passionless Droning about autism

Archive for the ‘Epigenetics’ Category

Hello friends –

One of the more beautiful and terrifying concepts I’ve come across in the last year or so is the idea of ‘developmental programming’, or sometimes fetal programming, or as I imagine it will eventually be recognized, the realization of subtle change is still change, and subtle change during critical timeframes can amplify into meaningful outcomes.  The underlying hypothesis is that environmental influences during early life, gestation, infancy, or even childhood, have the capacity to permanently influence physiological and behavioral state into adulthood.  The available evidence implicates the potential for developmental programming to be involved with an assortment of conditions that on the whole, you’d rather not have than have, including the spectrum sized set of disorders grouped as ‘metabolic syndrome’ that incorporates several risk factors for cardiovascular disorders, obesity, type II diabetes.  There is also less pronounced evidence for some autoimmune disorders, and perhaps, autism. 

Here is the most concise explanation of developmental programming I’ve seen so far, from Developmental Programming of Energy Balance and Its Hypothalamic Regulation

The concepts of nutritional programming, fetal programming, fetal origins of adult disease, developmental origins of health and disease, developmental induction, and developmental programming were all conceived to explain the same phenomenon: a detrimental environment during a critical period of development has persistent effects, whereas the same environmental stimulus outside that critical period induces only reversible changes.

I am absolutely in love with the importance of time dependent effects, a sort of combo pack of why the dose doesn’t always make the poison, and the importance of understanding subtle interactions in developing systems. 

The area of developmental programming that has a ton of research in the human field and animal models is the link between metabolic syndrome and a differently structured uterine and/or early postnatal environment.  A nice review from 2007, Developmental programming of obesity in mammals (full paper) has this:

Converging lines of evidence from epidemiological studies and animal models now indicate that the origins of obesity and related metabolic disorders lie not only in the interaction between genes and traditional adult risk factors, such as unbalanced diet and physical inactivity, but also in the interplay between genes and the embryonic, fetal and early postnatal environment. Whilst studies in man initially focused on the relationship between low birth weight and risk of adult obesity and metabolic syndrome, evidence is also growing to suggest that increased birth weight and/or adiposity at birth can also lead to increased risk for childhood and adult obesity. Hence, there appears to be increased risk of obesity at both ends of the birth weight spectrum.


Childhood and adult obesity are amongst the cardiovascular risk factors now considered to be ‘programmed’ by early life and, perhaps counter-intuitively, babies subjected either to early life nutritional deprivation or to an early environment over-rich in nutrients appear to be at risk. Supportive evidence includes the observation of a ‘U-shaped’ curve which relates birthweight to risk of adult obesity (Curhan et al. 1996).

[Check out that example of a hormetic dose curveTotally sweet!]

The list of papers supporting a link between abnormal gestational or birth parameters and subsequent obesity in the offspring is very, very voluminous.   The satellite level high view of the research starts with Dutch mothers during a time of famine, and the observations that these children were much more likely to be obese at nineteen in Obesity in young men after famine exposure in utero and early infancy.  Later, infants in England were found to have birth weight positively correspond to adult weight in Birth weight, weight at 1 y of age, and body composition in older men: findings from the Hertfordshire Cohort Study (full paper).  A study with twin pairs, Birth weight and body composition in young women: a prospective twin study  had similar findings, but with the additional coolness factor of being able to detect differences between genetically identical twins who happened to be born at different weights.  There are studies on infants that are born light but then ‘catch up’are consistently more likely to be obese, a review of which can be found in Rapid infancy weight gain and subsequent obesity: systematic reviews and hopeful suggestions.  Startlingly, Weight Gain in the First Week of Life and Overweight in Adulthood observed that formula fed babies who gained considerable weight during the first eight days after birth were more likely to be obese as adults, similar to other findings implicating formula fed babies with adult obesity.

Therearealsoconservativelya bazillionanimalmodelsthattellusthatthestudiesin humans are accurate.

Part of me hates the deterministic nature of these findings, it’s really just an extension of the fatalism of genetic assignment, but on the other hand, the data is the data.  I must admit, I am in love with the underlying evolutionary cleverness of the thrifty phenotype end of the U curve on display; a fetus or neonate that is deprived of nutrients, or perhaps, some types of nutrients, programs itself for an environment in which food is scarce, handling calories differently at a very fine grained metabolic level.  From a survival standpoint this modification is most definitely the smart move; all inbound indicators are signaling to the fetus that calorie acquisition is going to be tough on the outside, and as a result, the physiology is tweaked so that baby is ready to make the absolute most of any available nutrients.  If that child, however, is raised in a world with plentiful calories, if not always, beneficial calories, they tend to store fat more readily than a baby/child/adult that did not receive the same messages in utero.  Neat.

Like lots of things I seem to be running into, our observations of what is happening seem to be more advanced than our understanding of how it is happening.  The ideas of developmental programming have been around for a while, but we are still very much in the learning phase regarding mechanism of action, a very thorough review that I ran into can be found here:  Mechanisms of developmental programming of the metabolic syndrome and related disorders.   (full paper). 

Another example of programming a bit closer to home to the autism world has been in the news lately, namely the replication of findings that children who grow up around farm animals, or in some cases, pets, are less likely to suffer from allergies and /or asthma than children who grow up without that exposure.  These findings are also very robust, and appear to implicate similar critical developmental timeframes including the gestational environment, infancy, and toddlerhood. 

Here is an example of the kind of thing in this area,  Farming environment and prevalence of atopy at age 31: prospective birth cohort study in Finland

Cross-sectional studies have shown an association between the farming environment and a decreased risk of atopic sensitization, mainly related to contact with farm animals in the childhood. Objective Investigate the association of a farming environment, especially farm animal contact, during infancy, with atopic sensitization and allergic diseases at the age of 31. Methods In a prospective birth cohort study, 5509 subjects born in northern Finland in 1966 were followed up at the age of 31. Prenatal exposure to the farming environment was documented before or at birth. At age 31, information on health status and childhood exposure to pets was collected by a questionnaire and skin prick tests were performed. Results Being born to a family having farm animals decreased the risk of atopic sensitization [odds ratio (OR) 0.67; 95% confidence interval (CI) 0.56-0.80], atopic eczema ever (OR 0.77; 95% CI 0.66-0.91), doctor-diagnosed asthma ever (OR 0.74; 95% CI 0.55-1.00), allergic rhinitis at age 31 (OR 0.87; 95% CI 0.73-1.03) and allergic conjunctivitis (OR 0.86; 95% CI 0.72-1.02) at age 31. There was a suggestion that the reduced risk of allergic sensitization was particularly evident among the subjects whose mothers worked with farm animals during pregnancy, and that the reduced risk of the above diseases by farm animal exposure was largely explained by the reduced risk of atopy. Having cats and dogs in childhood revealed similar associations as farm animals with atopic sensitization. Conclusion and Clinical Relevance Contact with farm animals in early childhood reduces the risk of atopic sensitization, doctor-diagnosed asthma and allergic diseases at age 31.

That is one hell of a long running study and the findings are consistent with a wealth of similar studies across populations, including Exposure to environmental microorganisms and childhood asthma, and Effect of animal contact and microbial exposures on the prevalence of atopy and asthma in urban vs rural children in India.  These findings are part and parcel with the Hygiene Hypothesis, the idea that a relative reduction in ‘training’ of the immune system can lead to disturbances in normal immune system development and consequent development of autoimmune disorders.   (Here’s a nice review of the evidentiary backing for the Hygiene Hypothesis) From a clinical viewpoint, there are reasons to suspect this is a biologically plausible pathway; in Environmental exposure to endotoxin and its relation to asthma in school-age children the researchers reported an inverse relationship between the amount of endotoxin (i.e., a bacterial fingerprint that is recognized by the immune system) and the immune  response, stating, “Cytokine production by leukocytes (production of tumor necrosis factor alpha, interferon-gamma, interleukin-10, and interleukin-12) was inversely related to the endotoxin level in the bedding, indicating a marked down-regulation of immune responses in exposed children.”  We can also see immunomodulatory effects of farm or rural living in the cytokine profiles of breast milk between two populations, as reported in Immune regulatory cytokines in the milk of lactating women from farming and urban environments, which found much higher concentrations of TGF-Beta1, a critical immune modulator, in breastmilk and collustrum of ‘farm mothers’.  The concentration of TGF-Beta1 in breastmilk had already been implicated in infant development of atopic disease in Transforming growth factor-beta in breast milk: a potential regulator of atopic disease at an early age

The evidence supporting developmental programming in these instances is very problematic to overcome, clearly there are mechanisms by which the events of very early life can cause persistent changes to physiology into adulthood; be they changes ‘designed’ to be adaptive, or disturbed trajectories of usually tightly regulated systems that find inappropriate targets in an environment different than what our ancestors evolved in.  I’d note that none of what is above invalidates any findings of genetic involvement with cardiovascular problems, obesity, or asthma, but it should serve as a portrait of how genetic recipes are only part of the process. 

So, what about autism?  This is, admittedly, where things get a bit more speculative, there isn’t the same type of epidemiological evidence in the autism arena as what we see above.  Part of this discrepancy is an artifact of the fuzzy nature of autism, a bazillion different conditions each with their own personalized manifestation, a much more daunting set of variables to detangle compared with measuring BMI, triglyceride levels or asthma.  Those caveats in place, there is still room to discuss some potential examples wherein early life experiences might be participating in ‘programming’ some of what we see in autism. 

A nice review paper that speaks directly towards a developmental programming model that involves autism is Early life programming and neurodevelopmental disorders that includes as an author, Tom Insel, head of the National Institute of Mental Health, and generally, one of the good guys.   This is part of the abstract.

Although the hypothesized mechanisms have evolved, a central notion remains: early life is a period of unique sensitivity during which experience confers enduring effects. The mechanisms for these effects remain almost as much a mystery today as they were a century ago (Insel and Cuthbert 2009). Recent studies suggest that maternal diet can program offspring growth and metabolic pathways, altering lifelong susceptibility to diabetes and obesity. If maternal psychosocial experience has similar programming effects on the developing offspring, one might expect a comparable contribution to neurodevelopmental disorders, including affective disorders, schizophrenia, autism and eating disorders. Due to their early onset, prevalence and chronicity, some of these disorders, such as depression and schizophrenia, are among the highest causes of disability worldwide (World Health Organization, 2002). Consideration of the early life programming and transcriptional regulation in adult exposures supports a critical need to understand epigenetic mechanisms as a critical determinant in disease predisposition.


A concise explanation of the concept of developmental programming and the need for more finely detailed understandings of the likely epigenetic underpinnings.  Also included is a discussion of things like maternal stress during gestation, childhood environmental enrichment (or more specifically, ‘de-enriched’ or otherwise, terrible situations), and prenatal infection models.  Nice.  

What about specifics for the autism arena?  One environmental event that most everyone agrees can increase risk of an autism diagnosis is an immune challenge in the gestational period.  The animal models are robust and have been replicatedacross laboratories and epidemiological data supports an association.  A lot of groups have been studying the effects of maternal immune activation in animal models the past few years, what we can see are some striking parallel veins to what is observed in autism that involve the concept of developmental programming. 

One paper, with a title I love, is  Neonatal programming of innate immune function.  Here is a snipet of the abstract from the first paper:

There is now much evidence to suggest that perinatal challenges to an animal’s immune system will result in changes in adult rat behavior, physiology, and molecular pathways following a single inflammatory event during development caused by the bacterial endotoxin lipopolysaccharide (LPS). In particular, it is now apparent that neonatal LPS administration can influence the adult neuroimmune response to a second LPS challenge through hypothalamic-pituitary-adrenal axis modifications, some of which are caused by alterations in peripheral prostaglandin synthesis. These pronounced changes are accompanied by a variety of alterations in a number of disparate aspects of endocrine physiology, with significant implications for the health and well-being of the adult animal.

Another very cool, and very dense, paper with a salient title and content by the same group is  Early Life Activation of Toll-Like Receptor 4 Reprograms Neural Anti-Inflammatory Pathways (full paper) which reports that a single early life immune challenge results in persistently altered response to immune stimulants into adulthood, with differential responses in the CNS compared to the periphery.  Especially interesting in this paper is that the researchers have dug down a layer into the biochemical changes affected by early life immune challenge and found that alterations to HPA-Axis metabolites are responsible for the changes. 

Tinkering around with the HPA-Axis, an entangled neuroendicrine system that touches on stress response, immune function, mood, and more can have a lot of disparate effects.  It turns out, there is evidence that early life immune challenges can also modify behaviors in a way consistent with altered stress responses.

For example, the very recently published Peripheral immune challenge with viral mimic during early postnatal period robustly enhances anxiety-like behavior in young adult rats has a short, but to the point abstract:

Inflammatory factors associated with immune challenge during early brain development are now firmly implicated in the etiologies of schizophrenia, autism and mood disorders later in life. In rodent models, maternal injections of inflammagens have been used to induce behavioral, anatomical and biochemical changes in offspring that are congruent with those found in human diseases. Here, we studied whether inflammatory challenge during the early postnatal period can also elicit behavioral alterations in adults. At postnatal day 14, rats were intraperitoneally injected with a viral mimic, polyinosinic:polycytidylic acid (PIC). Two months later, these rats displayed remarkably robust and consistent anxiety-like behaviors as evaluated by the open field/defensive-withdrawal test. These results demonstrate that the window of vulnerability to inflammatory challenge in rodents extends into the postnatal period and offers a means to study the early sequelae of events surrounding immune challenge to the developing brain.

The methodology is very similar to what we see in a lot of animal models of early life immune activation, convince a young animals immune system that they are under microbial attack by mimicking either bacterial or viral invaders, and then measure behaviors, or physiology, later in life. This study could be seen as a complement to a much earlier (2005) paper, Early life immune challenge–effects on behavioural indices of adult rat fear and anxiety, which used a different immune stimulant (bacterial fingerprint/LPS versus viral fingerprint/Poly:IC), but which found generally consistent results.

There are more, for example, Early-Life Programming of Later-Life Brain and Behavior: A Critical Role for the Immune System (full paper), which reviews animal study evidence that early life immune challenges can have lifelong effects.  Here is part of the Introduction:

Thus, the purpose of this review is to: (1) summarize the evidence that infections occurring during the perinatal period can produce effects on brain and subsequent behavior that endure throughout an organism’s life span, and (2) discuss the potential role of cytokines and glia in these long-term changes. Cytokines are produced within the brain during normal brain development, but are expressed at much higher levels during the course of an immune response. In contrast to overt neural damage, we present data indicating that increased cytokine exposure during key periods of brain development may also act as a “vulnerability” factor for later-life pathology, by sensitizing the underlying neural substrates and altering the way that the brain responds to a subsequent immune challenge in adulthood. In turn, this altered immune response has significant and enduring consequences for behavior, including social, cognitive, and affective abilities. We discuss the evidence that one mechanism responsible for enduring cytokine changes is chronic activation of brain microglia, the primary immunocompetent cells of the CNS.

Check that out!  We have several papers showing, indeed, a ‘chronic activation of brain microglia’ in the autism population; one way, it seems, to achieve this, is ‘increased cytokine exposure during key periods of brain development’.  (Ouch!) 

Is developmental programming the mechanism by which gestational immune activation raises the risk of autism?  I don’t think we can answer that question with any authority yet, but the logical jumps to arrive at that conclusion are small, and  are supported by a great deal of evidence.  No doubt, we’ll be learning more about this in the years to come.

Ultimately, I think what all of this means is that, as usual, there is another layer of complexity thrown into the mix.  As far as autism goes, it seems likely that at least some of our children are manifesting behaviors consistent with autism as a result of things that happened to them very, very early in their life.  Figuring out if this is happening, how it is happening, and to which individuals, is a daunting, very difficult task; but at least we are approaching a level of knowledge to allow for such an endeavor.

This posting focused on the bad stuff, but the inverse is just as meaningful, having a ‘normal’ gestational period as far as nutrients go, programs you towards a more healthy weight, and being born to a mother exposed to a variety of microbial agents, as the overwhelming majority of mothers were for most of human existence, programs you away from asthma.  But from a broader standpoint, from a ‘every human on the planet’ view, I think we must begin to recognize that everyone is being programmed, in some ways for good, in others, for not so good.  Curiosity and thoughtful analysis is our way to illuminate the beautiful and dispassionate gears that propel the machinations of nature; developmental programming is one of the cogs in the natural world, hopefully, one day, we will acquire the wisdom to refine the program for our benefit, but in the meantime, it is still exciting to witness the discovery of the inner workings.


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.


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 activityBDNF 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

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:

Effects of perinatal hypothyroidism on regulation of reelin and brain-derived neurotrophic factor gene expression in rat hippocampus: Role of DNA methylation and histone acetylation

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

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:

Table 1

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).
Lastly, the participants were scanned for antibodies to CMV, a persistent herpesvirus found in almost all humans, and can be used as a biomarker to indicate compromised immune function.  Significant differences in antibodies were observed between the two groups.

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.


Hello friends –

I ran across this one on accident the other day (why wasn’t it in one of my pubmed alerts?):

Gestational Age at Delivery and Special Educational Need: Retrospective Cohort Study of 407,503 Schoolchildren


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.


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

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:

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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

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