a much broader range of genes seem to be affected, as we see in the wide range of over and under expressed genes.

While it would be logical to think about a specific dysfunction needing a therapy that targets just that gene, this appears not to be necessary.

It appears that downstream processes may be the most damaging/relevant, for example disturbances in Protein Kinase A and C (PKA and PKC) may play a key role in many cases of regressive autism, and this will feature in its own post, because it would be treatable today. 

Reduced activity of protein kinase C in the frontal cortex of subjects with regressive autism: relationship with developmental abnormalities.

Brain Region–Specific Decrease in the Activity and Expression of Protein Kinase A inthe Frontal Cortex of Regressive Autism

 

Both the above papers are by Abha and Ved Chauhan.  I put Abha on my Dean’s list long ago.  I did have a discussion with her a while back.  She is clearly a very nice person and intellectually towers over the Curemark lady (Joan Fallon) who gets $40 million to play with her pancreatic enzymes, but never publishes anything except very superficial patents.

I think for $40 million Abha and Ved could figure it all out.

PKB, otherwise known as Akt is also very relevant to some types of autism.

Tamoxifen, recently shown to reverse autism in a SHANK3 mouse model, is a PKC inhibitor.

Another epigenetic drug, Theophylline activates PKA.

Akt, also known as protein kinase B (PKB), is a central node in cell signaling downstream of growth factors, cytokines, and other cellular stimuli. Aberrant loss or gain of Akt activation underlies the pathophysiological properties of a variety of complex diseases, including type-2 diabetes and cancer.

If you could identify if a particular person was hypo/hyper in PKA, PKB and PKC, this might well open the door to an effective treatment.

Research on PKB, also known as AKT

Dysregulation of theIGF-I/PI3K/AKT/mTOR signaling pathway in autism spectrum disorders.

Decreased Phosphorylated Protein Kinase B (Akt) inIndividuals with Autism Associated with High Epidermal Growth Factor Receptor(EGFR) and Low Gamma-Aminobutyric Acid (GABA)

And a paper from the clever Japanese:-

Roles of PTEN/PI3K/AKT/GSK3β Pathway in Neuron Signaling Involved in Autism

Autism spectrum disorder is a set of neurodevelopmental disorders in terms of prevalence, morbidity and impact to the society, which is characterized by intricate behavioral phenotype and deficits in both social and cognitive functions. The molecular pathogenesis of autism spectrum disorder has not been well understood, however, it seems that PI3K, AKT, and its downstream molecules have crucial roles in the molecular pathogenesis of autism spectrum disorder. The PI3K/AKT signaling pathway plays an important role in the regulation of cell proliferation, differentiation, motility, and protein synthesis. Deregulated PI3K/AKT signaling has also been shown to be associated with the autism spectrum disorder. Discovery of molecular biochemical phenotypes would represent a breakthrough in autism research. This study has provided new insight on the mechanism of the disorder and would open up future opportunity for contributions to understand the pathophysiology

For those who favour dietary intervention:-

  
Based on the above chart curcumin should likely be good for my N=1 case of autism. Time will tell.

Consequences of upstream dysfunctions

So it might be better to consider autism as a disease of wider downstream gene expression, rather than necessarily of “faulty” genes.  Modulating the resulting wider gene expression may be much more realistic than fixing individual genes.

It is certainly plausible that the body has its own protective self-repair mechanism that might be somehow re-energized. Some people have pondered why so many highly intelligent mathematicians and computer scientists seem have relatives with autism.  The clever genes do associate with a type of autism plus ID/MR.  It was suggested that protective genetic changes might be in play, so that the people with the most genetic variance are actually the family members without the autism.

This does remain conjecture, but as more whole genome data is collected we are seeing some interesting findings.

A fascinating very recent study that looked at a group of 53 families with autism using the traditional approach of whole exome sequencing and also microarray. 

Using these methods, that are the current gold standard, the researchers found very little.  Dysfunctions in the 700 known autism genes were not detected.

However using more expensive whole genome sequencing, dysfunctions were identified in the “DNA junk” zone very close beside the known autism genes.  The researchers were then able to identify the genetic cause of 30% of the cases, a big improvement on 0%.  I expect if they looked a little harder the 30% would be higher.

“We performed whole-genome sequencing (WGS) of 208 genomes from 53 families affected by simplex autism.”

“For the majority of these families, no copy-number variant (CNV) or candidate de novo gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequencing (WES).

Comparing the sequences of the individuals with autism and those of their unaffected siblings, the researchers found that people with autism are more likely to have genetic variants — either single base-pair changes in the sequence or small CNVs — in swaths of DNA abutting known autism genes. But the researchers only found the variants after they restricted their search to regions of the genome already implicated in autism, and even then the statistical significance is modest.

Sequencing whole genomes could reveal the genetic cause of autism in as much as 30 percent of people for whom faster and cheaper sequencing methods come up short

“It’s increasing power even in areas that are supposed to be covered by whole-exome sequencing,” says Peixoto. “It seems that it’s clear that whole-genome sequencing will become the standard.”

Spaces near genes may harbor pitfalls for autism

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

One specific microRNA has strong links to autism spectrum disorder, say TSRI scientists

Epigenopathies

Many diseases have an epigenetic component. The severe progressive asthma that is COPD is a well-known example.  It appears that smoking in middle age often leads to permanent epigenetic changes that come back to haunt often then non-smokers in old age.  Even though they have not smoked for twenty years, there oxidative stress response has been permanently modified.  This results in a kind of steroid resistance, so that usually reliable drug therapies fail to work. 

It is thought that autism has an epigenetic component.  This would do some way to explaining 30-40% of the increase in prevalence in recent years that is not explained by ever widening diagnostic criteria.

Because epigenetic changes can be heritable and can be accumulated from all kinds of exposures, even simple ones like severe emotional stress and pollution, you can reconcile autism as being primarily a genetic condition even though incidence has clearly risen within one or two generations. So you can have an “epigenetic epidemic”, so to speak.

Epigenetics as a therapy

While much is written about epigenetic change being bad, it could also be good.

There are many known substances that affect gene expression; some are very target specific which is useful.

This answers a recent issue raised by a reader of this blog who did exome sequencing. What is the point of discovering a genetic dysfunction if there is no therapy? Medicine is some decades behind science, better to know what gene is affected because you well be able to affect its expression, you just need some help from Google.

Epigenetic therapy could be used to remove unwanted tags, but it could also be used to leave new ones to upregulate under-expressed genes.

Such epigenetic therapy is already a reality in COPD and is being considered for rare single autisms where one copy of the gene is not functional, so turn up the volume on the remaining copy.

As we saw in the post on epigenetics, one potential category of drugs are HDAC inhibitors, these would affect one epigenetic mechanism.

There are many such HDAC inhibitors and most have other modes of action, so you cannot be sure what is giving the noted effect.

Valproate

This epilepsy drug has numerous effects including as a HDAC inhibitor.  Given to mothers during pregnancy it can cause autism in the offspring, but when given to the affected offspring the autism can be reduced.

Valproate is given off label to treat autism even when no epilepsy is present.

As we saw in the comments section, long term valproate se can have side effects.

Sulforaphane

This substance derived from broccoli and patented by Johns Hopkins, is another HDAC inhibitor.  It also upregulates Nrf2, which turns on the oxidative response genes.  This was proposed as a COPD therapy by Professor Barnes.

We saw in a post that for Nrf2 to have its full effect there needed to be enough of a protein called DJ-1.  You can increase DJ-1 expression with cinnamon (sodium benzoate).

That was one reason to think that cinnamon would complement Sulforaphane as a therapy for both COPD and some autism.

Sodium Butyrate

Sodium Butyrate is an HDAC inhibitor that is available as a supplement. We came across it in an earlier post as a precursor to butyric acid.  Butyric acid plays a role in the permeability of the gut and the Blood Brain Barrier (BBB).  It also seems to protect from auto immune disease.

Butyrate is fed to millions of farm animals every day to increase their resistance to auto-immune disease.

Butyric acid is produced naturally in the gut by the bacteria living there, however the amount can be increased by the uses of a particular probiotic-bacteria.

This would support the uses of sodium butyrate and the Miyari 588 bacteria.

I have on my to-do-list to investigate higher doses of Miyari 588, but having read the comment by Alli that 500 mg of sodium butyrate is effective, I will try that first.  She also found higher doses ineffective, which was the same in a mouse study published last November,

The study below highlights which genes were down-regulated and which were up-regulated, the overall effect was beneficial

Sodium butyrate attenuate ssocial behavior deficits and modifies the transcription ofinhibitory/excitatory genes in the frontal cortex of an autism model.

 

The core behavioral symptoms of Autism Spectrum Disorders (ASD) include dysregulation of social communication and the presence of repetitive behaviors. However, there is no pharmacological agent that is currently used to target these core symptoms. Epigenetic dysregulation has been implicated in the etiology of ASD, and may present a pharmacological target. The effect of sodium butyrate, a histone deacetylase inhibitor, on social behavior and repetitive behavior, and the frontal cortex transcriptome, was examined in the BTBR autism mouse model. A 100 mg/kg dose, but not a 1200 mg/kg dose, of sodium butyrate attenuated social deficits in the BTBR mouse model. In addition, both doses decreased marble burying, an indication of repetitive behavior, but had no significant effect on self-grooming. Using RNA-seq, we determined that the 100 mg/kg dose of sodium butyrate induced changes in many behavior-related genes in the prefrontal cortex, and particularly affected genes involved in neuronal excitation or inhibition. The decrease in several excitatory neurotransmitter and neuronal activation marker genes, including cFos Grin2b, and Adra1, together with the increase in inhibitory neurotransmitter genes Drd2 and Gabrg1, suggests that sodium butyrate promotes the transcription of inhibitory pathway transcripts. Finally, DMCM, a GABA reverse agonist, decreased social behaviors in sodium butyrate treated BTBR mice, suggesting that sodium butyrate increases social behaviors through modulation of the excitatory/inhibitory balance. Therefore, transcriptional modulation by sodium butyrate may have beneficial effects on autism related behaviors.

  

Theophylline

Theophylline is an old asthma drug that is an HDAC inhibitor.

At low doses it is now being trialled as an epigenetic add-on therapy in COPD.  It pretty obviously does work, but data needs to be collected to measure how effective it is and what is the best dose.

It shows how the COPD researchers/clinicians like Professor Barnes are doing a good job and not frightened to experiment.

Would a similar low dose of theophylline benefit a sub-group of those with autism/schizophrenia?  I think it is quite likely.

COPD and autism/schizophrenia share the same impaired oxidative stress response.

A randomised, double-blind placebo controlled trial of the effectiveness of low dose oral theophylline as an adjunct to inhaled corticosteroids in preventing exacerbations of chronic obstructive pulmonary disease (TWICS)

Chronic Obstructive Pulmonary Disease (COPD) is a progressive lung disease characterised by progressive airflow limitation. In the UK, it affects around 3 million people, is the fifth leading cause of death and costs the NHS approximately £1 billion annually. Exacerbations of COPD account for 60% of NHS COPD costs and are associated with accelerated rate of lung function decline, reduced physical activity, reduced quality of life, increased mortality and increased risk of co-morbidities. COPD treatment guidelines recommend inhaled corticosteroids (ICS) to reduce exacerbations and improve lung function. However, in COPD, airway inflammation is relatively insensitive to the anti-inflammatory effects of ICS and even high doses fail to prevent exacerbations. Preclinical and pilot studies demonstrate that low dose theophylline may increase the sensitivity of the airway inflammation to ICS, and thus when used with ICS will reduce the rate of COPD exacerbation. In this study we will determine the clinical effectiveness and cost-effectiveness of adding low dose theophylline to ICS therapy in patients with COPD. The primary outcome is the number of exacerbations. The primary economic outcome is the cost-per-QALY gained during the one year treatment period. We will recruit 1424 participants from primary and secondary care across seven areas of the UK. Participants will be randomised to theophylline (200 mg once or twice daily depending on smoking status and weight) or placebo for 12 months. We will follow participants up at six and twelve months to assess the number of exacerbations. We will also collect data on adverse events, health care utilisation, quality of life and breathlessness, and lung function. Low dose theophylline is cheap (10p/day) and, if shown to make current ICS therapy more effective in a cost effective manner, it will improve the quality of life of COPD patients and reduce the burden of COPD on the NHS.

At large doses, Theophylline has long been a therapy for asthma and COPD, but as with Sodium Butyrate, it is quite possible that larger doses of Theophylline produce a different result.  In other words the epigenetic effect fortunately comes from the low dose.

Low doses mean less chance of side effects.

For example, in anyone predisposed to reflux/GERD/GORD many asthma drugs pose a problem because at the same time as opening the airways in your lungs they will relax the lower esophageal sphincter and allow stomach acid to rise upwards.

We saw in an earlier post that in some types of autism something called mGluR5 is dysfunctional in the brain. By chance mGluR5 is also involved in closing the lower esophageal sphincter.  In people with reflux/GERD/GORD a mGluR5 inhibitor was found to have promise for the management of their symptoms.

Randomised clinical trial:effects of monotherapy with ADX10059, a mGluR5 inhibitor, on symptoms and reflux events in patients with gastro-oesophageal reflux disease.

So it is not surprising that many people with autism also have reflux/GERD/GORD. 

But the dysfunction with mGluR5 in autism can be both hyper and hypo, so the therapy might be a positive allosteric modulator (PAM), or a negative allosteric modulator (NAM).  

In someone with autism + reflux/GERD/GORD  it would be reasonable to think a NAM, like ADX10059, might help both conditions.

Gene Repression and Genome Stability

There is another epigenetic process that may be disturbing gene expression in some people and may be treatable.

I have been trying to find why so many people with autism can benefit from biotin; I think I have found a plausible explanation.

“Biotinylation of histones plays a role in gene repression and repression of transposable elements, thereby maintaining genome stability”

I think in some people with autism and no clinical deficiency of biotin the continued “overdosing” of biotin might be having an effect on gene expression, bringing things a little closer to where they should be.

Rather beyond the scope of this blog, it appears that in some people the impaired genome stability, reversible with biotin(ylation), this might be a significant cancer risk.

In essence, for most people supraphysiological concentrations of biotin will do absolutely nothing, but in a sub-group it might do a lot of good.  It is epigenetic, but you do not have to understand it to benefit from it.  It is complicated.

Biotinylation of Histones Represses Transposable Elements in Human and Mouse Cells and Cell Lines and in Drosophila melanogaster

Transposable elements such as long terminal repeats (LTR) constitute ∼45% of the human genome; transposition events impair genome stability. Fifty-four promoter-active retrotransposons have been identified in humans. Epigenetic mechanisms are important for transcriptional repression of retrotransposons, preventing transposition events, and abnormal regulation of genes. Here, we demonstrate that the covalent binding of the vitamin biotin to lysine-12 in histone H4 (H4K12bio) and lysine-9 in histone H2A (H2AK9bio), mediated by holocarboxylase synthetase (HCS), is an epigenetic mechanism to repress retrotransposon transcription in human and mouse cell lines and in primary cells from a human supplementation study. Abundance of H4K12bio and H2AK9bio at intact retrotransposons and a solitary LTR depended on biotin supply and HCS activity and was inversely linked with the abundance of LTR transcripts. Knockdown of HCS in Drosophila melanogaster enhances retrotransposition in the germline. Importantly, we demonstrated that depletion of H4K12bio and H2AK9bio in biotin-deficient cells correlates with increased production of viral particles and transposition events and ultimately decreases chromosomal stability. Collectively, this study reveals a novel diet-dependent epigenetic mechanism that could affect cancer risk.

Here, we provide evidence for the existence of a novel diet-dependent epigenetic mechanism that represses retrotransposons. Importantly, we demonstrated that depletion of biotinylated histones in biotin-deficient cells increases LTR transcript levels, production of viral particles, and retrotransposition events, and ultimately decreases chromosomal stability. Both biotin deficiency and supplementation are prevalent in the US. For example, moderate biotin deficiency has been observed in up to 50% of pregnant women (35,36). About 20% of the US population reports taking biotin supplements (37), producing supraphysiological concentrations of vitamin in tissues and body fluids (23,28,35). The findings presented here suggest that altered biotin status in these population subgroups might affect chromosomal stability and cancer risk. 

Biotin and biotinidase deficiency

Biotin requirements for DNA damage prevention

  

Conclusion

I never got round to writing part 2 of my epigenetics post, but my experience of HDAC inhibitors to date has been very positive.

I would be the first to admit that this is rather hit and miss.  It was only when reading the paper on potential therapies for Pitt Hopkins, that was openly musing about HDAC inhibitors, in an equally hit and miss approach, that I thought I would write further about it.

It really seems totally haphazard, because you cannot predict the effect with any level of certainty.  If there is a self-repair mechanism trying to maintain homeostasis of the genome, haphazard may be good enough.

10mg of biotin twice a day does have a mild but noticeable stabilizing effect; is this caused by better maintaining genome stability? I have no idea. 

I will try sodium butyrate and if it works I will have to establish what dose of Miyari 588 produces the same effect.  Both are used in animal feed to reduce inflammatory disease, so you are already indirectly exposed to them if you eat meat.

Theophylline should also be investigated.  This is a very well understood drug and small doses really do seem to help people with COPD.

PKA, PKB and PKC are likely at the core of most people’s autism.  Many existing therapies can modify their expression.

Whole genome sequencing, carried out at great precision, is clearly the only satisfactory genetic testing method.  The other, cheaper, methods are just missing key data and giving many false negative results, i.e. saying there are no identifiable genetic dysfunctions, when this is not true.