Archive for the ‘Epigenetics’ Category
Elegant Observations, Feedback Loops Within Entangled Systems, and Possible Clues On Why So Many People With Autism Are Male – “Sex Hormones in Autism: Androgens and Estrogens Differentially and Reciprocally Regulate RORA, a Novel Candidate Gene for Autism”
Posted on: March 8, 2011
- In: Autism | Beautiful Complexity | Epigenetics | Epigenome | Feedback Loops | Genetics | Hu | RORA
- 2 Comments
Hello friends –
Whatever your take on the predominant cause of autism(s), your thoughts on the appropriateness, or inappropriateness of research allocations in the autism realm, one thing can’t be denied; collectively, a lot of researcher time and dollars have been poured into autism research. We’ve learned some important things, some cool things, some confusing things, some obscure things, and some useless things. But even with all of the resources we have applied towards understanding autism, one of the most curious unknowns is also one obvious to the most rudimentary observations, the persistently skewed male to female ratio, with a finding of three or four males to every female with autism. It is one of the most vexing questions, almost taunting us with seeming obviousness, but consistently elusive. It isn’t just autism, lots of other neurological conditions are similarly tilted, and in a bazillion animal models it seems an unfortunate fact that being born male simple predisposes you (or rat you) to a variety of things you’d rather not have.
The ideas I have seen floated most frequently to explain this observation involve the effect of prenatal testosterone and the associated ‘extreme male brain’ theory, a loss of genetic backups to compensate for mixups, and synergistic effects of testosterone on chemicals, notably, mercury; explanations which I generally like a little, a little less, and almost not at all, respectively. An idea I’ve floated a couple of times, but that seemed even less accepted (or, more likely, completely unnoticed), was that estrogen might be acting in a protective manner; as it is known to exhibit attenuate the effects of neuroinflammation and oxidative stress. Indeed, it is starting to look like estrogen receptors are expressed in a large variety of situations salient to CNS processes.
A few weeks ago, the same group that has published some immensely cool studies on epigenetics and brain proteins, genetic expression differentials within twin siblings with autism, and circadian rhythm alterations comes a paper which may give us insight into this question, so that is pretty exciting. Even cooler, it invokes a negative feedback loop in a complicated system and is built upon the foundation of several earlier studies on a protein implicated in lots of things we know are awry in autism. That study is Sex Hormones in Autism: Androgens and Estrogens Differentially and Reciprocally Regulate RORA, a Novel Candidate Gene for Autism (full paper). Here is the abstract:
Autism, a pervasive neurodevelopmental disorder manifested by deficits in social behavior and interpersonal communication, and by stereotyped, repetitive behaviors, is inexplicably biased towards males by a ratio of ~4:1, with no clear understanding of whether or how the sex hormones may play a role in autism susceptibility. Here, we show that male and female hormones differentially regulate the expression of a novel autism candidate gene, retinoic acid-related orphan receptor-alpha (RORA) in a neuronal cell line, SH-SY5Y. In addition, we demonstrate that RORA transcriptionally regulates aromatase, an enzyme that converts testosterone to estrogen. We further show that aromatase protein is significantly reduced in the frontal cortex of autistic subjects relative to sex- and age-matched controls, and is strongly correlated with RORA protein levels in the brain. These results indicate that RORA has the potential to be under both negative and positive feedback regulation by male and female hormones, respectively, through one of its transcriptional targets, aromatase, and further suggest a mechanism for introducing sex bias in autism.
The press release and google news cycle for this paper seemed to have been well ahead of the pubmed robot; Kev had a post on this study a few weeks before it hit pubmed with a postdate. I generally skip out on the interest story/vaccine fairytale story/vaccine nightmare story/lost child nightmare story that is the google news autism feed, but in this case, it harbored a story on a paper that I was actually interested in. In any situation, the paper landed in pubmed this morning, and is available in full via PLOS, so great stuff is available to us all.
The paper starts with some of the backstory, the ‘inexplicable’ male predominance in autism, some of the theories on why this might be the case, and most importantly, details on previous findings by this set of researchers on reduced levels of RORA in the CNS of people with autism, a protein with a great number of functions of interest to the autism community.
Together, these results link molecular changes in RORA in peripheral cells to molecular pathology in the brain of autistic individuals. These findings are particularly relevant to ASD as RORA is involved in several key processes negatively impacted in autism, including Purkinje cell differentiation, cerebellar development, protection of neurons against oxidative stress, suppression of inflammation, and regulation of circadian rhythm. Behavioral studies on the RORA-deficient staggerer (RORA+/sg) mouse, primarily used as a model to study ataxia and dystonia[13], further show that RORA is also associated with restricted behaviors reminiscent of ASD, such as perseverative tendencies, limited maze patrolling, anomalous object exploration as well as deficits in spatial learning.
It’s tough to find a protein with a greater key word hitlist for our population of interest than Purkinje cell differentiation, cerebellar development, protection from oxidative stress, suppression of inflammation, and regulation of the circadian rhythm. In fact, I’d be shocked to find a protein touching so many fracture points that wasn’t found altered in the autism population; it makes too much sense within the framework of an entangled system and what we already know about the physiology of autism. Remember that the previous paper found decreased RORA in the brain of people with autism; i.e., less of a protein that protects from oxidative stress, supports Purkinje cell development, and suppresses the inflammatory response. A relative lack of RORA makes a depressingly good amount of sense.
That being said, what makes the current paper so interesting is that they found the RORA is differentially, and inversely modulated by female and male hormones (i.e., testosterone and estrogen). But even more insidiously, one of the downstream products regulated by RORA, aromatase, participates in the cleavage of testosterone to estrogen; the authors essentially describe a negative feedback loop. It turns out, not only is RORA decreased in the CNS of autism, but so too is aromatase.
We also show that one of the transcriptional targets of RORA is aromatase, which is a crucial enzyme in the biosynthesis of estrogen from testosterone. It is noteworthy that both RORA and aromatase proteins are decreased in the frontal cortex of autistic subjects, and that the level of aromatase protein is strongly correlated with the level of RORA protein in the brain tissues. We therefore propose that the reduction of RORA observed in autism is exacerbated by a negative feedback mechanism involving decreased aromatase level, which further causes accumulation of its substrate, testosterone, and reduction of its product, estradiol. Testosterone and estradiol respectively exhibit negative and positive feedback regulation of RORA expression as illustrated in Fig. 5, which summarizes the principal findings of this study. Thus, a deficiency in RORA in autistic brain is expected to be further aggravated by increased levels of testosterone due to suppression of aromatase, a transcriptional target of RORA.
This is pretty neat; it shows how simply being male can lead to the downregulation of a system with tendrils attached to a great number downstream processes we know to be disturbed in autism.
I particularly liked that this paper established a chain of learning more, something I think we can all agree is a great idea. Some of the people on this study have been plugging away with some interesting ideas for a while, all of which, I believe, are ancestors of these findings. They had two really neat papers on genetic expression in autism twins with differential degrees of autism severity, both of which used genomic bioinformatic tools to understand which the genetic pathways were affected. This is actually rather brilliant; they essentially leveraged the genetic uniqueness of the twins to gain more insight into which processes were being affected in autism by seeing which genes were differentially expressed in identical twins that manifested differently, using genetics to learn about what is happening a layer above the genome. Next, the original RORA paper began to probe the mechanism by which the previously observed expression was achieved, they found that a particular protein, RORA, was overmethylated and consequently at depressed levels. Another bioinformatic approach told them that RORA was a particularly attractive candidate for further evaluation based on its descendant interactions, and the association between RORA, aromatase, and sexual hormones appeared. Beautiful.
All that coolness not withstanding, some of the articles I saw on this lacked the caution and nuance we ought to see with these kinds of findings; the paper was pretty clear that previous CNS studies hadn’t shown decreased RORA in all of their samples, just most of them. This doesn’t answer all of our questions about the male dominance of autism, but we do know more than when this study was published, and that is pretty cool. Hooray for knowledge.
– pD
The Beautiful, Dispassionate, and Humbling Complexity of Environmental Enrichment, Butterfly Wings, and How the Granularity of Our Filters Control What We Think We Know
Posted on: November 5, 2010
- In: Autism | BDNF | Brain | Epigenetics | Epigenome | Intriguing | Mr. Rat | Some Jerk On The Internet
- 4 Comments
Hello friends –
I’ve been planning to write something about the idea of environmental enrichment for a while now but other stuff kept on popping up. At a broad level, researchers are finding that the type of external stimulation an animal is raised or housed in can have dizzyingly unpredictable effects on a range of physiological and behavioral endpoints, many of which are of great interest to the autism community. This is a tough area to dance through in the autism world; the available literature has shades of refrigerator mothers, and TV based causation; yet, the underlying idea of environmental enrichment, that the external environment can affect a person in a very physical way, is something known to the autism community in concrete ways. What’s more, much of our data in the environmental enrichment realm is nothing less than compelling. It is exciting to know that we are beginning to have insight into the molecular mechanisms by which the environment can affect the body and brain, and with that insight, just maybe the wisdom to help our children and help ourselves.
From the biomarker side, a couple of neat studies would include Environmental enrichment reduces Abeta levels and amyloid deposition in transgenic mice, wherein striking reductions in amyloid proteins were found in knockout mice housed in a stimulating environment compared to those in standard housing. Or the very recently published, Complex environment experience rescues impaired neurogenesis, enhances synaptic plasticity, and attenuates neuropathology in familial Alzheimer’s disease-linked APPswe/PS1DeltaE9 mice which hits a lot of keywords with parallels to the autism research world. There are many, many others including hits like Altered plasticity in hippocampal CA1, but not dentate gyrus, following long-term environmental enrichment, or hilariously named, soundbyte laden, Hippocampal epigenetic modification at the brain-derived neurotrophic factor gene induced by an enriched environment. The lower level details of these studies and their many ancestors are beyond the scope of what I have time for now, but clearly anything that can be affecting synaptic plasticity, BDNF expression, and neurogenesis should be of interest to the autism community.
If we turn to measurements that go beyond frozen slices of tissue (but do not necessary exclude them), our data regarding behavioral differences in EE housed animals is also robust. For example, we could look at Environmental enrichment delays the onset of memory deficits and reduces neuropathological hallmarks in a mouse model of Alzheimer-like neurodegeneration, which found that EE housed mice performed significantly better at memory tasks that other mice housed in non stimulatory environments. Environmental-enrichment-related variations in behavioral, biochemical, and physiologic responses of sprague-dawley and long evans rats concludes by saying, The data support the claim that environmental enrichment may render animals more resilient to challenges. Ouch. Forgetting chronic diseases such as Alzheimer’s or Parkinson’s, which get a lot of attention in the EE world, even things like traumatic brain injury or lack of oxygen to the brain seem to show benefits from a stimulating environment, as we can see from studies like Environmental Enrichment Influences BDNF and NR1 Levels in the Hippocampus and Restores Cognitive Impairment in Chronic Cerebral Hypoperfused Rats or Empirical comparison of typical and atypical environmental enrichment paradigms on functional and histological outcome after experimental traumatic brain injury. The flip side, a ‘de-enriched’ environment has findings along the lines of what you might expect; i.e., Environmental impoverishment and aging alter object recognition, spatial learning, and dentate gyrus astrocytes. Ouch.
So what is, exactly, an enriched environment? The methods section from Environmental enrichment reduces Abeta levels and amyloid deposition in transgenic mice says this:
Animal experiments were conducted in accordance with institutional and NIH guidelines. Male offspring of transgenic breeding pairs APPswe × PS1 were separated from their mother at 3 weeks of age (after weaning), genotyped, and housed four males to a cage. Enriched environment was composed of large cages running wheels, colored tunnels, toys, and chewable material. For 1 month, mice were exposed to enriched environment every day for 3 hr and were returned to their original cages for the remaining 21 hr. After 1 month of daily enrichment, mice were introduced to the enriched environment three times a week for an additional 4 months. Mice were sacrificed at age of 6months. Following weaning, a control group of animals was maintained for 5 months in standard housing conditions.
Lets consider the implications of these findings. Reducing amyloid buildup has been a holy grail of the pharmaceutical companies for a long time now, though it is possible that this plan of attack was based on bad assumptions. Tens of millions of dollars (or hundreds of millions) have been thrown at synthetic ways to reduce or eliminate the buildup of amyloid plaque in mice, rats, and recently, people with mixed to poor results. Even if it turns out that amyloid isn’t causing Alzheimer’s, that doesn’t do anything to change the fact that these researchers were able to make very significant changes to biological systems by setting their rats up in a rat mansion with rat delivered food and a rat tennis court for a few hours a day. Despite the mixed findings as of late on the effect of brain training in order to stave off dementia, I think most of us have known someone, or Kevin Baconed one degree out to know someone who has seemingly either degenerated with a stagnant environment, or kept on trucking through old age with a more active lifestyle. Is their environment participating?
So what about autism? The most extreme and tragic parallels can be seen in studies of children from orphanages, notably in Romania, where children were raised in absolutely destitute surroundings. A recent study is entitled Stereotypies in children with a history of early institutional care with these findings:
RESULTS: At the baseline assessment prior to placement in foster care (average age of 22 months), more than 60% of children in institutional care exhibited stereotypies. Follow-up assessments at 30 months, 42 months, and 54 months indicated that being placed in families significantly reduced stereotypies, and with earlier and longer placements, reductions became larger. For children in the foster care group, but not in the care as usual group, stereotypies were significantly associated with lower outcomes on measures of language and cognition.
CONCLUSIONS: Stereotypies are prevalent in children with a history of institutional care. A foster care intervention appears to have a beneficial/moderating role on reducing stereotypies, underscoring the need for early placement in home-based care for abandoned children. Children who continue to exhibit stereotypies after foster care placement are significantly more impaired on outcomes of language and cognition than children without stereotypies and thus may be a target for further assessments or interventions.
Another study that looks specifically towards autistic like behaviors in children raised in orphanages is Early adolescent outcomes of institutionally deprived and non-deprived adoptees. III. Quasi-autism.
BACKGROUND: Some young children reared in profoundly depriving institutions have been found to show autistic-like patterns, but the developmental significance of these features is unknown.
METHODS: A randomly selected, age-stratified, sample of 144 children who had experienced an institutional upbringing in Romania and who were adopted by UK families was studied at 4, 6, and 11 years, and compared with a non-institutionalised sample of 52 domestic adoptees. Twenty-eight children, all from Romanian institutions, for whom the possibility of quasi-autism had been raised, were assessed using the Autism Diagnostic Interview-Revised (ADI-R) and the Autism Diagnostic Observation Schedule (ADOS) at the age of 12 years.
RESULTS: Sixteen children were found to have a quasi-autistic pattern; a rate of 9.2% in the Romanian institution-reared adoptees with an IQ of at least 50 as compared with 0% in the domestic adoptees. There were a further 12 children with some autistic-like features, but for whom the quasi-autism designation was not confirmed. The follow-up of the children showed that a quarter of the children lost their autistic-like features by 11. Disinhibited attachment and poor peer relationships were also present in over half of the children with quasi-autism.
CONCLUSIONS: The findings at age 11/12 years confirmed the reality and clinical significance of the quasi-autistic patterns seen in over 1 in 10 of the children who experienced profound institutional deprivation. Although there were important similarities with ‘ordinary’ autism, the dissimilarities suggest a different meaning.
Similarly depressing findings can be found in places like Institutional rearing and psychiatric disorders in Romanian preschool children, or Placement in foster care enhances quality of attachment among young institutionalized children. There is a gripping This American Life about a child adopted from Romania. Please be sure your head is in the right place before listening to part II, which describes a family trying to decide of their very severely autistic son should be placed in residential care. I ran into this episode on accident one day in the car when I was already feeling bleak and walked out the other end pretty fucked up for a few days; those guys are really good and the narrative can hit very close to home for some.
Calling up images from the dark(er) days of autism and Bettleheim we have an array of studies on the effect of maternal separation and subsequent physiological and behavioral effects that have parallels in autism findings. For example, here is an abstract from Behavioural and neurochemical consequences of early weaning in rodents
Among all mammalian species, pups are highly dependent on their mother not only for nutrition, but also for physical interaction. Therefore, disruption of the mother-pup interaction changes the physiology and behaviour of pups. We review how maternal separation in the early developmental period brings about changes in the behaviour and neuronal systems of the offspring of rats and mice. Early weaning in mice results in adulthood a persistent increase in anxiety-like and aggressive behaviour. The early-weaned mice also show higher hypothalamic-pituitary-adrenal activity in response to novelty stress. Neurochemically, the early-weaned male mice, but not female mice, show precocious myelination in the amygdala, decreased brain-derived neurotrophic factor protein levels in the hippocampus and prefrontal cortex, and reduced bromodeoxyuridine immunoreactivity in the dentate gyrus. Because higher corticosterone levels are persistently observed up to 48 h when the mice are weaned on postnatal day 14, the exposure of the developing brain to higher corticosterone levels may be one of the effects of early weaning. These results suggest that deprivation of the mother-infant interaction during the late lactating period results in behavioural and neurochemical changes in adulthood and that these stress responses are sexually dimorphic (i.e. the male is more vulnerable to early weaning stress).
The rapidfire analysis tells us that altered HPA-Axis activity, BDNF levels, and anxiety all have parallels in autism, along with perhaps the most consistent finding in animal studies that have interest to autism, the problems of being born male and consequent risk factors from nearly everything. This is a review paper, but there are a gazillion others with titles like Maternal separation disrupts dendritic morphology of neurons in prefrontal cortex, hippocampus, and nucleus accumbens in male rat offspring, Short- and long-term consequences of different early environmental conditions on central immunoreactive oxytocin and arginine vasopressin levels in male rats, or Prolonged maternal separation decreases granule cell number in the dentate gyrus of 3-week-old male rats.
Though I’m pretty sure that this should be clear to everyone, just to be sure, I’m not proposing a refrigerator mother theory of autism. But the data is the data and the logical opposite of an enriched environment is also born out.
So what? Well, this reminded me of the “Rat Park” studies an Internet friend told me about, wherein researchers seemed to find that animals dosed with opiates for several weeks would voluntarily wean themselves from the drugs if moved to much larger enclosures where they had access to either drugged water or plain water. The startling thing about the Rat Park studies isn’t so much what was learned about opiate addiction, so much as the broader implications that the existing studies on drug addiction might not be studying the right thing; that instead of testing the effects on opiate availability on rodents, they were testing the effects of opiate availability on chronically depressed rodents. Following through, it occurs to me that in addition to the bazillion other problems we have moving from rodent to human with anything other than a hopeful educated guess, we must grudgingly admit that the condition the animals were housed in may be affecting a lot of findings. As if we didn’t have enough confounders already!
But more importantly, these types of findings are beautiful portraits of complexity, the dispassionate hand of nature and the dangers of thinking you understand.
There are so many instances where we have found that as we gain the ability to make more detailed observations, we learn that our existing conclusions were crude facsimiles of reality, and oftentimes, conclusions that had been formed on dangerously unsound foundations. By way of example, exposure to lead and consequent effects on neurodevelopment. At one point, lead was used as a pesticide, eventually we figured out that wasn’t such a good idea, but it should be fine in paint and gasoline. Then we removed it from paint. Then gasoline. And just a few years back, the ‘safe’ level of lead was deemed to be zero; and even the tiniest increases in lead were associated with developmental problems. Of course, this was always the reality, but it was not until we applied filters of sufficient sophistication that our observations were adequately powered to understand the reality. Are our studies of any number of factors clever enough to discern the changes we’d like to understand when we realize that subtle changes are still changes?
It gets thornier for the autism community in particular. One thing a lot of our kids aren’t very good at are “complex environmental interactions”, in fact, a lot of our kids are flat out terrible at them. After a couple of weeks/months/years of soul crushing experiences trying new things out with kid autism, some parents might start to think to themselves that a trip to the zoo, or the museum, or the movie theater or even the super market just isn’t worth it. The result, while not necessarily an abject environment can start to resemble a single square mile of ocean, indistinguishable from the sea for backwards or forwards; the real world equivalent of a DVD set on repeat play. I speak from experience, a rule in our household when one of the parents had to leave the other home for a weekend with kid autism was ‘survive, don’t thrive’. If that meant a trip to the same lake, spinning the same DVD, and a meal of the same food, but a relatively meltdown free weekend, that was OK.
We survived, but did we spite ourselves in the process? Were we reinforcing at a neurochemical level some of the causes of the very behaviors that were causing us to retreat to the middle of the ocean? We are starting to learn that this might be somewhat of a self fulfilling prophecy; taking a child who already does very poorly in new environments and run him or her through the same things over and over could be exacerbating their ability to handle new environments in a physiological way. The data is the data.
That being said, there is an upside, a big one; the flip side is that parents have a chance to make real and salient changes in their child by the least controversial methods possible; gentle but repeated exposure to new things. For some of us, this means a lot of shitty days and late night drinks to get through to the other side. That’s OK. It’s worth it. Steel yourself for a meltdown and turn off the goddamned TV, take kid autism to the zoo, or the bounce house playground, or art festival, or a ‘non-autism’ friends house. A lot of our children might need a helping hand, a gentle push, or a well meaning shove into the world, but someone has to do it, and the world isn’t going to get any less complicated while we wait. When it works out, and you have even a single new experience your child enjoys, that is an enriched environment for you, and enriched environments aren’t just for rats and kids.
– pD
- In: Autism | BDNF | Biological Plausibility | BPA | Brain | Epigenetics | Epigenome | Genetics | Impending Doom | Intriguing | PBDE | Pesticides | Prevalence | Purkinje | Reelin | Some Jerk On The Internet | Synthetics | The Fairytale | Uncategorized
- 33 Comments
Hello friends –
I ran into a few abstracts, read a few papers, and tried to get my way through one really dense paper in the past few weeks that got me thinking about this post. It’s all shook up, like pasta primavera in my head, but hopefully something cogent will come out the other end. (?)
Of the metabolic conditions known to be associated with having a child with autism, hypothyroidism is one that I keep on running into by way of the pubmed alert grapevine. By way of example, we have two studies that looked for autoimmune conditions in family members which found hypothyroidism to be one of many autoimmune diseases as a risk factor for autism, including, Familial clustering of autoimmune disorders and evaluation of medical risk factors in autism, and Increased prevalence of familial autoimmunity in probands with pervasive developmental disorders. This shouldn’t be too surprising, we know that, for example, perinatal hypothyroidism is a leading cause of mental retardation, with similar findings for the condition during pregnancy. It turns out, it appears that rates of hypothyroidism are slightly increasing, though at this time, the increases are of relatively small proportions, and as such, may be artifacts unrelated to an actual increase in classically recognized hypothyroidism. In any case, I think it is safe to say that interference with thyroid metabolism is something to be avoided at all costs when possible.
So after having read about that, this paper showed up in my inbox a while ago:
Thyroid hormones have long been known to play important roles in the development and functions of the central nervous system, however, the precise molecular mechanisms that regulate thyroid hormone-responsive gene expression are not well understood. The present study investigated the role of DNA methylaion and histone acetylation in the effects of perinatal hypothyroidism on regulation of reelin and brain-derived neurotrophic factor (BDNF) gene expression in rat hippocampus. The findings indicated that the activities of DNA methyltransferase (DNMT), methylated reelin and BDNF genes were up-regulated, whereas, the activities of histone acetylases (HAT), the levels of global acetylated histone 3 (H3) and global acetylated histone 4 (H4), and acetylated H3, acetylated H4 at reelin promoter and at BDNF gene promoter for exon II were down-regulated in the hippocampus at the developmental stage of the hypothyroid animals. These results suggest that epigenetic modification of chromatin might underlie the mechanisms of hypothyroidism-induced down-regulation of reelin and BDNF gene expression in developmental rat hippocampus
This gets interesting for autism because reelin, and bdnf levels have been found to be decreased in several studies in the autism population, with direct measurements, genetic expression, mouse knockout based models of autism , and genomic alterations all being implicated. There have been some negative genetic studies, but considering that it isn’t always the genes you have, but the genes you use, our other available evidence certainly points to BDNF and reelin involvement with some percentage of children with autism, and the association is such that a reduction in reelin or BDNF is a risk factor for developing autism. It would seem that the paper above might give some insight into the lower level details of the effects of hypothyroidism and subsequent developmental trajectories; modifications of reelin expression; through epigentic mechanisms, no less!. That’s pretty cool!
Then, I got my hands on a review paper that tries to go into detail as to the functional mechanism by which reelin deficiency could contribute to ASD, Neuroendocrine pathways altered in autism. Special role of reelin. It is a review that touches on a variety of ways that reelin contributes to neurodevelopment that have findings in the autism realm, including neuronal targeting and migration during brain formation, interactions with the serotonin and GABA systems, testosterone, and oxytocin. In short, there are plenty of ways that decreased reelin expression can impact development in ways that mirror our some of our observations in autism.
Of the many things that convince me that we are doomed, the proliferation of chemical compounds whose interactions within our bodies we scarcely understand is among them. In my readings on endocrine disruptors, one thing I found that seemed to be worrying lots of researchers was that some classes of these chemicals are capable of interfering with thyroid metabolism, and in some cases interfering with development of cells known to be associated with autism. Terrifyingly enough, since I read those papers, several others have come out, including Polybrominated Diphenylether (PBDE) Flame Retardants and Thyroid Hormone during Pregnancy and Mini-review: polybrominated diphenyl ether (PBDE) flame retardants as potential autism risk factors. At this point, it is important to point out that, as far as I know, there have not been any studies showing that non occupational exposure to PDBEs or other environmental pollutants can lead to classically defined hypothyroidism, at least none that I know of. (?) Be that as it may, I think it is realistic to assume any interference in thyroid metabolism is a bad thing, and while finding people in the outlier regions of hypo (or hyper) thyroidism gives us information on extreme environments, it would take someone with a lot of misplaced faith to assume that we can safely disturb thyroid metabolism just a little bit, and everything will come out in the wash.
I’ve had the argument made to me in the past that environmental pollutant driven increases in autism lacked biological plausible mechanisms; this argument is almost always made within a context of trying to defend the concept of a static rate of autism. While the papers I’ve linked to above do not provide conclusive proof that our changing environment is causing more children to be born with autism, they do provide increasing evidence of a pathway from pollutants to ASD, and indeed, the lack of biological plausibility becomes an increasingly flacid foundation on which to assume that our observations of an increased rate of autism are illusory. Unfortunately, in my opinion, the focus on vaccines has contributed to the mindset that a static rate of autism (or nowadays, maybe a tiny increase), must be protected at all costs, including some ideas on the application of a precautionary principle that seem outright insane to me (or at least, the exact opposite of what I would consider to be a precautionary path).
One thing is for certain, the number of child bearing women in developing countries with measurable concentrations of chemicals known to interferre with thyroid metabolism nears 100% in the industrialized nation as we eat , drink, breathe and bathe in the microscopic remnants of packaging materials, deteriorating carpet fibers, and baby clothes that are made to be fire resistant. This is an environment unambiguously different than that encountered by any other generation of infants in the history of mankind. To believe that we can modify our environment so drastically without having an impact seems incredibly naive to me, or on some days, just plain old stupid.
– pD
Implications for Autism Or Just Interesting? “Epigenetic and immune function profiles associated with posttraumatic stress disorder”
Posted on: June 25, 2010
Hello friends –
One of my tangential pubmed alerts notified me of this study the other day: Epigenetic and immune function profiles associated with posttraumatic stress disorder
The biologic underpinnings of posttraumatic stress disorder (PTSD) have not been fully elucidated. Previous work suggests that alterations in the immune system are characteristic of the disorder. Identifying the biologic mechanisms by which such alterations occur could provide fundamental insights into the etiology and treatment of PTSD. Here we identify specific epigenetic profiles underlying immune system changes associated with PTSD. Using blood samples (n = 100) obtained from an ongoing, prospective epidemiologic study in Detroit, the Detroit Neighborhood Health Study, we applied methylation microarrays to assay CpG sites from more than 14,000 genes among 23 PTSD-affected and 77 PTSD-unaffected individuals. We show that immune system functions are significantly overrepresented among the annotations associated with genes uniquely unmethylated among those with PTSD. We further demonstrate that genes whose methylation levels are significantly and negatively correlated with traumatic burden show a similar strong signal of immune function among the PTSD affected. The observed epigenetic variability in immune function by PTSD is corroborated using an independent biologic marker of immune response to infection, CMV—a typically latent herpesvirus whose activity was significantly higher among those with PTSD. This report of peripheral epigenomic and CMV profiles associated with mental illness suggests a biologic model of PTSD etiology in which an externally experienced traumatic event induces downstream alterations in immune function by reducing methylation levels of immune-related genes.
Essentially the authors took a bunch of people that are more likely to experience stressful situations and PTSD, urban Detroit residents, who amazingly report PTSD symptoms at twice the level that previous studies have found in analysis of larger areas. [Apparently, getting physically attacked is more common there, which gives rise to PTSD even more than ‘other traumatic event types’, and was reported by 50% of the participants from a larger study which formed the population pool of this study. (!!)] With this population base, blood was drawn and methylation profiles were analyzed between participants who reported PTSD symptoms (n=23) and those who ‘only’ had ‘potentially traumatic events’ (PTE). PTSD and ‘controls’ where matched by race, age, sex, and blood profiles.
Once methylation levels were identified, a functional annotation clustering analysis was performed, which I believe is similar a pathway analysis; essentially a bioinformatic tool to gain insight into which biological functions were being manipulated as a result of differential methylation of the genome. This is a powerful new tool in discerning what is happening in autism and elsewhere, and I expect it will provide some surprising answers in the future. Here is their text on what they found:
Consistent with previous findings from gene expression (4, 5) and psychoeneuroimmunologic studies (3), each of the top three FACs determined from uniquely unmethylated genes among PTSD-affected individuals shows a strong signature of immune system involvement. This signature includes genes from the innate immune system (e.g.,TLR1 andTLR3), as well as from genes that regulate innate and adaptive immune system processes (e.g., IL8, LTA, and KLRG-1). In contrast, pathways and processes relevant to organismal development in general—and neurogenesis in particular—figure prominently among the genes uniquely unmethylated in the PTSD-unaffected group (e.g., CNTN2 and TUBB2B; Fig. S2). Notably, similar clusters were obtained using an alternative approach based on genes differentially methylated between the two groups at P < 0.01, with annotations in the top five FACs that include signal, cell proliferation, developmental process, neurologic system process, and inflammatory response
Keeping in mind that reduced methylation results in increased gene expression, if we take a look at Table 1, some of the parallels to autism jump out a little more robustly:
In the ‘Uniquely Unmethylated’ (i.e., higher expression), area, we find that participants affected by PTSD had showed greater enrichment in genes related to the immune response, and specifically the inflammatory response and innate immune response. Our evidence for similar immunological profiles in the autism realm is deep, and includes multiple observations of an active immune response in the CNS, highly significant over expression of genes related to immune function in the CNS, several observations of known upregulators of the innate immune response that are associated with inflammatory conditions, and multiple studies finding an exaggerated innate immune response in vitro when compared to controls. The correlations with developmental process and neuron creation are pretty straightforward.
In the ‘Uniquely Methylated’ area (i.e., lower expression), the sensory perception differences hit close to home, and xenobiotic metabolism has been implicated by several studies.
Going further, the researchers attempted to evaluate for correlations between the number of potentially traumatic experiences and the methylation profile, and somewhat unsurprisingly found that as the number of experiences increased, the methylation differentials showed wider variation.
Here again we see a distinct signature of immune-related methylation profiles among the PTSD-affected group only. More specifically, we see methylation profiles that are suggestive of immune activation among persons with more PTE exposure in the genes that are significantly negatively correlated with increasing number of PTEs—a pattern reflective of that observed for the uniquely unmethylated genes in this same group (Table 1).
From the discussion section:
Among the many analyses performed in this work, the immune related functions identified in the PTSD-affected group were consistently identified only among gene sets with relatively lower levels of methylation (Tables 1 and 2). Demethylation has previously been shown to correlate with increased expression in several immune system–related genes (reviewed in ref. 22), including some identified here [e.g., IL8 (23)]. In contrast, methylation profiles among the PTSD-unaffected are distinguished by neurogenesis-related functional annotations. Neural progenitor cells have previously been identified in the adult human hippocampus (24); however, stress can inhibit cell proliferation and neurogenesis in this brain region (reviewed in ref. 25), and recent work suggests that adult neurogenesis may be regulated by components of the immune system (reviewed in ref. 26). Thus, immune dysfunction among persons with PTSD may be influenced by epigenetic profiles that are suggestive of immune activation or enhancement and also by an absence of epigenetic profiles that would be consistent with the development of normal neural-immune interactions (27).
Among the genes uniquely methylated in the PTSD-affected group, it is striking that the second most enriched cluster—sensory perception of sound—directly reflects one of the three major symptom clusters that define the disorder (Fig. 3B). Genes in this FAC thatmay be particularly salient to this symptom domain include otospiralin (OTOS),which shows decreased expression in guinea pigs after acoustic stress (28) and otoferlin (OTOF), mutations in which have been linked to nonsyndromic hearing loss in humans (29). Exaggerated acoustic startle responses, often measured via heart rate or skin conductance after exposure to a sudden, loud tone, have been well documented among the PTSD affected (30) and are indicative of a hyperarousal state that characterizes this symptom domain. Notably, prospective studies have demonstrated that an elevated startle response is a consequence of having PTSD, because the response was not present immediately after exposure to trauma but developed with time among trauma survivors who developed the disorder (30, 31).
My son had some very severe auditory related problems earlier in his life, and still occasionally struggles with either sudden loud noises, or some very specific noises, such as some dog barks, or the sound of an infant crying. Previously the only physiology based attempt at an explanation I’d heard of for this type of response involved fine grained brain architecture and consequent filtering and/or overexcitation problems. The idea that sound sensitivities in particular can be obtained environmentally is of particular interest to the autism community.
From the common sense angle, I find this completely fascinating; we’ve known for a long time that living with consistent stress is bad for you with a variety of nasty endpoints, but this type of finding narrows down the means by which this happens. In the far off future, perhaps targeted methyl affecting drugs could be considered for people who experience extremely stressful events, as sort of a ‘PTSD vaccine’ [hehe] could be developed.
From an ASD perspective, increased feeling of anxiety, or just generally being ‘stressed out’ is a consistent finding both in research and from what I’ve read of readings from people with autism on the Internet. I’ve seen several explanations, with sensory based problems being mentioned several times. From a biological standpoint we seem to have a growing body of evidence of an abnormally regulated stress response in the autism cohort. An internet friend of mine, Loftmatt, has written extensively on his thoughts concerning the increase in stress in modern society and the mechanisms by which this could be contributing to our apparent observations of an increase in autism. This study would seem to provide insight towards a possible mechanism by which a frequent state of stress could lead to some of our immunological findings in the autism realm; a possibility I hadn’t considered previously when trying to detangle a means by which our observations of immune activation were not participating in autistic behavior. The thought of a feedback loop also strikes me looking at this, something causes a feeling of extreme stress, which leads to abnormal methylation levels and genetic expression, which leads to increased physiological (and behavioral?) alterations, and even more stress.
I may try to poke through the supplementary materials to see if any specific genes or pathways found to be differentially regulated have parallels in some of the other studies we’ve seen recently such as Garbett or Hu, although this may be somewhat of a crapshoot unless I could figure out how to actually submit gene lists to GSEA and read the responses.
And we may need to consider the possibility that these types of effects can be trans-generational. One of the most fascinating studies I’ve seen on epigentics involved exactly that, a multi-generational effect of famine in Holland, wherein the grandchildren of women who were pregnant during a time of famine bore striking differences in a variety of endpoints compared to children whose grandmothers were not pregnant during that time.
The more we learn, the more complicated the world becomes.
-pD
Confusing and Fascinating Findings – Gestational Age at Delivery and Special Educational Need
Posted on: June 11, 2010
Hello friends –
I ran across this one on accident the other day (why wasn’t it in one of my pubmed alerts?):
Background
Previous studies have demonstrated an association between preterm delivery and increased risk of special educational need (SEN). The aim of our study was to examine the risk of SEN across the full range of gestation.
Methods and Findings
We conducted a population-based, retrospective study by linking school census data on the 407,503 eligible school-aged children resident in 19 Scottish Local Authority areas (total population 3.8 million) to their routine birth data. SEN was recorded in 17,784 (4.9%) children; 1,565 (8.4%) of those born preterm and 16,219 (4.7%) of those born at term. The risk of SEN increased across the whole range of gestation from 40 to 24 wk: 37–39 wk adjusted odds ratio (OR) 1.16, 95% confidence interval (CI) 1.12–1.20; 33–36 wk adjusted OR 1.53, 95% CI 1.43–1.63; 28–32 wk adjusted OR 2.66, 95% CI 2.38–2.97; 24–27 wk adjusted OR 6.92, 95% CI 5.58–8.58. There was no interaction between elective versus spontaneous delivery. Overall, gestation at delivery accounted for 10% of the adjusted population attributable fraction of SEN. Because of their high frequency, early term deliveries (37–39 wk) accounted for 5.5% of cases of SEN compared with preterm deliveries (<37 wk), which accounted for only 3.6% of cases.
Conclusions
Gestation at delivery had a strong, dose-dependent relationship with SEN that was apparent across the whole range of gestation. Because early term delivery is more common than preterm delivery, the former accounts for a higher percentage of SEN cases. Our findings have important implications for clinical practice in relation to the timing of elective delivery
[Full paper from link. Emphasis is mine]
Essentially the authors evaluated gestational lengths with a fine tooth comb to discern if ‘early’, though not technically ‘pre-term’ delivery was associated with a ‘special education need’ (SEN), which in this case embodies a range of developmental problems including dyslexia, autism, or even physical problems like deafness or vision problems.
What the authors found was that there were subtle, but real effects in the likelyhood of having a special education need for non full term births that was dose dependent, but even included children that would not necessarily be considered early by existing standards.
Our study demonstrated a strong trend of decreasing risk of SEN with advancing gestational age at birth. The key finding of the present analysis is that this trend continued across gestational ages classified as term. Although the risk of SEN was highest among infants who were delivered preterm (<37 wk gestation), these accounted for only 5.1% of deliveries. Therefore, only a relatively small proportion of SEN (3.5%) could be attributed to preterm delivery. By contrast, 39.6% of infants were delivered between 37 and 39 wk gestation. Therefore, whilst these early term infants had only a moderately increased risk, 5.3% of SEN cases could be attributed to early term delivery.
The authors claim that the finding of effects at early, but not pre-term gestational lengths is one that is largely missing from existing studies, which have not taken these date ranges into consideration, or the ones that did, were not studying for cognitive problems, and indeed, excluded children with these criteria. Curiously, they also report an increase in SEN in children who had extra gestational periods, i.e., > 41 weeks in some studies.
The authors make absolutely no speculation as to what might be driving increased special education needs as the result of premature or early birth.
Looking at their results, one of the most striking things is that the impact did not alter if elective (i.e. C-Section) versus non-elective births were used as a variable. But this has deep ramifications for the autism storyline, which holds that if there are environmental factors that can contribute to autism, they are prenatal, and indeed, are often thought to involve insults very early in the prenatal period. In this case, we know that a genetic or environmental force isn’t contributing to the early birth, because it didn’t matter if the birth was spontaneous or not. The only area for an effect is postnatal. That is a big, big difference in the narrative.
Is this a matter of some just in time epigenetic programming happening in the womb that doesn’t get a chance to finish up in early births? Alternatively it could be that early birth allows for environmental exposures that the infant is not quite prepared to deal with. Or it could be both, or neither, or an illusory finding, but if these findings can be replicated, it raises a lot of questions about the sacred line between prenatal and postnatal environmental influences.
Unfortunately, the raw data for this project doesn’t seem to be available online; it might be really nice to see if there were patterns to be observed had particular salience to our population of interest.
– pD
Fascinating Study – Immune transcriptome alterations in the temporal cortex of subjects with autism
Posted on: June 7, 2010
Hello friends –
I’ve been referencing this paper in some discussions online for a while; I’ve read it, and in fact, while working on another project, got the opportunity to speak with one of the authors of the paper. It’s a very cool paper with a lot of information in it, some of which, could be considered inconvenient findings. Here is the abstract:
Immune transcriptome alterations in the temporal cortex of subjects with autism
Autism is a severe disorder that involves both genetic and environmental factors. Expression profiling of the superior temporal gyrus of six autistic subjects and matched controls revealed increased transcript levels of many immune system related genes. We also noticed changes in transcripts related to cell communication, differentiation, cell cycle regulation and chaperone systems. Critical expression changes were confirmed by qPCR (BCL6, CHI3L1, CYR61, IFI16, IFITM3, MAP2K3, PTDSR, RFX4, SPP1, RELN, NOTCH2, RIT1, SFN, GADD45B, HSPA6, HSPB8and SERPINH1). Overall, these expression patterns appear to be more associated with the late recovery phase of autoimmune brain disorders, than with the innate immune response characteristic of neurodegenerative diseases. Moreover, a variance-based analysis revealed much greater transcript variability in brains from autistic subjects compared to the control group, suggesting that these genes may represent autism susceptibility genes and should be assessed in follow-up genetic studies.
(emphasis is mine) [Full paper freely available from that link]
I am particularly intrigued by the second bolded sentence regarding the “these expression patterns appear to be more associated with the later recovery phase of autoimmune brain disorders, than the innate immune response characteristic of neurodegenerative diseases”. I’ve had it put to me previously that we should not necessarily implicate neuroinflammation in autism, the argument being that even though we had evidence of chronically activated microglia, what we do not seem to have evidence for is actual damage to the brain, and ergo, the neuroinflammation may actually be a byproduct of having autism, as opposed to playing a causative role, or that in fact, the neuroinflammation might even be beneficial. There have been some other places where the claim has been made that because our profile of neuroinflammation doesn’t match more classically recognized neurodegenerative disorders (i.e., MS/Alzheimer’s/Parkinson’s), that therefore, certain environmental agents need not be fully investigated as a potential contributor to autism. This is the first time that I am aware that someone has attempted to classify the neuroinflammatory pattern observed in autism not only as distinctly different from classical neurodegenerative diseases, but to also go so far as to provide a more refined example.
From the Introduction:
In order to better understand the molecular changes associated with ASD, we assessed the transcriptome of the temporal cortex of postmortem brains from autistic subjects and compared it to matched healthy controls. This assessment was performed using oligonucleotide DNA microarrays on six autistic-control pairs. While the sample size is limited by the availability of high-quality RNA from postmortem subjects with ASD, this sample size is sufficient to uncover robust and relatively uniform changes that may be characteristic of the majority of subjects. Our study revealed a dramatic increase in the expression of immune system-related genes. Furthermore, transcripts of genes involved in cell communication, differentiation, cell cycle regulation and cell death were also profoundly affected. Many of the genes altered in the temporal cortex of autistic subjects are part of the cytokine signaling/regulatory pathway, suggesting that a dysreactive immune process is a critical driver of the observed ASD-related transcriptome profile.
I was initially very skeptical about this, with a sample set so small, wasn’t it difficult to ascertain if their findings were by chance or not? It turns out, the answer depends on the type of datapoint you are evaluating against. A powerful tool in use by the researchers is a recent addition to the genetic analysis research suite, not only the ability to scan for thousands of gene activity levels simultaneously, but the use of known gene networks to identify if among those thousands of results, related genes are being expressed differentially. This is important for some amazingly robust findings presented later in the paper, so lets sidetrack a little bit. Here is a nice overview of the process being used:
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. A common approach involves focusing on a handful of genes at the top and bottom of L (i.e., those showing the largest difference) to discern telltale biological clues. This approach has a few major limitations.
(i) After correcting for multiple hypotheses testing, no individual gene may meet the threshold for statistical significance, because the relevant biological differences are modest relative to the noise inherent to the microarray technology.
(ii) Alternatively, one may be left with a long list of statistically significant genes without any unifying biological theme. Interpretation can be daunting and ad hoc, being dependent on a biologist’s area of expertise.
(iii) Single-gene analysis may miss important effects on pathways. Cellular processes often affect sets of genes acting in concert. An increase of 20% in all genes encoding members of a metabolic pathway may dramatically alter the flux through the pathway and may be more important than a 20-fold increase in a single gene.
(iv) When different groups study the same biological system, the list of statistically significant genes from the two studies may show distressingly little overlap (3).
So, back to Garbett, not only did the authors find a great number of genes overexpressed in the autism group (and a smaller number, underexpressed), when they threw their thousands of results of individual genes into the GSEA, what came back was that several genetic pathways were very significantly altered, many of them immune mediated. This is a big step in understanding in my opinion. I believe we have likely come full circle on our understanding of very high penetrance genes that might be driving towards a developmental trajectory of autism; i.e., Rhett, Fragile-X. But using this technique we can determine if entire biological pathways are altered by measuring the output of genes. Specifically the point made in bullet (iii) stands out to me; having a twenty fold increase in a single gene might not be too big a deal if the other participants in the proteins function cannot be altered by twenty fold as a result due to other rate limiting constraints; but if we can see related sets of genes with similar expression profiles, we can get a much better picture of the biological results of different expression.
The methods get dense pretty quickly, but are worth a shot to show how thorough the researchers were to insure that their findings were likely to be signficant. Essentially they performed three different statistical tests against their results of differentially expressed genes and broke their results down into genes that passed all three tests, two of three test, or one of three tests. Furthermore, a selected twenty genes were targeted with qPCR validation, which in all cases showed the expected directionality; i.e., if the expression was increased in the transcriptome analysis, qPCR analysis confirmed the increased expression.To provide another benchmark, they tested for other genes known to be associated with autism, REELN, and GFAP and found results consistent with other papers.
Having determined a large number of differentially expressed genes, the authors then went to try to analyze the known function of these genes.
These classifications were performed on a selected gene set that is differentially expressed between AUT and CONT subjects; based on the success of our qPCR validation, we decided to perform this analysis using transcripts that both reported an |ALR>1| and that reached p<0.05 in at least 2/3 statistical significance comparisons. Of 221 such transcripts, 186 had increased expression in AUT compared to CONT, while only 35 genes showed reduced expression in the AUT samples. We subjected these transcripts to an extensive literature search and observed that 72 out of 193 (37.3%) annotated and differentially expressed transcripts were either immune system related or cytokine responsive transcripts (Supplemental Material 2). Following this first classification, we were able to more precisely sub-classify these 72 annotated genes into three major functional subcategories, which overlap to a different degree; 1) cell communication and motility, 2) cell fate and differentiation, and 3) chaperones (Figure 3). The deregulation of these gene pathways might indicate that the profound molecular differences observed in the temporal cortex of autistic subjects possibly originate from an inability to attenuate a cytokine activation signal.
That last sentence packs a lot of punch for a couple of reasons. It would seem to be consistent with their statements regarding a “late recovery phase” of an autoimmune disorder; i.e., an immune response was initiated at some point in the past, but has yet to be completely silenced. This also isn’t the first time that the idea of problems regulating an immune response (i.e., the inability to attenuate a cytokine activation signal) has been suggested from clinical findings, for example, in Decreased transforming Growth Factor Beta1 in Autism: A Potential Link Between Immune Dysregulation and Impairment in Clinical Behavioral Outcomes, the authors found an inverse correlation between TGF-Beta1 and autism behavioral severity:
Given that a major role of TGFβ1 is to control inflammation, the negative correlations observed for TGFβ1 and behaviors may suggest that there is increased inflammation and/or ongoing inflammatory processes in subjects that exhibit higher (worse) behavioral scores.
As such, TGFβ has often been considered as one of the crucial regulators within the immune system and a key mediator in the development of autoimmune and systemic inflammation.
In summary, this study demonstrates that there is a significant reduction in TGFβ1 levels in the plasma of young children who have ASD compared with typically developing children and with non-ASD developmentally delayed controls who were frequency-matched on age. Such immune dysregulation may predispose to the development of autoimmunity and/or adverse neuroimmune interactions that could occur during critical windows in development.
[full paper from the link]
The theme of a critical window of development and enduring consequences of insults during that window is one that is getting more and more attention recently; this is an area that is going to get more and more attention as time goes by, and eventually, as the clinical data continues to pile up, meaningless taglines aren’t going to be enough to keep us from dispassionately evaluating our actions.
The Discussion section is particularly nice, I’ll try not to just quote the entire thing. Here are the really juicy parts.
The results of our study suggest that 1) in autism, transcript induction events greatly outnumbers transcript repression processes; 2) the neocortical transcriptome of autistic individuals is characterized by a strong immune response; 3) the transcription of genes related to cell communication, differentiation and cell cycle regulation is altered, putatively in an immune system-dependent manner, and 4) transcriptome variability is increased among autistic subjects, as compared to matched controls. Furthermore, our study also provides additional support for previously reported involvement of MET, GAD1, GFAP, RELN and other genes in the pathophysiology of autism. While the findings were obtained on a limited sample size, the statistical power, together with the previously reported postmortem data by other investigators suggest that the observed gene expression changes are likely to be critically related to the pathophysiology seen in the brain of the majority of ASD patients.
There is some description of studies using gene expression testing in the autism realm where the authors ultimately conclude that technical and methodological differences between the studies make them difficult to tie together coherently. There is another small section re-iterating the findings that were similar to single gene studies; i.e., REELN, MET, and GAD genes.
The most prominent expression changes in our dataset are clearly related to neuroimmune disturbances in the cortical tissue of autistic subjects. The idea of brain inflammatory changes in autism is not novel; epidemiological, (DeLong et al., 1981; Yamashita et al., 2003; Libbey et al., 2005) serological studies (Vargas et al., 2005; Ashwood et al., 2006) and postmortem studies (Pardo et al., 2005; Vargas et al., 2005; Korkmaz et al., 2006) over the last 10 years have provided compelling evidence that immune system response is an essential contributor to the pathophysiology of this disorder (Ashwood et al. 2006). Finally, converging post-mortem assessments and measurements of cytokines in the CSF of autistic children (Vargas et al., 2005), may indicating an ongoing immunological process involving multiple brain regions
Nothing really new here to anyone that is paying attention, but good information for the extremely common, gross oversimplification that ‘immune abnormalities’ have been found in autism, but we don’t have any good reason to think they may be part of the problem. Of course, this is an argument you’ll see a lot of the time regarding everyone’s favorite environmental agent.
Altered immune system genes are often observed across various brain disorders, albeit there are notable differences between the observed transcriptome patterns. The majority of neuroimmune genes found activated in the autistic brains overlap with mouse genes that are activated during the late recovery or “repair” phase in experimental autoimmune encephalomyelitis (Baranzini et al., 2005). This suggests a presence of an innate immune response in autism. However, the altered IL2RB, TH1TH2, and FAS pathways suggest a simultaneously occurring, T cell-mediated acquired immune response. Based on these combined findings we propose that the expression pattern in the autistic brains resembles a late stage autoimmune event rather than an acute autoimmune response or a non-specific immune activation seen in neurodegenerative diseases. Furthermore, the presence of an acquired immune component could conceivably point toward a potential viral trigger for an early-onset chronic autoimmune process leading to altered neurodevelopment and to persistent immune activation in the brain. Interestingly, recently obtained gene expression signatures of subjects with schizophrenia (Arion et al., 2007) show a partial, but important overlap with the altered neuroimmune genes found here in autism. These commonly observed immune changes may represent a long-lasting consequence of a shared, early life immune challenge, perhaps occurring at different developmental stages and thus affecting different brain regions, or yielding distinct clinical phenotypes due to different underlying premorbid genetic backgrounds.
The last sentence, regarding ‘long-lasting’ consequences of early life immune challenges is one that has a large, and growing body of evidence in the literature that report physiological and behavioral similarities to autism. We also have recent evidence that hospitilization for viral or bacterial infection during childhood is associated with an autism diagnosis. There is, of course, a liberal sprinkling of ‘mays’, ‘propose’, and ‘conceivably’ caveats in place here.
Earlier I mentioned that the authors studied gene networks in addition to single gene expressions., and that some of those findings were very significant. The results of this are found in Table 2. In one discussion, I had it pointed out to me by ScienceMom that it appeared that some of the networks were not found to be statistically significant (and ergo we should not necessarily assume that immune dysfunction was a participant in autism). [If you look at Table 2, some networks like a p value of 0000]. I decided to use the data in this paper for another project that isn’t ready yet, but in that process I was able to speak directly with one of the authors of this paper. I asked him about this, and he told me that this was a function of space limitations; all of the gene networks described were found to be statistically signficant, but in some instances there wasn’t enough space to typeset the p value. In fact, some networks were found to be differentially expressed with a p-value of .000000000000001. (!!!!!!!!) That isn’t a value that you see very often.
I recently got a copy of Mitochondrial dysfunction in Autism Spectrum Disorders: cause or effect, which shares an author with this paper, Persico. In that paper, they reference Immune Transcriptome Alterations In the Temporal Cortex of Subjects With Autism, invoking a potential cascade effect of prenatal immune challenge, inherited calcium transport deficiencies, and resultant mitochondrial dysfunction that could lead to autism. I’ve generally stayed away from the mitochondria stuff in the discussion realm; even though I think it is probably somewhat important to some children, and critically important to a select few children, I’ve mostly found that the discussion of mitochondrial issues is comprised of two sets of people talking past one another so as to prove something, or disprove something about everyones favorite environmental agent; but this is a neat paper that I’d like to get to eventually.
– pD
Super Cool Study: Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain
Posted on: April 25, 2010
- In: Autism | BCL-2 | Brain | Epigenetics | Epigenome | Fatemi | Genetics | Hu | Immunology | Inflammation | Intriguing | Oxidative Stress | Purkinje | RORA | Some Jerk On The Internet | The Fairytale | Uncategorized
- 4 Comments
So this is a really cool paper by some folks that have a series of interesting stuff: Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. Here is the abstract:
Autism is currently considered a multigene disorder with epigenetic influences. To investigate the contribution of DNA methylation to autism spectrum disorders, we have recently completed large-scale methylation profiling by CpG island microarray analysis of lymphoblastoid cell lines derived from monozygotic twins discordant for diagnosis of autism and their nonautistic siblings. Methylation profiling revealed many candidate genes differentially methylated between discordant MZ twins as well as between both twins and nonautistic siblings. Bioinformatics analysis of the differentially methylated genes demonstrated enrichment for high-level functions including gene transcription, nervous system development, cell death/survival, and other biological processes implicated in autism. The methylation status of 2 of these candidate genes, BCL-2 and retinoic acid-related orphan receptor alpha (RORA), was further confirmed by bisulfite sequencing and methylation-specific PCR, respectively. Immunohistochemical analyses of tissue arrays containing slices of the cerebellum and frontal cortex of autistic and age- and sex-matched control subjects revealed decreased expression of RORA and BCL-2 proteins in the autistic brain. Our data thus confirm the role of epigenetic regulation of gene expression via differential DNA methylation in idiopathic autism, and furthermore link molecular changes in a peripheral cell model with brain pathobiology in autism.
[As always, any emphasis is my own.]
This group has published a couple of papers that utilized similar study groups, methodologies, and means to display their findings, all of which I would recommend to anyone interested in learning; specifically, Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes [full paper available!], Gene expression profiling differentiates autism case-controls and phenotypic variants of autism spectrum disorders: evidence for circadian rhythm dysfunction in severe autism [full version available!], and Gene expression profiling of lymphoblasts from autistic and nonaffected sib pairs: altered pathways in neuronal development and steroid biosynthesis [full paper available!].
There are a couple of things I really like about their methodology and presentation style.
1) Several studies, including the most recent, included twins with discordant autism severity as study participants as a way to gain insight into the impact of genetic expression, as opposed to genetic structure on autistic behaviors. The highly cited heritability of autism in twins is used as evidence that the condition is predominantly mediated through genetics, and while no doubt genetic structure is important, by using genetic clones with different manifestations of autism severity, the authors are able to ascertain information about which genes are being affected in twins.
2) The two stage nature of the study design allows for both large scale analysis of a great number of genes being expressed differentially by genome wide scan, the results of which can be used for highly targeted confirmation by tissue analysis. Further, the use of cells available in the periphery, lymphobastoid cell lines (LLCs) as measurement points for genetic expression, allows for well thought out investigations of a very rare resource, post morten brain tissue from autistics. In this instance, different methylation profiles identified from LLCs from blood samples gave the researchers a starting point for what to look for in the brain tissue.
3) This paper ties together both genetic expression and epigenetics; i.e., not only that genes are being used differently, but it forwards our understandings of the means by which this is happening. Earlier studies by this group have found differences in genetic expression previously, but hadn’t elucidated on the specific mechanisms of action, in this case, over methylation, and consequent silencing of genetic protein production.
4) This is the first group of papers I’ve seen that have been using a bioinformatics approach to understanding the pathways affected by their findings; there may be other papers out there in the autism realm, (and almost certainly in others), that have been performing this type of analysis, but I haven’t run into them. Several of their papers, including the circadian rhythm paper, provide illustrations of associations to biological conditions and pathologies associated with affected networks. Here is an example from the latest paper. (Sarcastic apologies for those running at 800 / 600)
This type of illustration is the death knell for the argument that autism is a condition to be handled by psychologists; there are a couple of similar ones in the paper.
Considering those points, here are some juicy parts from the paper itself. From the introduction:
In this study, we use global methylation profiling of discordantly diagnosed monozygotic twins and their nonautistic siblings on CpG island arrays to test the hypothesis that differential gene expression in idiopathic autism is, at least in part, the result of aberrant methylation. Our study reveals distinct methylation differences in multiple genes between the discordant MZ twins as well as common epigenetic differences distinguishing the twins (the undiagnosed twin exhibiting milder autistic traits that are below the threshold for diagnosis) from nonautistic sibling controls.
There are essentially three groups, twins with different autism severity, and non autistic siblings. One thing that I’m not cerrtain of here is whether or not there were methylation differences found between the twins and their non autistic siblings or not; the text above is a little unclear; i.e., as there are different mechanisms by which genetic expression can be modified besides methylation, this may mean that while there were expression differences found between autism and controls, those differences were not found to be attributed to differential methylation levels. (?)
From the results:
Network analysis was then performed to examine the relationship between this set of genes and biological processes. As shown in Fig. 1B, many of the associated processes within the network, including synaptic regulation, fetal development, morphogenesis, apoptosis, inflammation, digestion, steroid biosynthesis, and mental deficiency, have been associated with autism. Two genes from this network, BCL-2 and RORA, were selected for further study because of their respective roles in apoptosis and morphogenesis/inflammation. Interestingly, BCL-2 protein has been previously demonstrated to be reduced in the cerebellum and frontal cortex of autistic subjects relative to control subjects (31, 32), but RORA, a nuclear steroid hormone receptor and transcriptional activator that is involved in Purkinje cell differentiation (33) and cerebellar development (34), has never before been implicated in autism. In addition, RORA, a regulator of circadian rhythm (35), is also neuroprotective against inflammation and oxidative stress (36), both of which are increased in autism (37, 38).
Several of the tables are pretty cumbersome to paste in, but do provide more detailed functional level impacts of some of the functions of the differentially methylated genes identified. Even with the text above, however, we can see a lot of sweet spots being touched on, including several that were identified in previous studies by this group of researchers. It also illustrates some of the very powerful techniques in use; a broad array of genes were scanned for differential expression, some with different expression and significant roles in processes known to be abnormal in the autism population are identified, and used for further, more pinpointed analysis.
As noted, Fatemi found reduced BCL-2 in post mortem brain samples in two studies; one of the roles played by BCL-2 is apoptosis, or programmed cell death. By way of example, here is a study that shows that knockout (or in this case, knockup) mice that overexpress BCL-2 have more Purkinje cells than their non modified counterparts, which states, in part:
Because bcl-2 overexpression has been shown to rescue other neurons from programmed cell death, the increase in Purkinje cell numbers in overexpressing bcl-2 transgenics suggests that Purkinje cells undergo a period of cell death during normal development.
Considering that reductions in Purkinje cells is among the most commonly found brain difference in autism, a reduction in BCL-2 seems appropriate. The fact that it in this case it was methylation levels leading to a reduction in BCL-2 might also be of interest in regards to the Fairytale Of The Static Rate of Autism; here we have evidence that mechanisms other than genetic structure are leading to decreases in a protein known to protect Purkinje cells from apoptosis.
I don’t know anything about RORA, but its list of functions make a lot of sense when we consider other findings; a relative dearth of a protein known to protect against neuroinflammation and oxidative stress and a regulatory role in the sleep cycle.
The authors also noticed a dose dependent relationship between expression levels, which in this case represented a silencing of genes and autism severity.
Quantitative RT-PCR was used to confirm decreased expression of BCL-2 and RORA in autistic samples and to evaluate the effect of a global methylation inhibitor, 5-Aza-2-deoxycytidine, on gene expression. For both BCL-2 and RORA, gene expression was significantly higher (P_0.05) in the unaffected control than autistic co-twins (Fig. 4A). Generally, the diagnosed autistic co-twin (_A) had the lowest level of expression of BCL-2 and RORA, while the milder undiagnosed co-twin (_M) exhibited transcript levels between that observed for unaffected sibling controls and autistic co-twins. This suggests a quantitative relationship between phenotype and gene expression of these 2 genes, although additional studies are required to confirm this observation
Again, this makes plenty of sense if we believe that things like a neuroinflammation, oxidative stress have parts to play in the behavioral manifestation of autism; in this case, get more methylation, and hence, less RORA and BCL-2, which, in turns, makes you more susceptible to neuroinflammation, oxidative stress, and Purkinje cell development abnormalities.
If we take the predisposition towards problems with inflammation for a closer look, we can find that several other papers, including Grigorenko, Enzo, and Ashwood have all found that a propensity for inflammation, or a propensity towards abnormal regulation of inflammation have correlations with autism severity. Though potentially inconvenient, this would seem to lend additional evidence for a causal role of immune based pathology in autism, as opposed to autism causing immune abnormalities.
The discussions section has a lot of good text that is largely a touch up on what we already have here. Here are some good quotes:
In particular, functional and pathway analyses of the differentially methylated/expressed genes showed enrichment of genes involved in inflammation and apoptosis, cellulardifferentiation, brain morphogenesis, growth rate, cytokine production, myelination, synaptic regulation, learning, and steroid biosynthesis, all of which have been shown to be altered in ASDs. The candidate genes were prioritized for further analyses by identifying the overlap between the differentially methylated genes and those that had been shown to be differentially expressed in the same set of samples in previous gene expression analyses (18). Pathway analyses of this filtered set of genes thus focused our attention on 2 genes, BCL-2 and RORA, as potential candidate genes for ASDs whose expression may be dysregulated byaberrant methylation. As shown in Figs. 3 and 4, respectively, RORA was confirmed to be inversely differentially methylated and expressed in LCLs from autistic vs. nonautistic siblings,with expression dependent on methylation, as demonstrated by the absence of methylation in the presence of 5-Aza-2-deoxycytidine. Notably, we also show by immunohistochemical staining of cerebellar and frontal cortex regions of autistic vs. normal brain (Figs. 5, 8), that RORA protein is noticeably reduced in the majority ofthe autistic samples relative to age- and sex-matched controls. This reduction is also specifically demonstrated in Purkinje cells, which are dependent on RORA for both survival and differentiation (Fig. 7). These findings thus link molecular changes identified in a peripheral cell model of ASDs to actual pathological changes in the autistic brain, suggesting that LCLs is an appropriate surrogate for studies on autism.
Finally, this paper generated a lot of press, in part (I think), because somewhere, someone (the authors?), apparently made note of the fact that this type of feature, hypermethylation, is potentially treatable, raising the possibility of palliative avenues. (Or was this just a function of the fact that it was a finding that wasn’t truly genetic, and thus, ‘fixable’?) While technically true, I am of the opinion that this is a long ways off; the authors found large numbers of differentially methylated genes; some were also hypomethylated. The drugs that we know are capable of epigenomic modifications right now, some are used in advanced cancer patients, for example, are not discriminatory in their actions. What we really would need would be targeted unmethylators that we could use to attach to RORA and BCL-2 genes and specifically free them up to produce more protein. The same week that this paper came out, another paper was published, entitled Epigenetic approaches to psychiatric disorders which speaks towards this complexity.
– pD
- In: Autism | Epigenetics | Epigenome | Genetics | Phenotypes | Uncategorized
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Hello friends –
A while ago I saw a completely fascinating Nova called Ghost In Your Genes concerning the nascent field of epigenetics, the study of the relative expression of genes, which is a bit different than the presence or absence of genetic differences. I’d recommend this program to anyone interested in learning.
In a general sense, our genes are simply blueprints for the production of proteins; the traditional model of genetic research involves structural changes in the genetic blueprints, so that we might understand that a person with a particular mutation might produce more, or less, of a particular protein than someone without that mutation. As protein gradients are altered, physiological effects accumulate, and we can begin to associate genetic differences with identifiable classifications.
But. It turns out, structural differences in the DNA aren’t the only way to affect the production of genes. Genes can also be regulated by a variety of factors, and these changes in regulation, in turn, are measured as expression of genes, essentially a measure of which genes are active, or inactive, and to what extent.
From Wikipedia:
In biology, epigenetics is the study of inherited changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence, hence the name epi- (Greek: επί– over, above) –genetics. These changes may remain through cell divisions for the remainder of the cell’s life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism;[1] instead, non-genetic factors cause the organism’s genes to behave (or “express themselves”) differently.[2]
For another interesting write up, see this one by PZ Meyers; it gets technical quickly, but is a nice read. Specific mechanisms aside, it is sufficient for our purposes that epigenetics is the study of how a variety of non structural changes can affect how our genes operate.
An analogy might of a series of car engines, sitting at idle. All of them power a car, but at a structural level there are differences, most models are roughly generating the same amount of force at idle, but, for example, the Prius engine is generating much lower force than Porsche engine. At a very general level, we might consider physical mutations of our genome and protein generation capacities to be equivalent to the difference between the Porshce and the Prius at idle. But there are other means to affect the energy being put out by the engine, the accelerator, tweaking the cylinders, or a variety of other means. This is a big shift and weights heavily on the ‘genetic and environment interaction’ theme that gets a lot play in the autism realm. Despite a lot of studies, and spectrums of dollars there have been very few findings involving autism genes that do anything but confer a very limited risk of a diagnosis. Furthermore, a lot of the studies are finding that seemingly very common mutations are implicated, but with very delicate effects. An example of this might be the MET genes, that have several neat papers (here, here, here), but the specific MET-C allele associated with autism is still very common, found in nearly fifty percent of everyone. None the less, it is just a little more prevalent in the autism cohort, but the impact is very subtle, and likely dependent on the presence of a variety of other genes (or expression patterns), or other factors. Excepting known genetic conditions that confer great risk, but can be responsible for only a fraction of our autism, mutations such as Fragile-X or Rhett Syndrome, the vast majority of genetic findings impart small increases in risk.
But once we start looking at the wide array of different genetic expression in autism, it becomes clear that which genes you use, and to what extent, might be as important as which genes you are born with. By way of example, a very cool paper out recently, “Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain ” that is available in full online and I would recommend to anyone interested in how analyzing epigenetic changes and the accompanying differential gene expression can teach us more about autism. A lot of the press around this study involves the hope that eventually this kind of finding might lead a treatment opportunities, something I personally consider to be a long term goal that still faces significant technical hurdles; but it does gives us insight into the nature of autism, and the usefulness of the half truth ‘differently wired’ argument concerning autism treatments.
– pD
Note: Updated link to PZ.
passionless Droning about autism 
