Archive for the ‘The Fairytale’ Category
The Fairytale of a Static Rate of Autism Part 5 – The Prevalence Jackpot Versus The Prevalence Hookup, Futilely Struggling To Making Sense Out of Static, And How Journey Autism Flavors Our Path Of Moving Forward
Posted on: April 17, 2013
Hello friends –
There used to be a poker room about twenty miles from my home; it sat above a run down greyhound racing track and smelled like an old shoe on the best day. But they had poker. They hosted an accumulating jackpot hand, usually worth a couple of thousand dollars, sometimes quite a lot more, which you could win if you got a royal flush in the current suit; i.e., if the suit was hearts, and you wound up with 10-J-Q-K-A hearts, you’d win the Jackpot. This could lead to some unusual cost/reward analysis scenarios.
Let’s say you sit down to play and buy in for a hundred dollars. Then, three hands later, you look at your two hole cards and you have 10-J hearts. Not really a great hand, but if the board winds up showing Q-K-A hearts somewhere in the next five cards, you win fifteen thousand dollars (or whatever the Jackpot had accumulated to). Almost everyone folds, but before you get a chance to see the next three cards for the two measly dollars you put up as a blind, an aggressive, serial over-better to your right raises to fifteen dollars. You are in a tough spot, you know the guy bets like crazy anytime he thinks he can steal a pot, but you still are losing to anyone with a queen. If you had 10-J spades, or clubs, or mixed, or (nearly) whatever else, this is easy; you dump your shitty cards. But with your two royal heart cards, you *could* win the jackpot; your odds still totally suck, even if you were getting paid off a thousand to one you still didn’t have the ‘right’ odds to make the call, but if you inhabit a place where losing fifteen dollars won’t kill you, but winning fifteen thousand would definitely be a game changer, the magnitude of the potential winnings must be part of your decision making process.
I called the raise a few times, but never hit the jackpot. Or even came close.
I keep coming back to the idea of incorporating the scale of potential outcomes when I think about the non event of the hilarious prevalence numbers that came out a while, one in fifty with ‘autism’. Nobody outside of Journey Autism fucking cared and the responses were depressingly predictable; the media and the Internet skeptics went ‘full awareness’, and found nothing of any alarm in these numbers, the Internet vaccine crazies went ‘full autism’, and assumed the numbers were solely comprised of individuals who would need 24×7 assistance for forever. It was all a big joke. Haha.
I don’t know how large the real increase in autism is (the older parental age data tells us unambiguously that some of the increase is non-imaginary), but I do know that as our best efforts at figuring this thing out has left us skipping from one in two hundred and fifty, to one in a fifty in eight short years. To my eye, this means a real increase of fifty percent (or more!) could easily be hiding in the static and we’d never know. Most everyone doesn’t seem to care, that is the way of the Prevalence Hookup, quickly embracing whatever prevalence numbers come out, coupling until a set of newer, bigger, even more ‘greater awareness’ numbers come along.
But my thoughts continue to be formed by concept of a sort of missed jackpot opportunity when I see a sense of complacency about our ever growing autism population; it isn’t that I don’t believe that diagnostic changes and the watering down of what a diagnosis means in terms of life skills aren’t affecting rates, those factors are clearly at play, but the ramifications of just “some” of the increase being real seems like a big, big, big deal to me. When your population of interest is every child, a small real increase means a lot of individual children are affected. Sure, it is, possible that older parental age is the only recent development that is affecting rates upward, with all of the rest being diagnostics, but I find little comfort in this notion. If the soft social scientists are wrong, even a little, and there is a true increase in incidence, we may come to regret the solace provided by our collective bobbleheading at the mantra of ‘greater awareness’, for it enabled us to waste a great amount of precious time.
The thing is, it doesn’t really cost us that fucking much to apply more resources to the unimportant, nagging question on the neurodevelopment of a generation of infants. In 2006, Bush signed the ‘Combating Autism Act’, a bill included a billion of dollars for ‘research, surveillance, and treatment’. That’s two hundred million a year. Last year, The Avengers, a stupid and shitty movie, made over a billion dollars. Now, I know there are other funding sources for research, surveillance, and treatment, but there were also a lot of other stupid movies.
I believe that this prioritization is the equivalent of folding 10-J hearts to a dinky four dollar raise; the knowledge we could gain from a relatively small outlay is worth a lot. We shouldn’t be worrying about the cost, we should be considering the payoff; the question we are trying to understand, “are today’s infants neurobiologically different than infants of the last generation?” has a difficult to understate payoff. We shouldn’t be embracing reasons to stop playing, we should chomping at the bit to see the next three cards. This is an easy call.
And yet, there was a collective yawn when the CDC announced 2%.
Funny enough, it was just a few years ago that the UK NHS study of adults found a prevalence of 1%, a finding which was heralded as remarkably strong evidence that autism rates are stable (at the time, 1% was the general value for US children. Oh well.). For some reason, the robustness of the NHS adult findings didn’t cause anyone to exclaim that there is a sort of epidemic-lite, what with US kids having autism as twice the rate as NHS adults. It was a classic case of doublethink; US kids have autism at 2%, England adults have autism at 1%, and autism rates are stable. (Believing that any of the numbers have validity might be closer to triplethink!)
A while ago I saw an interview with Fombonne on the SFARI site that contained the unsurprising byline: ‘Eric Fombonne says that the new CDC report does not necessarily mean that prevalence is increasing’. [Note: This was BEFORE the 2% numbers were reported!] Anyway, he made some interesting points about the messiness of the autism data showing how silly the state by state numbers are; Utah has four times the cases that Alabama does, and utilized different diagnostic methods. In the text of the interview, he reveals Utah also had very low levels of MR (~ 13% instead of ~ 28%), AND had a creepy low male to female ratio. Either there is something really weird going on in Utah, or the ‘numbers’ from Utah and Alabama are not measuring the same thing. It could also be that the numbers are measuring some of the same thing, and there are a couple of weird things going on in Utah (heh). But the bigger point should be that we shouldn’t expect to get a decent understanding of autism rates at a national level by clumping together Alabama numbers, Utah numbers, and whatever other numbers, shaking up them up, and averaging them out. Maybe the headline ought to read, ‘Pretty much somewhere between half a percent, and two percent of children might have something a psychologist, or a doctor, or both, have something called autism, the manifestations and lifelong impact of which vary considerably individually and regionally’, or maybe ‘Autism Rates: Your guess is as good as ours!’.
I don’t trust any set of numbers more than an educated stab in the dark.
[Note: for a slightly different take on ADDM numbers, you can see this interview on SFARI, where Walter Zahorodny reports that detailed analysis of NJ data indicates a likely real increase in rates. Doh!]
I began to wonder; if almost nobody really seems worried about an ‘epidemic lite’, if no almost no one is alarmed that the confidence intervals in our data could incorporate huge numbers of actual people, why am I so concerned? Is my version of the precautionary principle overly cautious? I don’t know the answer to these questions, but I think that part of the answer lies within my journey autism, watching my son’s challenges (and triumphs) unfold, and the knowledge that whatever we find about autism incidence, he will be reliant on other people for his survival for his entire life. That is the gift autism has given him; it doesn’t mean he can’t be happy, it doesn’t mean he can’t experience love, but so far, we cannot detect that autism has provided him anything other than near debilitating OCD, an imperfect sense of dangerous situations, and a lifelong requirement of the kindness and capabilities of others.
I am filled with a pervasive and soul crushing sadness at the possibility of one ‘extra’ child having the same challenges because of changes we have collectively made to the environment, and that is the heart of the semantic dance over how much of the increase is real. That is the Jackpot.
But, your mileage may vary. I know that there are some parents and people out there who have challenges as heavy as my son’s, and they don’t share my sense of panic over the issue. A lot of people credit their autism with benefits. I won’t discount their experiences. Part of the reason we don’t see eye to eye may be that we look at the same question, but see different risks, and different payoffs.
– pD
Piling Up Small Changes, The Selective Skepticism Of Replacing One Fallacy With Another, And The Seductive Lure of Hubris Versus The Dispassionate Rules Of Nature
Posted on: September 28, 2012
Hello friends –
We keep on finding things that seem to very gently alter developmental trajectory towards (or away from) an eventual diagnosis of autism; a genetic variant here or there, an environmental exposure, or one of our very many experiments in cultural engineering. When these nudges are founded on genetic variances, they are often referred to as “low penetrance” risk factors; here is a snipet from the wiki definition for “Penetrance”
An allele with low penetrance will only sometimes produce the symptom or trait with which it has been associated at a detectable level.
I would argue, and have previously on this blog, that there isn’t a good reason that the descriptive of low penetrance should be relegated solely to genetic inputs. The ‘non-genetic’ factors we seem to have associated with autism risk, or protection, seem to inherit the same quality of a low grade impact; the risk of an autism diagnosis isn’t altered by too much, but instead, just a little.
There are a great number of examples of environmental impacts that seem to follow a low penetrance model of effect; maternal obesity, paternal age, cesarean section, maternal asthma, maternal folate ingestion [protective!], maternal use of anti-depressants (or being depressed?), low birth weight, and some perhaps some drugs given during pregnancy.
[Please, please note: I’m not “blaming the mother” here, but we do not have the luxury of invoking Bettleheim as a mechanism for avoiding evident truths. A dispassionate analysis of the data mandates we accept that the prenatal environment is critical.
If you think that some percentage of the autism ‘epidemic’ is real, you should realize that this issue is too important to be scuttled by emotional hotspots. You cannot blame yourself for things that were unknown to you during your pregnancy. If, instead, you don’t think autism rates have changed, none of the above impacts can be meaningful. Finally, if you believe that autism is more gift than disorder, then you aren’t getting blamed for anything anyways.]
Unfortunately, a mixture of subtle changes makes for a messy situation for our researchers for a few reasons; environmental studies contain a difficult to contend with set of confounders; knowing what to measure, when to measure it, and the often times necessary evil of usage of self reporting, computer models, or other proxies for exposure measurements. Making things even worse, it is biologically plausible, indeed, mandatory, that low penetrant effects operate with each other. What we will eventually need to be working on, for example, is determining the specific genetic dispositions that act in concert with a low birth weight and with gestational anti-depressant exposure to perturb neurodevelopment toward autism. That’s a tough thing to do.
Throwing this kind of disparate data into a blender at study time looks to be largely beyond our current capacities; researchers are struggling to identify single gene-environment interactions, for example, MET-C/pollutants, or the terrifying notion of RORA demythlation/endocrine disruptors interacting together. Looking at more, or a handful, as is likely necessary, is a long ways off.
I’ve been thinking about the intersection of these two things lately; our relative inability to evaluate for several, subtle, interacting forces, with the growing evidence that a great many mysterious conditions, including autism, seem to be governed by lots of small things occurring differently. I am left with the idea that are woefully unready to understand the participating factors in any particular case of autism, with similar reservations regarding our ability to know how much, if any, of the autism ‘epidemic’ is real.
A few weeks ago, there was an Op-Ed in the New York Times that speculated on the link between an in-utero environment characterized by increased inflammation and an eventual diagnosis of autism. I was largely in agreement with Moises Velasquez-Manoff on a the basic premise of his argument; especially regarding the state of the science on the immune findings in the autism realm, the use of helminths, not so much. A very widely read response by Emily Willingham accused the author of the piece of invoking a naturalist theory of the past:
Whether he means to or not, Velasquez-Manoff then echoes one of the favorite refrains of the anti-vaccine movement, that back when the world was a beautiful place of dirty, worm-infested children, clean water, 100% breastfeeding, and no television, it was a place where the immune system could do its work peacefully and with presumably Zen-like calm, weeding out the weak among us and leaving behind the strong.
I don’t think that the NYT article did anything of the sort, the author merely stated that there seem to be fewer signs of immune dysregulation and autoimmune conditions in some types of living conditions.
Then, a few weeks later, a widely publicized metadata study on organic eating came out. Again, the skeptics were ready to pummel the bruised body of the naturalistic fallacy, in this case, Stephen Novella at SBM:
Environmental claims for organic farming are complex and controversial – I will just say that such claims largely fall prey to the naturalistic and false dichotomy fallacies.
Stephen Novella’s version here is terse, but I think it is fair to say that in this context, the idea is that that if something is labeled as ‘natural’, that it then must be somehow superior to a ‘non-natural’ alternative, is a fair characterization of a naturalistic fallacy.
[The masochist could read through a few comments on that thread to see my take on the organic/non organic study; but the TL;DR version is, the study could have just as easily been titled, “Evaluations of Organic Eating Insufficiently Powered Or Designed To Know More Than The Most Primitive Endpoints, At Best”. Here is an NPR transcript where the presenter is a little more up front in that the state of the science is that health benefits have not been evaluated for.
But what I should point out here is that the studies of people were very limited. They were short-term and, like, narrowly focused. So they would look at pregnant women, for instance, and say, are pregnant women eating organic, are their children – did their children have left eczema or allergic conditions? So these are sort of narrowly focused studies. They were short-term, and there weren’t very many of them.
One of the few human studies in this metadata analysis involved a dietary intervention of one apple. What we have is a lack of evaluation, as opposed to a lack of findings, a familiar situation.]
Even so, it must be stated: The naturalistic fallacy(ies), as presented by the skeptics, and as believed by some fraction of grape-nut-eating-tarot-card-flipping people out there, is bogus. Things weren’t better way back then. Just because something is ‘natural’ doesn’t mean it is better, or without unknown consequences. Washing your hands is good, but antibiotics are also good, and work better when necessary. Breastfeeding is good, but it doesn’t keep your infant from getting cholera. Vaccines work. Modern agriculture is feeding a lot more of us than we used to be able to feed, and the hard truth be told, it is policies and habits that are leaving lots of people hungry. I don’t know if eating a organic diet is better for you or not, but I do know that I do like supermarkets.
But.
Our history is littered with the discarded arguments of people just as smart as us using rudimentary tools to understand complicated systems, declaring a lack of effect and throwing a contemptuous look over their shoulder at the rubes who long for the hilariously outdated solutions of yesteryear. We shouldn’t be concerned with the fact that the naturalistic fallacy is intellectually bankrupt; we should be concerned with the fact that our incredibly stupid species is changing our environment with reckless abandon on the assumption that we are smart enough to understand what we are doing. If the naturalistic fallacy is bad, the perfection-of-progess fallacy is almost as bad, with bonus negative points of being invoked by people who should know better.
How many examples do we need of our previous hubris until we realize that we are just barely less dumb now than we were then?
First we thought lead was safe as a pesticide, in paint, and as a gasoline additive. Then, we figured out it was only safe for paint and gasoline; then just in gasoline. Now, we know that any amount of measurable levels of lead are associated with cognitive effects. Any individual reader of this column was very likely an adult in 2002, and at that time, the state of our knowledge didn’t tell us that any amount of lead was less safe than no amount of lead. Ten goddamn years ago, the FDA thought there was a level of lead that in the bloodstream that did not affect cognitive function in children.
We have been performing increasingly optional cesarean sections for decades before starting to figure out that they are associated with adverse health effects for the lifespan. Only within the past few years have we discovered that this procedure is associated with altered microbiomes, obesity, and asthma.
We have been so successful at distributing products with based on plastic that over 90% of every human on the planet has detectable levels of component chemicals in their bloodstream. Only now that we have insured that nearly every human has been touched, we consistently find associations with metabolic and reproductive changes.
After near thirty years, the recommendations over administering Tylenol to infants was changed. In the 1980s we saw Reyes syndrome, made the association with aspirin, failed to observe any acute differences in infants given Tylenol, and pulled the trigger on global recommendation to replace aspirin with acetaminophen. It took decades before we were clever enough realize that eliminating Reyes might not have been the only thing we did, because we were too stupid to realize that effects do not have to be immediately obvious in order to have profound outcomes.
Human bodies were forged through the crucible of evolution, thousands of generations of adaptation, to be ready to start reproducing by the teens, and we have decided to start putting that process of for a decade, or two.
All of these examples are founded of the specificity of our analytical abilities, or rather a relative lack of specificity. We weren’t clever enough to understand to look for associations, so they remained invisible to us. A question never asked is never answered. Even worse, some of these are discrete events, disturbances orders of magnitude more simplistic to analyze compared to ‘eating organic’.
A lot of the skeptical sites will utilize the idea that humans are ‘pattern seekers’, especially when it comes to people reporting temporal associations with development of autistic behaviors and vaccination. I kind of like the idea of the pattern seeking human in general; the biggest pattern we seem to be seeing is the one that tells us that our current state of knowledge gives us enough information to understand what we are doing, a type of uber-pattern.
The idea that we have a decent understanding the effect of ingesting increased pesticide residue, a finding included in the organic metadata study, is a joke. The idea that we have the faintest clue of the outcomes of replacing infection with inflammation, a practice we have embraced with great enthusiasm, is a total fucking joke. We have barely bothered to look. Do not believe anyone who tells you otherwise.
This is what bothers me so much about a casual wielding of the naturalistic fallacy; it is so frequently a feint from critical questions. The discordance with reality of the naturalist fallacy has been established. It is great how much less suffering there is now, compared to then, but let’s not rest on our laurels. Am I the only one worried about how wrong we are here, now?
I don’t know if eating less pesticide is better than eating more pesticide, and I also can’t be sure that a lifestyle characterized by increased inflammation is a risk factor for developmental differences. I do know that the rules implemented by the natural world have no care for our hubris. Those same rules have violated our once pristine knowledge so dispassionately and with such regularity that I can find no pleasure in hurling the accusation of the naturalistic fallacy at anyone. Instead, the idea fills me with a sense of honorable mention at best; we are more capable than last century, last generation, last year, but we remain at the mercy of machinations which hold no regard for such incremental progress in knowledge in the face of unprecedented changes to our environment.
– pD
A Sense Of Relief After (Some Of) Your Phantoms Are Observed By Others, A Distillation of Humbling Complex Early Life Neuroimmune Literature: “Microglia in the developing brain: a potential target with lifetime effects”, and The Need For Dispassionate Analysis
Posted on: June 15, 2012
Hello friends –
I have a confession to make. The fact that a lot of very smart people have ignored or flat out laughed at my arguments bothers me sometimes. I have applied non-trivial, not to be rebated time and effort to put forth what I considered to be logical views, scientifically defendable and important ideas; and yet people I knew were otherwise rational, and in some cases, very intelligent, just hadn’t seemed to get what I was saying. Often this was within the context of a discussion argument of vaccination, but my larger concern, that of a non-imaginary, non-trivial increase in children with autism in the past decades, also usually falls on deaf ears. If “environmental changes” incorporate the chemical milieu of our mother’s wombs, the microbial world our infants are born into, or the ocean of synthetic chemicals we all swim through every day, we have no rational conclusion but that our environment has changed a lot in the past few decades. Considered within the context of the reality based model where the events of early life can be disproportionally amplified through the lifetime of an organism, clinging to the idea that there has been a stable incidence of autism seems dangerously naïve, at most charitable.
And yet, for the most part, many or most of the people who are alarmed are crackpots. There were times I questioned myself. Am I missing something? Am I chasing phantoms? Why aren’t any of these other smart people as worried as I am?
A while ago I got a copy of Microglia in the developing brain: A potential target with lifetime effects (Harry et all), a paper that tells me that if nothing else, I have some good company in pondering the potential for disturbances in early life to uniquely affect developmental outcome, in this instance through alterations to the neuroimmune system. If I am incorrect about the validity of a developmental programming model with lifetime effects, lots of prolific researchers are wrong about the same thing in the same way. Harry is a very thorough (and terrifying) review of the relevant literature. Here is the abstract:
Microglia are a heterogenous group of monocyte-derived cells serving multiple roles within the brain, many of which are associated with immune and macrophage like properties. These cells are known to serve a critical role during brain injury and to maintain homeostasis; yet, their defined roles during development have yet to be elucidated. Microglial actions appear to influence events associated with neuronal proliferation and differentiation during development, as well as, contribute to processes associated with the removal of dying neurons or cellular debris and management of synaptic connections. These long-lived cells display changes during injury and with aging that are critical to the maintenance of the neuronal environment over the lifespan of the organism. These processes may be altered by changes in the colonization of the brain or by inflammatory events during development. This review addresses the role of microglia during brain development, both structurally and functionally, as well as the inherent vulnerability of the developing nervous system. A framework is presented considering microglia as a critical nervous system-specific cell that can influence multiple aspects of brain development (e.g., vascularization, synaptogenesis, and myelination) and have a long term impact on the functional vulnerability of the nervous system to a subsequent insult, whether environmental, physical, age-related, or disease-related.
Hell yeah!
The body of Microglia in the developing brain: A potential target with lifetime effects has tons of great stuff. From the Introduction
The evidence of microglia activation in the developing brain of patients with neurodevelopmental disorders(e.g., autism) and linkage to human disease processes that have a developmental basis (schizophrenia) have raised questions as to whether developmental neuroinflammation actively contributes to the disease process. While much of the available data represent associative rather than causative factors, it raises interesting questions regarding the role of these ‘‘immune-type’’ cells during normal brain development and changes that may occur with developmental disorders. Within the area of developmental neurotoxicology, the potential for environmental factors or pharmacological agents to directly alter microglia function presents a new set of questions regarding the impact on brain development.
There is a short section on what is known about the colonization of the brain by microglia, it is a busy, busy environment, and while we are just scratching the surface, microglia seem to be involved in scads of uber-critical operations, many of which pop up in the autism literature. It is just being confirmed that microglia constitute a distinct developmental path that diverges as an embryo, two papers from 2007 and 2010 are referenced as reasons we now believe microglia are a population of cells that migrate into the CNS before birth and are not replaced from the periphery in adulthood. From there, the beautiful complexity is in full effect; as the microglia develop and populate the brain there are specific spatial and morphological conditions, microglia are first evident at thirteen weeks after conception, and do not reach a stable pattern until after birth. In fact, it appears that microglia aren’t done finishing their distribution in the CNS until the postnatal period, “With birth, and during the first few postpartum weeks, microglia disseminate throughout all parts of the brain, occupying defined spatial territories without significant overlap (Rezaie and Male, 2003) suggesting a defined area of surveillance for each cell.”
It occurred to me to wonder if there are differences in microglia settlement patterns in males and females in human infants, as has been observed in other models? Could a spatially or temporally different number of micoglia, or different developmental profiles of microglia based on sex be a participant in the most consistent finding in the autism world, a rigid 4:1 male/female ratio?
Speaking towards the extremely low replacement rates for microglia in adulthood, the authors wonder aloud on the possible effects of perturbations of the process of microglial colonization.
The slow turn-over rate for mature microglia raises an issue related to changes that may occur in this critical neural cell population. While this has not been a primary issue of investigation there is limited data suggesting that microglia maintain a history of previous events. Thus, if this history alters the appropriate functioning of microglia then the effects could be long lasting. Additionally, a simple change in the number of microglia colonizing the brain during development, either too many or too few, could have a significant impact not on only the establishment of the nervous system network but also on critical cell specific processes later in life.
(Emphasis mine)
Perhaps coincidentally (*cough*), we have abundant evidence of an altered microglial state and population in the autism population; while we do not know that these findings are the result of a disturbance during development, it is an increasingly biologically plausible mechanism, and thus far, I’ve yet to see other mechanisms given much thought, excepting the chance of an ongoing, undetected infection.
There is a brief section concerning the changes found in adult microglial populations in terms of density, form, and gene expression in different areas of the brain, “With further investigation into the heterogeneity of microglia one would assume that a significant number of factors, both cell membrane and secreted, will be found to be differentially expressed across the various subpopulations.” Nice.
There is a section of the paper on microglial phenotypes, there are a lot of unknowns and the transformation microglia undergo between functional states is even more nebulously understood during brain development. “It is now becoming evident that in the developing brain, many of the standards for microglia morphology/activation may require readdressing.” We haven’t even figured out what they’re doing in the adult brain!
There is a really cool reference for a study that shows altered microglial function dependent on the age of the organism.
In the adult rodent, ischemia can induce microglia to display either a more ramified and bushy appearance or an amoeboid morphology depending on the level of damage and distance from the infarct site(s). In the immature rodent, ischemia-induced changes in capillary flow or, presumably, altered CNS vascularization can retain the microglia in an amoeboid phenotype for longer and delay the normal ramification process (Masuda et al., 2011).
One way of looking at this would be to say that we should exercise extreme caution in trying to translate our nascent understanding of how mature microglia react when speculating on how immature microglia will act. To follow up on just how little we know, there is a long discussion about the shortcomings of a the term ‘activated’ microglia with some details on chemical profiles of broadly generalized ‘classically inflammatory, ‘alternatively activated’, ‘anti-inflammatory’, and ‘tissue repair’ phenotypes.
Next up is a dizzyingly list of brain development functions that microglia are known, or suspected to participate in. Without getting too deep in the weeds, of particular interest to the autism realm, that list includes neurogenesis and differentiation in the cortex [related: Courchesne, me], cell maturation via cytokine generation, axon survival and proliferation [related: Wolff, me], programmed cell death of Purkinje cells, clearance of ‘early postnatal hippocampul neurons’, and the ‘significant contribution to synaptic stripping or remodeling events’, i.e., pruning (Paolicelli / fractaltine), and even experience dependent microglia / neuron interactions. Taking all of this (and more) into consideration, the authors conclude “Thus, one can propose that alterations in microglia functioning during synapse formation and maturation of the brain can have significant long-term effects on the final established neural circuitry. “ Ouch.
Next up is a summary of many of the animal studies on microglial participation in brain formation, there is a lot there. Interestingly (and particularly inconvenient) is the finding that a lot of the functional actions of microglia during development appear to operate after birth. “Overall, the data suggest that microglial actions may be most critical during postnatal brain maturation rather than during embryonic stages of development.” Doh!
Early life STRESS gets some attention, and for once there is some good news if you look at it the right way. There is something about a very cool study from Schwarz (et all / Staci Bilbo!) involving drug challenge that peered deep into the underlying mechanisms of an environmental enrichment model; animals given a preferential handling treatment were found by two metrics to have differential microglia response in adulthood with (biologically plausible) observations, increased mRNA levels for IL-10 production, and decreased DNA methylation; i.e., less restriction on the gene that produces IL-10, and more messenger RNA around to pass off the production orders [totally beautiful!]. There is more including thyroid disruption (though in a way that I found surprising), and the observations of time dependent effects on immue disturbances. (super inconvenient)
There is so much data that keeps piling on that the authors end up with “Overall, the existing data suggest a critical regulatory role for microglia in brain development that is much expanded from initial considerations of microglia in the context of their standard, immune mediated responses.”
A terrifying concept that I haven’t found time to dedicate a post towards is microglia priming, which gets some attention in Harry.
There is a significant amount of evidence regarding what is often termed ‘‘priming’’ and ‘‘preconditioning’’ events that serve to either exacerbate or provide neuroprotection from a secondary insult, respectively. In these states, the constitutive level of proinflammatory mediators would not be altered; however, upon subsequent challenge, an exaggerated response would be induced. The phenomena of priming represent a phenotypic shift of the cells toward a more sensitized state. . . Exactly how long this primed state will last has not been determined; however, data from microglia suggest that it can extend over an expanded period of time. Preconditioning can also represent changes that would occur not only over the short term but may be long lasting.”
I happen to think that microglia priming is going to be a very important cog in the machinery for this journey when all is said and done; the evidence to support a preconditioning system is strong, and in parallel, the things we see different in autism (and elsewhere) is consistent with a different set of operations of microglia, AND we also have evidence the disturbances that would invoke microglial change are subtle but real risk factors for autism.
What comes next is a type of greatest hits mashup of very cool papers on developmental programming in the CNS.
Galic et al.(2008) examined age related vulnerabilities to LPS in rats to determine critical age periods. Postnatal injection of LPS did not induce permanent changes in microglia or hippocampal levels of IL-1b or TNFa; however, when LPS was given during the critical postnatal periods, PND 7 and 14, an increased sensitivity to drug induced seizures was observed in 8-week-old rats. This was accompanied by elevated cytokine release and enhanced neuronal degeneration within the hippocampus after limbic seizures. This persistent increase in seizure susceptibility occurred only with LPS injection at postnatal day 7 or 14 and not with injections during the first day of life or at PND 20. Similar long-lasting effects were observed for pentylenetetrazol-induced seizures when PND 11 or 16 rat pups were subjected to LPS and hyperthermic seizures (Auvin et al., 2009). These results again highlight this early postnatal period as a ‘‘critical window’’ of development vulnerable to long-lasting modification of microglia function by specific stimuli. Work by Bilbo and co-workers demonstrated LPS-induced deficits in fear conditioning and a water maze task following infection of PND 4 rats with Escherichia coli. In the young adult, an injection of LPS induced an exaggerated IL-1b response and memory deficits in rats neonatally exposed to infection (Bilbo et al., 2005). Consistent with the earlier work by Galic et al. (2008), an age dependency for vulnerability was detected with E. coli-induced infection at PND 30 not showing an increased sensitivity to LPS in later life (Bilbo et al., 2006).
In particular, Galic 2008, or Postnatal Inflammation Increases Seizure Susceptibility in Adult Rats (full paper) was a very formative paper for me; it was elegant in design and showed alarming differences in outcome from a single immune challenge experience, if it occurred during a critical developmental timeframe. If you haven’t read it, you should.
This paper has a nice way of distilling the complexity of the literature in a readable way.
One hypothesis for developmental sensitivity is the heterogeneous roles for inflammatory factors and pro-inflammatory cytokines during development, including their timing-, region and situation-specific neurotrophic properties. Many of the proinflammatory cytokines are lower at birth with a subsequent rapid elevation occurring during the first few weeks of life. In an examination of the developing mouse cortex between PND 5 and 11, mRNA levels for TNFa, IL-1b, and TNFp75 receptor remained relatively constant while a significant increase in mRNA levels of CR3, macrophage-1 antigen (MAC-1), IL-1a, IL-1 receptor 1 (IL- )R1, TNFp55 receptor (TNFp55R), IL-6, and gp130 occurred (Fig. 2). This data suggests that an upregulation of interleukins and cytokine receptors may contribute to enhanced cytokine signaling during normal cortical development.
One hypothesis put forward using a model reliant on postnatal exposure to LPS suggests that these types of exposure may ‘‘reprogram’’ neuroimmune responses such that adult stress results in hyperactivation of the hypothalamic pituitary adrenal (HPA) axis (Mouihate et al., 2010) and corticosterone changes (Bilbo and Schwarz, 2009).While limited, the available data suggest that events occurring during development, especially postnatal development, have the potential to cause long term alterations in the phenotype of microglia and that this can be done in a region specific manner.
[extremely inconvenient]
In what could, conceivably, be a coincidence, our available information on the autism brain also shows region specific changes in microglia populations, microglial activation profiles, and oxidative stress. I do not believe the findings reviewed in Microglia in the developing brain: A potential target with lifetime effects will be meaningless artifacts; the likelihood that our observations of an altered neuroimmune state in autism are not, at least, participatory has become vanishingly small.
Can these findings inform us on the incidence question? I was lurking on a thread on Respectful Insolence a while ago, and someone gave what I thought was a very succinct way of thinking about the changes that our species has encountered the past few decades; it went something like “we have replaced infection with inflammation”. That’s a pretty neat way of looking at how things have gotten different for humanity, at least lots of us, and especially those of us in the first world. We used to get sick and die early; now we live longer, but oftentimes alongside chronic disorders that share a common underlying biological tether point, inflammation.
Any dispassionate analysis of the available data can tell us that we have, indeed, replaced infection with inflammation; we suffer from less death and misery from infection, but more metabolic disorder, more diabetes, more hypertension, more asthma and autoimmune conditions than previous generations. We have largely replaced good fatty acids with poor ones in our diet. All of these conditions are characterized by altered immune biomarkers, including an increase in proinflammatory cytokines. Those are the facts that no one can deny; we have replaced infection with inflammation.
But when we look to the findings of Microglia in the developing brain: A potential target with lifetime effects, it becomes clear that our newfound knowledge of microglial function and crosstalk with the immune system raises some very troubling possibilities.
Lately it has been quite in vogue among a lot of the online posting about autism to at least mention environmental factors which could participate in developmental trajectory leading to autism; that’s a big step, an important and long overdue acknowledgement. If you pay close attention, you will notice that 99% of these admissions are handcuffed to the word “prenatal”. This is likely an attempt to deflect precise questions about the robustness of our evaluation of the vaccine schedule, but the big question, the incidence question, still hinges on fulcrum of the genetic versus environmental ratio ; that is a problem for the purveyors of the fairytale because the prenatal environment of our fetuses, the chemical milieu of their development, is qualitatively different compared to generations past. That chemical soup is their environment; and that environment has unquestionably changed in the past decades as we have replaced infection with inflammation.
Our previous analysis tells us that invoking inflammation outside the brain modifies microglial function inside the wall of the blood brain barrier; good or bad, no honest evaluation of the literature can argue against a lack of effect. What happens outside the brain affects what happens inside the brain. If, however, microglia are active participants in brain formation, as a swath of recent research indicates, can this fact give us insight into the incidence question?
Is a state of increased inflammation the pathway between maternal asthma, depression, stress, and obesity being associated with increased risk of autistic offspring? Have we replaced infection with inflammation plus?
What could be more lethal to the fairytale of a static tale of autism than a positive relationship between a lifestyle characterized by increased inflammation and the chances of having a baby with autism?
Are we totally fucked?
We cannot know the answers unless we have the courage to ask the difficult questions with methods powerful enough to provide good data, and it won’t be easy. The static rate of autism fairytale is a comforting notion; it expunges responsibility for the coronal mass ejection sized change to our fetuses developing environment, and while hiding behind the utterly frail findings of social soft scientists, we can happily place tin foil hats and accusations of scientific illiteracy on anyone who might be worried that our abilities have outstripped our wisdom. That is a terrible, cowardly way to approach the incidence question, what we should be doing is exactly the opposite, ridiculing the epidemic sized error bars in prevalence studies and demanding more answers from the hard scientists. Eventually we will get there and it will be a critical mass of information from studies like Harry that will propel decision makers to abandon the fairytale for a course regulated by dispassionate analysis.
– pD
The Fairytale of a Static Rate of Autism Part 4: Troubling Realities Acknowledged, The Incredible Shrinking Gods of the Gaps, and Otherwise Rational People Using ‘Small’ As An Empirical Measure To Answer A Critical Question
Posted on: August 19, 2011
Hello friends –
These have been rough times for the people who are heavily invested in the kissing cousin theories of autism as a predominantly genetic disorder and the static, or near static rate of autism. The California twin study that is old news by the time I get this finished showed much different rates of genetic participation than previously believed. These findings exposed the underlying frailty of gene-based causation theories, namely that some of the most widely referenced studies in the autism literature, studies used repeatedly as a basis for the notion that autism was ‘the most highly heritable neurodevelopmental disorder’, were, in fact, relatively underpowered, and suffered from serious temporal and methodological shortcomings.
By contrast, the California study looked at two hundred twin pairs, a lot more twins than any previous study and actually performed autism diagnostics on all of the participating children, whereas other studies relied on medical records. Performing dedicated ADOS diagnosis prospectively on the children allowed the researchers to discern between autism and PDD-NOS, something that not all previous studies were not able to perform, if for no other reason than the DSM-IV wasn’t even released when several of the most often cited studies were published. This is from the Comment section of the California twin study:
The results suggest that environmental factors common to twins explain about 55% of the liability to autism. Although genetic factors also play an important role, they are of substantially lower magnitude than estimates from prior twin studies of autism. Nearly identical estimates emerged for ASD, suggesting that ASD presents the same liability spectrum as strict autism.
This is on top of the fact that there is a quiet, but growing acknowledgement of the fact that literally decades of genetic studies have failed to be able to explain more than a fraction of autism cases despite sequencing of tens of thousands of genomes. This is a very similar situation to a great number of other disorders which we thought we would cure once the human genome was decoded. [Note: That isn’t to say that we haven’t learned a lot from sequencing the genome, just that we didn’t quite get what we thought we were going to get.]
This ‘double hit’, so to speak, has reached a critical mass such that health officials are making politically shrewd, but refreshingly realistic statements, and dare I say, a sliver of common sense may be about to infiltrate the discussion about autism prevalence. For example, as pointed out by Sullivan, Tom Insel, head of the National Institute of Mental Health keeps a blog where he recently blogged ‘Autism Spring’, which included this nugget within the context of continued failure of genetic studies to explain any substantial part of autism, “It is quite possible that these heritability estimates were too high. . .” Ouch. (I would recommend the entire blog posting by Mr. Insel.)
The high heritability estimates, and implicit genetically-mediated cause of autism, are foundational pillars of the argument that autism rates have not changed over time. Though overused, or used wrongly in many instances, there is a kernel of dispassionate reality behind the statement, ‘there is no such thing as a genetic epidemic’. Without the crutch of exceedingly high heritability to rely on, the notion of a stable rate of autism loses the only hard science (read: replicable, biologically-plausible), i.e.,genetics, it ever had, and must place complete reliance on the softer sciences (read: unquantifiable, ‘greater awareness’), i.e.,sociology. This is great news if you love impossible to verify estimates of prevalence and anecdotes about crazy uncle George who would have been diagnosed with autism forty years ago. However, if you think we should be relying less on psychologists and cultural anthropologists to answer critical questions, and rely more on hard science, this means that the old narrative on autism prevalence holds even less allure than it did in the past, for those of you who thought this was possible.
Before Kid Autism came around, I would occasionally read discussion boards on the creationism versus evolution ‘debate’. One thing that I noticed was that the creationists would often employ a ‘God of the Gaps’-style argument: anything that couldn’t be explained by science (yet), or anything necessary to support whatever fanciful construct had been erected to protect biblical creation fables, was ascribed to the work of God. That’s one thing you have to give to God, he (or she!) can handle it all; it didn’t matter what primitive logical test biblical creation was failing to pass, the golden parachute clause was always that God could have just made things that way. It was a nifty out on the part of the creationists, kind of like a get out of jail free card. The autism prevalence discussion has been working just like this, and the funny part is that the people that are always claiming to have the intellectual high ground, the supposed skeptics, are playing the part of the creationists! Zing!
Here is how it works:
Concerned Parent: It sure does seem like there is more autism than there used to be, what with there being X in a thousand kids with it! That’s much, much more than even ten years ago! My brothers, sisters and I all knew kids with mental retardation and Down’s syndrome, but we just don’t remember kids like we see today.
Supposed Skeptic: It is diagnostic substitution and ‘greater awareness’; autism incidence has been stable. The DSM was changed which resulted in more children being labeled.
Concerned Parent: It sure does seem like there’s more autism than there used to be. Now there are Y kids in a thousand having autism! Why does my son’s preschool teacher keep insisting something is changing?
Supposed Skeptic: It is diagnostic substitution and ‘greater awareness’; autism incidence has been stable. The DSM was changed which resulted in more children being labeled.
Concerned Parent: What the hell? Now there are Z kids in a thousand having autism! When are those genetic studies going to figure autism out, anyway?
Supposed Skeptic: It is diagnostic substitution and ‘greater awareness’; autism incidence has been stable. When does the new DSM come out again?
(Replace X/Y/Z with any progressively larger numbers.)
It doesn’t matter what prevalence number is thrown about–even the astronomical one in thirty-eight figure bandied about for South Korean children didn’t cause so much as a raised eyebrow; the autism equivalent of God of the Gaps, greater awareness and loosening of diagnostic criteria can handle any amount of increase gracefully. It is the equivalent of an uber-absorbent autism paper towel, capable of soaking up any number of new children with a diagnosis; there is, literally, no amount of an increase that the God of the Gaps can’t handle.
If, instead the question was posed like this, ‘How much of the apparent increase in autism is real?’, the answer was always, ‘Zero’, regardless of what the current rates of autism were when you asked the question
Then a funny thing happened, a series of studies from several researchers showed a consistent trend of older parents giving rise to more children with autism than younger parents. There were differences between the studies on just how much of an effect an older parent had, but the overall direction of association was clear. In this instance, there was also the luxury of a plausible biological mechanism that involved the mediator in favor, genetics. The idea is that advancing age in the parent meant more years for gametes to get knocked by a random cosmic zap or other environmental nastygram and this disturbance created genetic problems down the line for the offspring, a theory I think is probably pretty good. Once a couple of these studies started to pile up, there was a small shift in the narrative regarding autism prevalence; after all, nobody could bother to try to deny that parents were getting older compared to past generations. Here is how it looked:
Concerned Parent: What the hell? Now there are X kids in a thousand having autism!
Supposed Skeptic: Greater awareness and diagnostic substitution are primarily responsible for our observations of increased autism, although, ‘a real, small increase’ cannot be ruled out.
And with that, there was a little less autism prevalence for the God of the Gaps to handle. It never seemed to bother anyone that implicit in this argument is an impossible to quantify concept ‘small increase’. If you were to ask someone what rate of autism ‘a small increase’ amounted to with more precision, the answer is whatever amount rises to the level of autism minus the difficult to quantify effect of older parents. That is some lazy stuff.
Here are some examples of prominent online skeptics discussing the possibility of a true rise in autism. See if you can detect a pattern.
Here is Stephen Novella pushing The Fairytale in 2009:
While a real small increase cannot be ruled out by the data, the observed increase in diagnostic rates can be explained based upon increased surveillance and a broadening of the definition – in fact autism is now referred to as autism spectrum disorder.
[Here we see the notion that everything can be explained by the God of the Gaps.]
Here is an example of Orac toying around with this filibuster just the other day, in August of 2011:
True, the studies aren’t so bulletproof that they don’t completely rule out a small real increase in autism/ASD prevalence, but they do pretty authoritatively close the door on their being an autism “epidemic.”
These aren’t the only examples, far from it. Check it out:
It should be noted that the data cannot rule out a small true increase in autism prevalence. (Stephen Novella in 2008)
If the true prevalence rate of autism and ASDs has increased, it has not increased by very much. (David Gorski, 2010)
We should have the curiosity to wonder, what, exactly, does small mean in these contexts? What percentage size increase should we consider small enough to hide within the data? Five percent? Ten percent? What does ‘small’ mean, numerically, within a range? Is a ten to twenty percent rise in autism rates reason for us to take comfort in the fact that the effect of greater awareness is real? At what level does the percentage of ‘real’ autism increase mandate more than superficial lip service, more than a paragraph about ‘gene-environment interactions’ at the end of a two-thousand word blog post that takes pride in the intellectual chops of outthinking Jenny McCarthy? You won’t get anyone to answer this question; they can’t, because they don’t really know what they mean when they say, ‘small’, other than, ‘it can’t be vaccination’.
How do we know the amount of this increase must, in fact, even be ‘small’? This becomes especially problematic when we consider the smackdown that the canard of autism as ‘among the most heritable neurological conditions’ has taken as of late. If the high heritability estimates of autism are incorrect, yet so often repeated as gospel, why should we also assign confidence to the idea that the increase is trivial? Isn’t one argument the foundation of the other? Did either really have quality data behind them?
This is a terrible, awful, horrible, completely fucking idiotic way to address a question as important as whether or not a generation of children is fundamentally different. We cannot afford the ramifications of being wrong on this, but we seem to find ourselves in an epidemic of otherwise intelligent people willing to accept the pontifications of cultural anthropologists and the feebleness of social scientists on this critical question. I am not arguing against the realities of diagnostic switching and greater awareness affecting autism diagnosis rates. But we can understand that while they are a factor, we must also admit that we have little more than a rudimentary understanding of these impacts, and when we consider the implications of being incorrect, the potential disaster of a very real, not ‘small’ increase in the number of children with autism, we shouldn’t be overselling our knowledge for the sake of expedient arrival at a comforting conclusion. We should be doing the opposite.
If we can’t have the robustly defendable values on autism rates right now, that’s fine, because that is the reality, but we should at least have the courage to acknowledge this truth. This is the nature of still learning about something, which we are obviously doing in terms of autism, but in that situation, we don’t have the currency of scientific debate, decent data, to be saying with authority that any true increase in autism is small.
Unfortunately for the purveyors of The Fairytale, things are going to get a lot worse. The problem is that we are starting to identify extremely common, in some cases, recently more common, environmental influences that subtly increase the risk of autism. These are further problems for a genetic dominant model and effectively mandate that the ‘small increase’ is going to have to start getting bigger as a measurement, with a correlated decrease in the amount of autism that cultural shuffling can be held responsible for. Will anyone notice?
By way of example, we now have several studies that link the seasons of gestation with neurodevelopmental disorders including autism and schizophrenia; i.e., Season of birth in Danish children with language disorder born in the 1958-1976 period, Month of conception and risk of autism, or Variation in season of birth in singleton and multiple births concordant for autism spectrum disorders, which includes in the abstract, “The presence of seasonal trends in ASD singletons and concordant multiple births suggests a role for non-heritable factors operating during the pre- or perinatal period, even among cases with a genetic susceptibility.” Right! As I looked up some of these titles, I found that the evidence for this type of relationship has been well known for a long time; schizophrenia, in particular has a lot of studies in this regard, i.e., Seasonality of births in schizophrenia and bipolar disorder: a review of the literature, which is a review of over 250 studies that show an effect, and I also found Birth seasonality in developmentally disabled children, which includes children with autism and was published in 1989, which is like 1889 in autism research years.
Our seasons have remained constant (but probably won’t stay too constant for much longer. . . ), but this still throws a whole barrel of monkey wrenches into the meme of a disorder primarily mediated through genetics.
More damning for the Fairytale are some studies presented at this year’s IMFAR, and some others just published, that tell us that abnormal immune profiles during pregnancy appear to provide slightly increased risk for autism, roughly doubling the chance of a child receiving a diagnosis. The groovy part is that the studies utilized both direct and indirect measurements of an activated immune system to draw similar conclusions, a sort of biomarker / phenotype crossfire.
From the direct measurement end, we have Cytokine Levels In Amniotic Fluid : a Marker of Maternal Immune Activation In Autism?, which reports that mothers with the highest decile of tnf-alpha levels in the amniotic fluid had about a one and a half times increased risk for autism in their children. This makes a lot of sense considering the robustness of animal models of an acute inflammatory response during pregnancy and its impact on behavior.
Another study, this one from the MIND Institute in California (which I love), is Increased mid-gestational IFN-gamma, IL-4, and IL-5 in women giving birth to a child with autism: a case-control study (full paper). They found that in pregnant mothers, increased levels of IFN-gamma led to a roughly 50% increased risk of an autism diagnosis. Here is a snipet:
The profile of elevated serum IFN-γ, IL-4 and IL-5 was more common in women who gave birth to a child subsequently diagnosed with ASD. An alternative profile of increased IL-2, IL-4 and IL-6 was more common for women who gave birth to a child subsequently diagnosed with DD without autism.
This study took a lot of measurements, and goes to great lengths to explicitly call for additional analysis into the phenomena. IFN-gamma is typically considered pro-inflammatory, while IL-4 and IL-5 are considered regulatory cytokines. In order to determine if these findings were chance or not, the researchers determined if there was a correlation between the levels of IFN-gamma, IL-4, and IL-5, which they reported with very robust results. Less clear is what might be causing these profiles, or how, precisely, they might give rise to an increased risk of autism. The interconnectedness of the brain and the immune systemwould be a good place to start looking for an answer to the last question though.
What about indirect measurements? It just so happens, another paper was published at IMFAR this year that observed the flip side of the coin, conditions associated with altered cytokine profiles in the mother and this study also found an increased risk of autism. The Role of Maternal Diabetes and Related Conditions In Autism and Other Developmental Delays, studied a thousand children and the presence of diabetes, hypertension, and obesity in their mothers in regards to the risk of a childhood autism diagnosis. The findings indicate that having a mother with one or more of those conditions roughly doubles the chances of autism in the offspring. Obesity, in particular, has an intriguing animal model Enduring consequences of maternal obesity for brain inflammation and behavior of offspring, a crazy study that I blogged about when it was published. A variety of auto immune disorders in the parents have been associated with an autism diagnosis in several studies.
The obesity data is particularly troublesome for the idea of a ‘small’ increase in autism, just like parents have been getting older, parents have also been getting fatter, waaaay fatter, (and more likely to have diabetes) the last few decades. There isn’t any squirming out of these facts. If, indeed, being obese or carrying associated metabolic profiles is associated with an increased risk of autism, ‘small’ is getting ready to absorb a big chunk of real increase. But is there any clinical data to support this possible relationship, do we have any way to link obesity data with this autism data from the perspective of harder figures?
It further turns out, there are some very simple to navigate logical jumps between the above studies. Remembering that our clinical measurements indicated that increased INF-gamma, IL-4, and IL-5 from the plasma of the mothers was associated with increased risk, we can see very similar patterns in Increased levels of both Th1 and Th2 cytokines in subjects with metabolic syndrome (CURES-103). Here is part of the abstract, with my emphasis.
Metabolic syndrome (MS) is a cluster of metabolic abnormalities associated with obesity, insulin resistance (IR), dyslipidemia, and hypertension in which inflammation plays an important role. Few studies have addressed the role played by T cell-derived cytokines in MS. The aim of the tudy was to look at the T-helper (Th) 1 (interleukin [IL]-12, IL-2, and interferon-gamma [IFN-gamma]) and Th2 (IL-4, IL-5, and IL-13) cytokines in MS in the high-risk Asian Indian population.
Both Th1 and Th2 cytokines showed up-regulation in MS. IL-12 (5.40 pg/mL in MS vs. 3.24 pg/mL in non-MS; P < 0.01), IFN-gamma (6.8 pg/mL in MS vs. 4.7 pg/mL in non-MS; P < 0.05), IL-4 (0.61 pg/mL in MS vs. 0.34 pg/mL in non-MS; P < 0.001), IL-5 (4.39 pg/mL in MS vs. 2.36 pg/mL in non-MS; P < 0.001), and IL-13 (3.42 pg in MS vs. 2.72 pg/mL in non-MS; P < 0.01) were significantly increased in subjects with MS compared with those without. Both Th1 and Th2 cytokines showed a significant association with fasting plasma glucose level even after adjusting for age and gender. The Th1 and Th2 cytokines also showed a negative association with adiponectin and a positive association with the homeostasis model of assessment of IR and high-sensitivity C-reactive protein.
Check that shit out! Seriously, check that out; increased IFN-gamma, IL-4, and IL-5 in the ‘metabolic syndrome’ group, comprised of people with, among other things, obesity, insulin resistance, and hypertension; the same increased cytokines and risk factors found to increase the risk of autism.
If we look to studies that have measured for TNF-alpha in the amniotic fluid during pregnancy, we quickly find, Second-trimester amniotic fluid proinflammatory cytokine levels in normal and overweight women
There were significant differences in amniotic fluid CRP and TNF-alpha levels among the studied groups: CRP, 0.018 (+/-0.010), 0.019 (+/-0.013), and 0.035 (+/-0.028) mg/dL (P=.007); and TNF-alpha, 3.98 (+/-1.63), 3.53 (+/-1.38), and 5.46 (+/-1.69) pg/mL (P=.003), for lean, overweight, and obese women, respectively. Both proinflammatory mediators increased in women with obesity compared with both overweight and normal women (P=.01 and P=.008 for CRP; P=.003 and P=.01 for TNF-alpha, respectively). There were significant correlations between maternal BMI and amniotic fluid CRP (r=0.396; P=.001), TNF-alpha (r=0.357; P=.003) and resistin (r=0.353; P=.003).
Nice.
What we are really looking at are five studies the findings of which speak directly to one another; a link to metabolic syndrome during pregnancy and increased IFN-gamma, IL-4, and IL-5, a link to obesity and hypertension in pregnant mothers and autism risk, and an increased risk of autism in mothers wherein IFN-gamma, IL-4, and IL-5 were found to be increased outside of placenta. Further, we have a link between amniotic fluid levels of TNF-alpha and metabolic syndrome, metabolic syndrome in mothers and autism risk, and increased risk from increased tnf-alpha in the amniotic fluid.
As I have said previously, one thing that I have learned during this journey is that when we look at a problem in different ways and see the same thing, it speaks well towards validity of the observations. What we see above is a tough set of data to overcome; we need several types of studies looking at the relationship between metabolic syndrome, immune profiles during pregnancy, and autism from different angles to have reached the same wrong conclusion, something that is increasingly unlikely. We are in an epidemic of obesity and the associated endocrine mish mash of metabolic syndrome, there simply isn’t any diagnostic fuzziness on this. It is happening all around us. Even though the total increase in risk is relatively small, the sheer quantity of people experiencing this condition of risk mandates that the numbers game looks favorable towards a real increase in autism. If we acknowledge this, how can we continue to have faith in the concept that any true increase in the autism rates must be ‘small’?
Is the next argument going to be that besides increased parental age, and heavier or more diabetic mothers, the rest of the autism increase is the result of diagnostic three card monte? (Just how much is the rest, anyways?)
And even though these studies, and likely more in the future, expose the crystal delicate backbone of the ‘small true increase’ argument, I have great pessimism that the people so enamored with invoking this phrase will ever acknowledge its shifting size, much less the implications of being wrong on such a grand scale.
– pD
The Fairytale of a Static Rate of Autism Part III – Prevalence Hookups or What if They Threw An Autism Epidemic And Nobody Cared?
Posted on: May 30, 2011
- In: Autism | Hilarious | Prevalence | The Fairytale | Willing Disbelief
- 8 Comments
Hello friends –
The osmotic pressure of cool people and pop culture tells me that what we used to call one night stands are now called ‘hookups’, casual sexual encounters as convenient that don’t necessarily mean people are dating, but some release can be found, and everyone moves on with their lives until the next time. This reminds me a lot of how people that ought to know better have been treating autism prevalence studies lately. The results are useful in cementing an already reached conclusion, but ultimately, the findings are only used as isolated ejaculations of the same ideological tweets. Last week’s hookup doesn’t mean anything come this Saturday night, and there is absolutely no reason, no reason, anyone should be troubled to compare this weeks findings used to trumped a static rate of autism with last weeks findings. What we are witnessing is the equivalent of a scientific one night stand, and anyone who doesn’t think the scientific method should be framed for the sake of expediency ought to be furious.
These posts can oftentimes take me a long while to complete, so dating my start point a bit, about two weeks ago, the NHS study from England came out that described a near 1% prevalence of ‘autism’ in adults. The ‘findings’ from this study actually came to light and received attention in the autism community over a year ago, but the real publication happened in May 2011, so there you are.
About a week ago, the Korea ‘study’ on autism came out; it hit the web with a large footprint, and amazingly, described an atmospheric autism ‘prevalence’ of autism of near 2.5%, with 1 in 38 (!!!!) Korean children ‘estimated’ to be on the autism spectrum. If it has not happened already, this study and ‘conclusions’ will soon became part of the autism lexicon; an uber-Kevlar argument, impervious to any concerns involving the possibility of an actual increase in the number of children with autism.
Both of these studies share very similar methodologies; essentially a lot of people were screened through a questionnaire, a subset of people with ‘high’ scores on the questionnaire were subsequently retested with standard tools for assessing autism. Based on how well the questionnaire did at predicting autism spectrum diagnosis, an extrapolation, with various ‘corrections’, was made as towards how many people in the general public are on the spectrum. In both studies, the overwhelming majority of people ‘estimated’ with autism were previously undiagnosed and were not receiving any services.
Here’s the thing that is driving me up the wall crazy, apeshit mystified and enraged. Nobody cared. Let’s look again at what these studies found and see if we can detect anything of potential interest in their conclusions when compared between one another.
Nobody, and I mean nobody, took these two studies as evidence of an autism epidemic, despite the fact that here we have two supposedly (?) well designed studies that found entire spectrum sized differences in the number of children and adults with autism! You could literally drive the old spectrum through the hole in the new spectrum! If both of these two studies are meaningful, if both have accurately captured autism in their respective target populations, we have no choice but to admit that the epidemic is real, and we have proof that children have an autism spectrum disorder two and a half times more frequently than adults. There is an epidemic of autism in our children; or at least, in Korean children!
Did anyone see those headlines that I somehow missed? Did the online skeptical community acknowledge that we now finally have some solid evidence that indeed, autism rates are higher in children than adults, and somehow I failed to see those conversations?
Here’s what really confuses me. Some of the same people, same ‘skeptics’, and same news organizations breathlessly reported both of these findings without, apparently, understanding their implications alongside one another. For example, in 2009, here’s a post from Stephen Novella at Science Based Medicine that touched on the England study that includes this nugget:
They found a consistent prevalence of 1% in all age groups they surveyed. This is remarkable for two reasons – first, they found the exact same 1% figure as the CDC US survey (assuming the CDC data is more accurate than the phone survey published in Pediatrics). This supports the conclusion that the 1% figure may be close to the true prevalence of ASD in the population.
Second, the NHS study found that the prevalence of autism was the same in all age groups, strongly suggesting that true ASD incidence has not been increasing over recent decades and supporting the increased surveillance and definition hypothesis.
Check out how ‘remarkable’ Mr. Novella thinks the 1% matchup between English adults and American children is in terms of making the case for a static rate of autism. This is a guy whose posts outside the autism realm I tend to enjoy in many instances, he is clearly a superior intellect, and applies a very skeptical eye towards his non-autism posts. My presumption is that he was well aware that the NHS study actually diagnosed a grand total of 19 adults, and had good reasons, which he declined to illuminate in that post, for why this relatively low number of results was immune to significant confounding problems, which is why it provided such ‘remarkable’ evidence ‘strongly suggesting that true ASD incidence has not been increasing’.
Then, in May 2011, Mr. Novella posted Autism Prevalence Higher than Thought, concerning the Korea study. Here is a snippet from the conclusions:
This study adds an interesting data point to the whole picture of ASD. If correct, then the theoretically upper limit of ASD prevalence is about 2.6% of the population, more than twice the previous estimate. It also indicates that when you undergo a program of thorough searching, you will find more diagnoses.
What is going on here? The England study, which found a prevalence of 1%, the study that previously was found to be remarkable evidence of a static rate of autism was exactly the same type of study, wide-scale screening for likely candidates within the general population, followed by targeted autism assessment of people with high scores, and backwards extrapolation. Does anyone think that the Korea study was that much more thorough than the England study? If a study came out tomorrow that reported 5%, or 10% prevalance, would we simply assign this to a even more strenously executed methodology? Is there any evidence that we might use to suspect a 5% prevalance reported next week in Columbia is faulty that could not also be applied against Korea?
For what reason should we, now, believe that the England study of adults was so fatally flawed that it missed more than one autistic adult for every one it found? Surely a study capable of missing more than half of the autistic adults had some type of warning signs back in 2009 that might indicate that the evidence might be less than remarkable, maybe questionable, or that, in fact, it might be a Fairytale?
Am I cynical to suggest that what really made the England study such remarkably ‘strong evidence’ of a static rate of autism was that, at the time, it had findings within the statistical range of existing CDC numbers in children? Was the online and media love affair with the England NHS study little more than prevalence hookup? Have I reached the theoretical limit of jadedness?
There really isn’t a way to reconcile these two findings without either accepting a two and a half times increase in autism in children versus adults, a sort of epidemic-lite, or accepting that one or both of the studies suffer from serious flaws. But if we start accepting that the studies might have serious problems, we shouldn’t be saying they are ‘strong evidence’ of anything, except, perhaps, the difficult to overstate problems of autism prevalence studies. Of course, it is a different ballgame if you are relieved of the intellectual responsibility of actually trying to reconcile the two findings; if you allow yourself the prevalence doublethink that England has meaningful data, and so does Korea, and that the rate of autism isn’t increasing, then, no harm, no foul Big Brother.
One prevalence study that didn’t get the booty call was Brief Report: Prevalence of Pervasive Developmental Disorder in Brazil: A Pilot Study, which came out in February, 2011; just three months before Korea. Methodology wise, this study is a kissing cousin to Korea and England, a screening was performed in the general population, and assessments were subsequently performed and then statistical extrapolations were performed to reach a prevalence rate. Let’s see what these values look like up against each other, and see if we can detect a pattern.
Can anyone see a pattern here?
Now the skeptic might tell you that the Brazil study was a lot smaller, which is true; the initial screening of children only contained a little less than 1,500 children. But it hardly matters; just to get to the level of English adults ‘found’, they would have had to miss two children for every child they found, and to approach Korea values, they needed to have missed almost nine children for every child actually diagnosed. Does anyone think this is reality? Why would prospective screening and backwards extrapolation be so accurate in one population, and so wildly inaccurate in another population? The Brazil and England study used versions of the same screening questionnaire!
I understand that being partially funded by Autism Speaks, and having a ‘cultural anthropologist’ with a book on the subject of autism carries some weight in the press conference area; so that might explain why one study got press, and another didn’t. Forgetting the press issue, where are the calls that we should try throwing four thousand Brazilian genomes at a sequencer to see what in their genetic makeup appears to be protecting them from autism so effectively? Why aren’t these studies meaningful evidence of some environmental force acting to create wildly different rates of autism in these different populations?
I would note that the press releases, media regurgitations, and skeptical viewpoints nearly all contained the boilerplate note that more studies are needed. Consider, however, if our need for ‘more study’ is so extensive, if we place so little confidence in our methodologies that papers published within months of each other, with nearly identical study methods, find literally nine times higher rates of autism in one population aren’t a warning sign of an real difference in incidence, what this ought to be telling us is that all of our prevalence data are crapshoots, at best. We shouldn’t get to pick and choose which studies we think are meaningful because they happen to meet comforting quotas, or discard those that fail to support those palliative notions.
It is tempting to look at the Brazil study and evaluate for design or implementation problems that could cause such startlingly low rates of autism; the authors go into some discussion about the reasons their findings might seem so low. Complicating matters along this line, however, is that the Brazil and Korea studies, shared a researcher, the relatively well known psychiatrist with a large pubmed autism prevalence footprint, Eric Fombonne. It occurred to me that it might be a fun experiment to see how reliable Mr. Fombonne has been regarding autism prevalence.
[Click on the image to get a bigger view / stupid wordpress template] Note that I have omitted review papers, or papers that had no abstracts, but it doesn’t really help. (How could it?)
All of these findings were wholly or partially authored by the same person. Is there anything more damning for the state of autism prevalence research than this person continues to be considered a source of reliable information?
I used to live with a fun dude in college; he went to engineering school and went on to work at a manufacturing facility near our town. One of the funniest things he told me about engineering was this quote:
Dilution is the solution to pollution!
In other words, if you have a hundred pounds of diethyl-pthylate-poisonate to dispose of, ship in a hundred thousand gallons of water, and start pumping; if you have two hundred pounds to eject, ship in two hundred thousand gallons of water. This is what is happening to the definition of autism, the quirky element, the ‘broad autistic phenotype’ is seeping into these studies. After dozens, or hundreds of prevalence studies we are ultimately left with as many portraits of different entities as envisioned by the researcher and width of spectrum de jour. The upshot of this, however, is that it makes no sense to try to compare these studies.
In the meantime, we are told time and time again that even though our common sense, our memories of childhood, and the repeated lamentations from every person who has worked with children for the last few decades, all of which are warning us that something is different; all of these things are all supposedly subject to an array of biases so strong that we cannot trust them to reach any conclusions. Only through carefully planned, objective analysis can we reach any conclusions on autism incidence. The results of this choreographed investigation looks like this:
Does anyone really think there aren’t some pretty serious biases operating here? If we cannot use common sense to try to reconcile the picture above, what can we use? If trusting common sense is dangerous to valid conclusions, so is trusting this.
If anyone really thought that Korea and Brazil were measuring the same condition, a condition that until very, very recently has been considered lifelong and severely debilitating, the two wildly different findings would be cause for alarm, undeniable evidence of a massive environmental force influencing the development of autism in some populations. But no one thinks this, no one cares, and that is because; no one really believes these studies are measuring the same thing. But admitting this is dangerous to too many, it is the implicit acknowledgement of just how little we understand, how beholden our policies and research prioritizations are guided by the softest of science and scientists, and ultimately, how frequently we’ve been sold a narrative with the scientifically defendable value of a set of monetized South Florida mortgages.
Such is the way of the prevalence hookup, transiently entertaining, but without meaning from week to week. Until we can find a way past this, past reliance on the shifting sands of behavioral assessments that can vary from researcher to researcher (or by the same researcher!), we can perform all of the ‘thorough investigations’ that we can afford and repeat the ‘findings’ that support our meme until we are blue in the face. None of it will mean a goddamned thing, though we may lose a generation of children while we bounce from one set of findings to another, feeling pleased with the ones that make doom seem unlikely, and discarding the ones that should be cause for great alarm.
-pD
Hello friends –
I have decidedly mixed feelings on the genetic side of autism research; clearly genetics plays a part, but it does appear that autism has largely mirrored other complicated conditions in that what we thought we were getting when we cracked the genetic code has, for all practical purposes, failed to materialize. To what extent our genetic makeup really plays a part in autism more than any other condition that is currently mystifying us, I don’t think we can say with much certainty; unless you want to count some.
To my mind, one particularly bright spot in the gene realm is the associations of the MET-C allele and an increased risk of an autism diagnosis. At first glance, MET doesn’t seem like a big deal; lots of people have the MET-C mutation, in fact, nearly half of everyone has it. But people with autism have it just a little more frequently, an observation that has been replicated many times. But what is exciting is not only that the MET-C findings are robust, but they can also affect a lot of implicated systems in autism in biologically relevant ways. From an ideological standpoint, the fissure in the autism community about research priorities regarding genetics versus environment, the MET-C studies are a superb example of just how much useful knowledge there is by starting at the genome and working upwards, and finding once we get there that the reality involves lots more than just genes. There is something for everyone!
Getting to the big picture where we can appreciate the beautiful complexity takes a little bit of digging, but it’s worth the effort.
Every now and again you’ll see a period piece about the forties, fifties or sixties, and you’ll get a glimpse of the female operator, someone who would take a call and literally connect two parties together; the gatekeeper. The operator’s actions were binary; either she connected the lines and the call went through, or she didn’t, and nothing happened. Of course, one operator couldn’t connect you to any other phone, but participated in groupings of phones with some logical or functional structure. Ultimately, the operators were the enabler of communication, physically putting two entities into contact to perform whatever business they had with each other.
Within our bodies, tyrosine kinases are enzymes responsible transferring phosphate to proteins; a chemical exchange critical towards a great number of cellular functions, and in a sense, the tyrosine kinases act as cellular operators, helping implement a physical swap of chemicals that ultimately set in motion a great number of processes. Some very rudimentary cellular functions are initiated by the tyrosine kinases; for example, cell division, which is why mutated kinases can lead to the generation of tumors; i.e., the signaling for cell division gets turned on, and never gets turned off. Inhibiting tyrosine kinases is the mechanism of action for some drugs that target cancer.
The MET gene is responsible for creating the MET receptor tyrosine kinase. This particular receptor is involved in lots of processes that are of great interest to autism; the MET receptor is expressed heavily during embryogenesis in the brain, has immune modulating capacities, and is associated with wound healing, and is particularly implicated in repair of the gastro-intestinal track.
Kinases don’t just fire away, shuttling phosphates around any old time, they must be activated by a triggering molecule, or a ligand. There is only one known ligand for the MET receptor; hepatocyte growth factor, or HGF (also sometimes referred to as HGF/SF, or hepatocyte growth factor/scatter factor). We’ll get to why we bother worrying about HGF a little later on, but it is important to keep in mind that without HGF, the functions affected by the MET-C receptor, early brain development, immune modulating, and wound repair cannot be achieved.
So what about autism, and why is it a beautiful illustration of complexity? Walking our way through the MET findings in autism is a rewarding task; it is one of the few instances I’ve seen where the glimpses of relevance gleaned from straight genetic studies have been incrementally built upon to achieve a much grander understanding of autism. This is the kind of thing that I think a lot of people who dismiss the utility of genetic studies are missing; genetics are only the first piece of the puzzle, it doesn’t only implicate genes, it tells us about the processes and the proteins disturbed in autism; and with that knowledge, we can perform targeted analysis for environmental participants.
The first clues about MET involvement with autism came in 2006, when A genetic variant that disrupts MET transcription is associated with autism (full paper) was published. The abstract is longish, but here is a snipet:
MET signaling participates in neocortical and cerebellar growth and maturation, immune function, and gastrointestinal repair, consistent with reported medical complications in some children with autism. Here, we show genetic association (P = 0.0005) of a common C allele in the promoter region of the MET gene in 204 autism families. The allelic association at this MET variant was confirmed in a replication sample of 539 autism families (P = 0.001) and in the combined sample (P = 0.000005). Multiplex families, in which more than one child has autism, exhibited the strongest allelic association (P = 0.000007).
I appreciate the pleiotropic nature of what we are seeing here, a gene that is involved with brain growth and maturation, immune function, and GI repair. The association in ‘multiplex’ (i.e., families with more than one child with autism) was very, very strong. Even still, this was a pretty short paper, and it was all genetics. Coolness factor: 3.
Neater studies were on the horizon shortly thereafter, a year later, some of the same group looked for expression of MET in post mortem brain tissue and found significantly decreased levels of MET protein in Disruption of cerebral cortex MET signaling in autism spectrum disorder.
MET protein levels were significantly decreased in ASD cases compared with control subjects. This was accompanied in ASD brains by increased messenger RNA expression for proteins involved in regulating MET signaling activity. Analyses of coexpression of MET and HGF demonstrated a positive correlation in control subjects that was disrupted in ASD cases.
This is a nice follow up; lots of times a genetic study might suggest a hit, but we really don’t even know how such a genetic change might manifest physiologically, like having a jigsaw puzzle of solid black and finding two pieces that fit together. In those instances, we can’t really go looking for different levels of the protein, so there you are. In this case, the authors found an allele worth investigating, and then went looking to see if relevant proteins were altered in the population, and in the CNS no less! Not only that, but they also looked at the initiating end of the process, the ligand, HGF, and found abnormalities. Good stuff. Unfortunately, I haven’t found myself a copy of this paper yet, but the fact that other proteins in the pathway were altered is another line of evidence that something is amiss. I’ve begun to appreciate the fact that I have spent a long time under appreciating the interconnectedness of biological systems; you aren’t going to have a disturbance in one system without altering the way upstream, and downstream processes are working; so the fact that we see other proteins, those related to MET functions, modified, makes beautiful sense. Coolness factor: 5.
Likely because of the mixed findings of skewed proteins in the MET pathway (?), the next study in line is, Genetic Evidence Implicating Multiple Genes in the MET Receptor Tyrosine Kinase Pathway in Autism Spectrum Disorder (full paper available). Here’s the abstract:
A functional promoter variant of the gene encoding the MET receptor tyrosine kinase alters SP1 and SUB1 transcription factor binding, and is associated with autism spectrum disorder (ASD). Recent analyses of postmortem cerebral cortex from ASD patients revealed altered expression of MET protein and three transcripts encoding proteins that regulate MET signaling, hepatocyte growth factor (HGF), urokinase plasminogen activator receptor (PLAUR) and plasminogen activator inhibitor-1 (SERPINE1). To address potential risk conferred by multiple genes in the MET signaling pathway, we screened all exons and 5′ promoter regions for variants in the five genes encoding proteins that regulate MET expression and activity. Identified variants were genotyped in 664 families (2,712 individuals including 1,228 with ASD) and 312 unrelated controls. Replicating our initial findings, family-based association test (FBAT) analyses demonstrated that the MET promoter variant rs1858830 C allele was associated with ASD in 101 new families (P=0.033). Two other genes in the MET signaling pathway also may confer risk. A haplotype of the SERPINE1 gene exhibited significant association. In addition, the PLAUR promoter variant rs344781 T allele was associated with ASD by both FBAT (P=0.006) and case-control analyses (P=0.007). The PLAUR promoter rs344781 relative risk was 1.93 (95% Confidence Interval [CI]: 1.12−3.31) for genotype TT and 2.42 (95% CI: 1.38−4.25) for genotype CT compared to genotype CC. Gene-gene interaction analyses suggested a significant interaction between MET and PLAUR. These data further support our hypothesis that genetic susceptibility impacting multiple components of the MET signaling pathway contributes to ASD risk.
We’ve got two new genes added to the mix, PLAUR and SERPINE. The juicy part here is that the authors didn’t look for these variants at random, but performed a targeted search; they knew that the proteins encoded by these genes interact with either MET receptor function or HGF, and they also had found altered expression of these genes in the CNS study. From the Introduction:
The hepatocyte growth factor (HGF) gene encodes the activating ligand for the MET receptor. HGF is translated as an inactive precursor protein that requires cleavage for efficient binding to the MET receptor [Lokker et al 1992]. The activating cleavage of HGF is achieved most efficiently by the enzyme plasminogen activator (urokinase-type; uPA; gene symbol: PLAU) under conditions in which uPA binds to its receptor, the urokinase plasminogen activator receptor (uPAR; gene symbol: PLAUR). Activating cleavage of HGF can be suppressed by the plasminogen activator inhibitor-1 (PAI-1; gene symbol: SERPINE1). Together, these proteins regulate the activity of MET receptor tyrosine kinase signaling, and our recent microarray analyses of postmortem temporal lobe of individuals with ASD indicate that disrupted MET signaling may be common to ASD pathophysiology [Campbell et al 2007]. For example, we found that there is increased expression of the HGF, PLAUR and SERPINE1 transcripts in ASD in postmortem cerebral cortex. The observation of disrupted expression suggests a general dysfunction of MET signaling in the cerebral cortex of individuals with ASD.
The proteins encoded by PLAUR and SERPINE were also found increased in the expression study; a finding further supported by the genetic study here. The really grand slice here is that the SERPINE protein suppresses cleavage of HGF; essentially another way MET function can be affected, from a disturbance upstream of HGF binding. In other words, more SERPINE (possibly as a result of a ‘promoter allele’) would result in less MET receptor activation because the SERPINE interferes with the cleavage of HGF, and thus, another pathway to reduced MET activation. In a finding that seems 20/20 with hindsight, a functional promoter of the SERPINE gene was found to increase autism risk; i.e., if you have more SERPINE, you get less functional HGF, and therefore less triggering of the MET receptor. This is cool and begins a portrait of the complexity; it shows how the effect of reduced MET functionality can come from multiple drivers; the reduced MET allele, or, the promoter SERPINE allele, and what’s more, having both is an even bigger risk; the authors are describing a synergy of low penetrance genes.
From the discussion section of the paper:
Beyond genetic susceptibility, the functional integrity of the MET signaling system also is sensitive to environmental factors. This concept is supported by bioinformatics analyses that identified PLAUR, SERPINE1 and HGF as genes active in immune response regulation, sensitive to environmental exposures, and within chromosomal regions previously implicated in ASD linkage studies [Herbert et al 2006]. Moreover, a recent cell biological study shows that chemically diverse toxicants reduce the expression of MET in oligodendrocyte progenitor cells, a result that is interpreted as the convergence of toxicant effects on oxidative status and the MET-regulating Fyn/c-Cbl pathway
Here are links to the Hebert paper, Autism and environmental genomics, and the Li paper, Chemically Diverse Toxicants Converge on Fyn and c-Cbl to Disrupt Precursor Cell Function. What is neat here is that we are starting to be able to see a pathway of genes, and resultant proteins, that can effect disparate systems. I believe that there is a subset of acupuncture, acupressure that relies on more knuckles than needles, and while the science on accu* based therapies isn’t very good, it does occur to me that in a sense, our lattice work of HGF-PLAUR-SERPINE proteins that participate in the MET-C process are pressure points in a delicate system, push a little bit and things will bend down the line accordingly. It also exemplifies why I am offended by highly negative attitudes on genetic studies held by people who believe in a non trivial, environmentally mediated increase in the rates of autism; we are approaching a nearly impossible to overturn reality that genes we know to be associated with autism are particularly sensitive to interference from environmental agents, and participate in immune function. That is important information. Coolness factor 8. First glimpse of beauty factor: 10.
Next up we have Dynamic gene and protein expression patterns of the autism-associated Met receptor tyrosine kinase in the developing mouse forebrain (full paper).
The establishment of appropriate neural circuitry depends upon the coordination of multiple developmental events across space and time. These events include proliferation, migration, differentiation, and survival – all of which can be mediated by hepatocyte growth factor (HGF) signaling through the Met receptor tyrosine kinase. We previously found a functional promoter variant of the MET gene to be associated with autism spectrum disorder, suggesting that forebrain circuits governing social and emotional function may be especially vulnerable to developmental disruptions in HGF/Met signaling. However, little is known about the spatiotemporal distribution of Met expression in the forebrain during the development of such circuits. To advance our understanding of the neurodevelopmental influences of Met activation, we employed complementary Western blotting, in situ hybridization and immunohistochemistry to comprehensively map Met transcript and protein expression throughout perinatal and postnatal development of the mouse forebrain. Our studies reveal complex and dynamic spatiotemporal patterns of expression during this period. Spatially, Met transcript is localized primarily to specific populations of projection neurons within the neocortex and in structures of the limbic system, including the amygdala, hippocampus and septum. Met protein appears to be principally located in axon tracts. Temporally, peak expression of transcript and protein occurs during the second postnatal week. This period is characterized by extensive neurite outgrowth and synaptogenesis, supporting a role for the receptor in these processes. Collectively, these data suggest that Met signaling may be necessary for the appropriate wiring of forebrain circuits with particular relevance to social and emotional dimensions of behavior.
Coooooool. Here we touch on the complexity of brain formation, all the little things that need to go exactly right, and how MET might play a role in that incredibly complicated dance. Even better, a mouse model is used to gain an understanding of where and when peak expression of MET proteins occur, a period of significant changes to neural structures and the formation of synapses, the physical structures that enable thought. This is a dense paper, too dense to get deeply into blockquoting for this posting, but there are some parts that deserve notice, namely, documentation of spatially localized MET expression in brain areas associated with social behaviors and some fine grained information on the specific parts of synapse formation that utilize MET. Coolness factor: 8. Complexity Factor: 12.
Here is a paper that a lot of people that play skeptics on the Internet ought to hate, Distinct genetic risk based on association of MET in families with co-occurring autism and gastrointestinal conditions. (full paper)
In the entire 214-family sample, the MET rs1858830 C allele was associated with both autism spectrum disorder and gastrointestinal conditions. Stratification by the presence of gastrointestinal conditions revealed that the MET C allele was associated with both autism spectrum disorder and gastrointestinal conditions in 118 families containing at least 1 child with co-occurring autism spectrum disorder and gastrointestinal conditions. In contrast, there was no association of the MET polymorphism with autism spectrum disorder in the 96 families lacking a child with co-occurring autism spectrum disorder and gastrointestinal conditions. chi(2) analyses of MET rs1858830 genotypes indicated over-representation of the C allele in individuals with co-occurring autism spectrum disorder and gastrointestinal conditions compared with non-autism spectrum disorder siblings, parents, and unrelated controls.
There is a lot of caution in this paper, but the nice part is that there are biologically plausible mechanisms by which a reduction in MET could snowball into problems in the gastro-intestinal track.
In the gastrointestinal system, MET signaling modulates intestinal epithelial cell proliferation, and thus acts as a critical factor in intestinal wound healing. For example, activation of MET signaling via application of exogenous hepatocyte growth factor has been shown to reduce the effects of experimentally induced colitis, inflammatory bowel disease, and diarrhea.
Pushing on the other end of the balloon, increasing MET signaling, has been shown to help GI problems; no less than evidence that a genetic change associated with autism has biologically plausible mechanisms by which GI problems would be more prevalent. In fact, unless our findings of MET alleles are in error, or our clinical findings of the effects of HGF are spurious, it is absolutely expected. There is also a section with the startlingly simple, and simultaneously great idea of why findings like these might be useful markers for phenotypic categorization in studies in the future; i.e., to discern the prevalence of GI problems in autism, it might, for example, make sense to design that study to take presence or absence of MET alleles into consideration. Nice. Coolness Factor: 7. Insidiousness factor: 9.
Here’s another one that found associations with MET and social behavior, and GI disturbances again. Association of MET with social and communication phenotypes in individuals with autism spectrum disorder
Autism is a complex neurodevelopmental disorder diagnosed by impairments in social interaction, communication, and behavioral flexibility. Autism is highly heritable, but it is not known whether a genetic risk factor contributes to all three core domains of the disorder or autism results from the confluence of multiple genetic risk factors for each domain. We and others reported previously association of variants in the gene encoding the MET receptor tyrosine kinase in five independent samples. We further described enriched association of the MET promoter variant rs1858830 C allele in families with co-occurring autism and gastrointestinal conditions. To test the contribution of this functional MET promoter variant to the domains of autism, we analyzed its association with quantitative scores derived from three instruments used to diagnose and describe autism phenotypes: the Autism Diagnostic Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule (ADOS), and both the parent and the teacher report forms of the Social Responsiveness Scale (SRS). In 748 individuals from 367 families, the transmission of the MET C allele from parent to child was consistently associated with both social and communication phenotypes of autism. Stratification by gastrointestinal conditions revealed a similar pattern of association with both social and communication phenotypes in 242 individuals with autism from 118 families with co-occurring gastrointestinal conditions, but a lack of association with any domain in 181 individuals from 96 families with ASD and no co-occurring gastrointestinal condition. These data indicate that the MET C allele influences at least two of the three domains of the autism triad.
Really sort of plain, but very nice to see the GI component validated in another data set. Coolness factor 5.
Then a few months ago, Prenatal polycyclic aromatic hydrocarbon exposure leads to behavioral deficits and downregulation of receptor tyrosine kinase, MET was released, an uber cool showcase of the autism bigfoot, the often regaled, only very rarely documented, gene/environment interaction.
Gene by environment interactions (G × E) are thought to underlie neurodevelopmental disorder, etiology, neurodegenerative disorders, including the multiple forms of autism spectrum disorder. However, there is limited biological information, indicating an interaction between specific genes and environmental components. The present study focuses on a major component of airborne pollutants, polycyclic aromatic hydrocarbons (PAHs), such as benzo(a)pyrene [B(a)P], which negatively impacts cognitive development in children who have been exposed in utero. In our study, prenatal exposure of Cpr(lox/lox) timed-pregnant dams to B(a)P (0, 150, 300, and 600 μg/kg body weight via oral gavage) on embryonic day (E14-E17) consistent with our susceptibility-exposure paradigm was combined with the analysis of a replicated autism risk gene, the receptor tyrosine kinase, Met. The results demonstrate a dose-dependent increase in B(a)P metabolite generation in B(a)P-exposed Cpr(lox/lox) offspring. Additionally, a sustained persistence of hydroxy metabolites during the onset of synapse formation was noted, corresponding to the peak of Met expression. Prenatal B(a)P exposure also downregulated Met RNA and protein levels and dysregulated normal temporal patterns of expression during synaptogenesis. Consistent with these data, transcriptional cell-based assays demonstrated that B(a)P exposure directly reduces human MET promoter activity. Furthermore, a functional readout of in utero B(a)P exposure showed a robust reduction in novel object discrimination in B(a)P-exposed Cpr(lox/lox) offspring. These results confirm the notion that common pollutants, such as the PAH B(a)P, can have a direct negative impact on the regulated developmental expression of an autism risk gene with associated negative behavioral learning and memory outcomes.
Oh snap. A common pollutant (well, common in the last few decades anyways), is shown to interact with MET in a dose dependent fashion to reduce protein expression in the brain during embryonic development and cause ‘a robust reduction in novel object discrimination’. (Ouch) This is an example of just what we mentioned above, referenced Herbert, concerning the possibility of MET as a gene sensitive to ‘environmental exposures’. Indeed. From the discussions section:
The results from the present study demonstrate that the transcription and developmental expression patterns of a replicated ASD risk gene, MET, are highly sensitive to a common PAH pollutant. In utero exposure to B(a)P produces an oxidative milieu of B(a)P metabolites in offspring during a key postnatal period of synapse development, providing evidence that environmental exposure creates a sustained cerebral cortical burden that likely contributes to an increased oxidative load. Oxidative stressors in the form of metabolites would be expected to negatively impact gene expression (Kerzee and Ramos 2000) and, more specifically, receptor tyrosine kinase function, including Met (Li et al. 2007). These data suggest that B(a)P-induced exposure would impact the expression of key neurodevelopmental genes, including Met. Additionally, the predominance of the 3-OH and 9-OH metabolites places a sustained burden in the brain because of the potential for further oxidization to form B(a)P quinones (McCallister et al. 2008, Hood et al. 2000, Brown et al. 2007) which undergo redox cycling to generate reactive oxygen species (Kerzee and Ramos 2000, Bolton et al., 2000).
And
In conclusion, specific developmental events such as glutamatergic excitatory synapse formation and maturation may be particularly vulnerable to G x E effects that impact regulatory and signaling proteins involved in this process. While we do not suggest that the current study reflects specific defects related to a complex clinical condition such as the ASDs, current molecular, behavioral and functional imaging data are converging on the concept that the ASDs are a manifestation of altered local and long-distance cortical connectivity (Geschwind et al. 2007, Bill and Geschwind 2009, Geschwind and Levitt, 2007, Levitt and Campbell 2009). Also, Met and other related signaling components of this receptor tyrosine kinase pathway have been implicated in both syndromic and idiopathic disorders where the ASDs are diagnosed at a high rate. In combination with risk alleles in key genes, the in utero exposure to PAHs such as B(a)P, which results in both a reduction in absolute levels and the mistiming of peak Met expression, could drive the system toward a pathophysiological threshold that neither genetic risk nor environmental factors could produce individually. The present study focused on the neocortex, but given the highly restricted spatial and temporal expression of Met in mouse limbic circuits associated with social-emotional development and cognition (Judson et al. 2009), it is likely that perturbations occur throughout these key circuits, including in the hippocampus.
Really cool stuff; particularly the finding that developmental, in utero exposure was capable of driving abnormal protein expression well after birth. This is the best of both sides of the genetics versus environment conundrum; the kind of finding that sheds light on how environmental pollutants could be participating in increasing the number of children with autism by interacting with genetically susceptible children. But what I love about this is that it is the death knell of the fairytale of a static rate, or near static rate of autism, just having the genes or the exposure isn’t enough; instead, the interaction of alleles and timed exposure ‘could drive the system toward a pathophysiolical threshold that neither genetic risk nor environmental factors could produce individually’. I think there are some more findings coming from this group soon that might be exciting, or terrifying, depending on how you see it. (or both). Coolness factor: 99.
So what have we learned and just how cool is it?
1) The MET receptor enables some types of cellular signaling that have relevance to the autism community including synapse formation, immune modulation, and gastro intestinal function. The ligand, or trigger of the MET receptor is HGF.
2) Certain alleles of the MET gene that result in decreased expression are more common in children with autism than people without autism.
3) Consistent with findings of increased prevalence of MET alleles, MET protein expression was found to be decreased in brain tissue from people with autism. Other, related proteins, HGF, PLAUR, and SERPINE were also found to be disturbed.
4) Following up on the differential findings of SERPINE and PLAUR, genetic studies found gene to gene interactions between the MET allele and alleles involved with production of SERPINE and PLAUR. Some of the proteins in question are known to be particularly vulnerable to environmental interference.
5) Animal models tell us that MET is heavily expressed in many areas of the mammalian brain during prenatal and postnatal development, and we gain insight into the spatial and temporal expression of MET during the intricate dance of brain formation.
6) Two studies add evidence that the one function of decreased MET expression, GI disturbances, are indeed found with greater consistency within children with autism and the MET allele. This should be a relatively unsurprising finding considering what we know about MET and children with autism.
7) Finally, a portrait of genetic / environmental interactions capable of disturbing physiology and behavior in ways consistent with findings in autism is rendered using an agent that is the product of the automobile age and already associated with decreased cognitive skills for groups with the highest gestational exposure.
It should be noted that this is just a slice of the MET papers out there in the autism realm; they all shared one or more authors, I picked them because they seem to show a nice progression of knowledge, and incremental approach towards learning more. There is a lof more to learn, in particular, I think that the immune modulating effects of reduced expression would be an interesting subject, but one that will have to wait for another posting.
– pD
Low Penetrance Environmental Impacts, Gene Environmental Interactions, and the Depressingly Bad Jokes that Infiltrate Autism Discussions
Posted on: January 8, 2011
Hello friends –
There’s been something at the back of my mind for a while now regarding the potential for environmental influences to participate in autism, and indeed, a true rise in the number of children that have developmental problems that I’ve been struggling with articulating elegantly. The right course came to me while reading threads where the recent autism risk as proximity to highways paper was discussed. I’m actually not too big on the paper, it is very preliminary, uses some terms that are kind of confusing, and at very best, should be used as a guide for more targeted studies. For anyone who didn’t see it when it came out, essentially it reported a small increase of risk of having a baby with autism as the pregnant mother lived closer to some types of highways.
What I liked about this study is that at the core, there was a twinge of a biologically plausible mechanism, specifically, exposure to pollutants during development and consequent interference with neural development. Examples given in the text including possible endocrine disrupting effects of some types of automotive exhaust, and studies showing altered glutamate expression and associated plasticity defects resulting from pollutants.
What I didn’t like about the study is that it didn’t include any biomarkers and seemed relatively soft on the definitional terms. It was essentially a GIS placement and association lookup; lots of data and easy to find phantoms. A methodologically similar study by Bearman was released a few months previously; purporting to assign a very specific percentage of autism increase (16%) to the spatial proximity of other parents with children with autism, with the idea being that those chatty parents convinced their close neighbors to get their child diagnosed, while those people who more than 500 meters from a child with autism, and therefore don’t talk to as many people, failed to get their child diagnosed. I came down pretty hard on Bearman and don’t see much difference to apply less skepticism here. I will note, however, with no small amount of amusement, that when Bearman was discussed, no one seemed too concerned about the lack of control for urbanicity in the ‘skeptical’ realm. Big surprise.
The skeptics took the freeway paper apart, or in some instances, took apart a reporter or blogger who was spinning the findings as stronger than they were. I was more or less in agreement with the skeptics ideas on this one; this paper certainly was not sufficiently strong to make any conclusive statements and as usual, some headlines got it way wrong.
On the other hand, according to my underlying principles of subtle change still being meaningful, the humbling complexity of poking around with systems like embryonic development, and the difficult to overstate gulf between what we know and what we think we know about the effects of our reckless introduction of a galaxy of sythentic chemicals into the environment our infants are born into, this study fit in pretty nicely; at the very least as a reason to perform bioinformatic analysis of pregnant women to test for biomarkers of exhaust exposure and cognitive outcomes a few years down the ‘road’.
It didn’t take long before the gross over simplifications started rolling in though; i.e., ‘If this study is valid, we should have seen the rise in autism when the Interstate program was initiated in the 1950’s!’ [cue laugh track], or ‘I guess I have genes that made me live near an Interstate’. [cue whoot whoot track] It occurred to me that the Interstate jokes are a good illustration of what is largely wrong with nearly every single discussion on environmental participation you stumble into on the Internet. On one hand, the notion that unless an environmental study has sufficient power to prove a causal relationship for autism, or indeed, can be shown to be unable to account for all autism cases, it is safe to be mocked, or for the more academically minded, accused of being the result of data dredging. Similarly, anything showing a glimmer of plausibility that isn’t a genetic finding can lends itself towards showing how worthless the genetic angle is. These are useful cards to play if your goal is to bash environmental causation theories (and thereby, vaccination causation theories), or if your goal is to bash genetic theories; but ultimately are wastes of time if we want to understand a condition with the murky history and multifaceted manifestations of autism. The crux of what really bothered me about both sides of the Internet joke is that they each ignore meaningful information that can be offered from the other side. It is worse than dumb, it is wasteful.
Stepping away from the environmental end for a moment, I think it is safe to say that everyone is beginning to realize that the hunt for high impact genetic changes that can explain more than a tiny fraction of our autism cases is an abject failure. While there are some genetic changes, like Fragile X, that confer extremely high risk of autism, the absolute number of people with such changes is relatively simple to determine, and they comprise a vanishingly small subset of the children with autism. What we do seem to be finding is that there are lots of genetic changes that confer a small risk of having autism, the so called, low penetrance genetic changes. The idea here is that if you have many, (maybe as many as a dozen or more) low penetrance genes, the cumulative effects build up until a physiological end point is reached wherein autistic behaviors manifest. I actually like the idea behind low penetrance genes a lot; it makes a lot of our finings of genetics make sense, and I absolutely believe in a strong genetic participation in autism.
Remember, at the end of the day, genes are nothing more than blueprints for building proteins. Most genetic alterations don’t involve complete additions, or removals, of proteins, but rather, creation of a little less, or a little more of a protein, or perhaps, creation of proteins that are just a tiny bit different than ‘normal’, sort of like autism itself. While the environment these proteins enter, or are regulated into entering, starts influencing the eventual biological outcome in the most immediate sense imaginable, the end points of genetics, these proteins and their precise structures are indisputably important in what is happening in everything our bodies do; including, in some instances, have autism.
Consider the tightly orchestrated formation of the microscopic chasms between neurons, the process of synaptogenesis. Dozens (or hundreds) of chemicals dance together in order to form the structures in our brains that exchange chemical messengers, neurotransmitters, that literally form the foundation of neuron to neuron communication, and thus, cognition; the physical constructs of thought. It is a biological cauldron that we are just beginning to comprehend, the mind formingly intricate, time dependent interplay of a chemical deck of cards orders of magnitude more complicated than sequencing the genome.
The evidence for altered synapses, and modified synaptic function in autism, and most (all?) other developmental disorders is impossible for an intellectually honest observer to deny. Some of the most commonly found genetic alterations in people with autism involve genes known to participate in the formation, maintenance, or functioning of synapses. For example, neurexin , shank, and neuroligin, are some well known, or at least, well reported reported genes intimately attached to synapse function also found associated with autism, and our list should also include calcium expression and adhesion genes (and many, many others). Each of these genes or processes contribute to the synapse in subtle, but different ways, at different times, and yet we can see that interferences anywhere down the functional class of chemicals is associated with autism. Yet, very few people, (I’ve read of none), have been found to have a neurixin allele, a shank allele, and a neruoligin mutation. And there are some people who have the same mutations, but do not exhibit autistic behavior. There are also a great many people that have no known mutations in any of these genes, and still, receive an autism diagnosis. What does this tell us?
It should tell us that while there are lots of genetic ways that synapse function can be altered in such a way that autistic behaviors bubble up to the diagnosis endpoint, but more importantly, the critical question need not necessarily revolve around what genes you have, but rather, is synapse function manipulated? Furthermore, we should be able to conclude that simply having a single modifier (i.e., one shank mutation) go wrong isn’t a guarantee of an autism diagnosis, and thus; the participation of individual mutations is real, but small. [I would also argue that it is likely that there are a great number of as of yet, undetected genetic misprints that contribute in the same real, but subtle ways.]
Another more accessible example of a low penetrance gene is the MET gene, which produces a protein known to interact with a lot of important processes involved in autism, including brain formation, immune system functioning, and intestinal repair. There have been a lot of high quality studies on the MET mutations in the past few years including those that report higher incidences of MET mutations in children with autism and gastrointestinal problems, higher findings of MET alleles in autism, association to communication phenotypes and MET expression, replication of above studies, evidence of interaction with other genes known to be associated with autism, decreased expression in post mortem brain tissue, and animal studies showing differential, time dependent expression of MET. (and many, many others).
The kicker towards this discussion, howeever, is that the changes to the MET gene are really, very, very common. Nearly one half of everyone has the low MET production gene, but even still, many more people with autism have it. So, while it is clearly implicated, other changes are obviously necessary for that particular genetic change to result in autism. What we are learning about the systems affected by MET, or lots of the genes implicated in autism, is that very subtle changes towards critical processes are sufficient to modify the course of development. Somewhat counter intuitively, I would argue that the implication of this is compelling evidence (or terrifying news) for those of us with worries about the possibility of an environmentally driven increase in the number of people with an autism diagnosis; indeed, it argues that just like genetics, we must admit the reality that if genes can be low penetrance, so too, then, can environmental impacts.
For example, back to brain formation. We know that the neurexin proteins participate in forming our synapses. But we have evidence that hypo
thyroidism can lead to structural changes during development, and we also know that there is increasing evidence that endocrine disruptors can interferre with thyroid metabolism, or for that matter, a wide range of findings on endocrine disruptors and cognitive function. Or if we look to pesticides, we have evidence that developmental exposure to diazonon can modify neurotransmitter function, with similar findings are available for other classes of pesticides. Similarly with heavy metals.
The skeptics would claim with some legitimacy that there are significant dose dependency problems to be addressed before we should start pointing to every experimental slice of evidence of potential harm and claiming that the sky is falling. But. What if, in fact, we need only perturb the process of brain development a little bit, and with a little help from other, low penetrance genes or other exposures, developmental trajectories begin to alter? This would seem to be precisely what we are learning from the genetic angle; it isn’t one big thing incorrectly designed, it is lots of small things. And while our genetic code has, for the most part, remained stable; our environment today is vastly overpopulated with chemicals capable of minor, but real, effects when compared to yesteryears past.
The search for a single environmental impact with the ability to explain a significant portion of autism diagnosis is as futile as the hunt based on genetics. This makes for a far messier landscape, but also one that fits my terrifying, over arching principle of the Fairytale of a static (or near static) rate of autism, that our uncontrolled experiment of introducing synthetic chemicals into our environment coupled with widespread social changes with real physiological impacts, a set of experiments absolutely unprecedented in the history of living things on planet Earth, that changes to our offspring are unavoidable. To suggest otherwise, strikes me as either the height of arrogance, or the depths of ignorance.
Going back to the freeway study for a minute, I ran into a paper while writing this piece that involves pollutants, interaction with the MET gene, gene x environment interactions, and low penetrance impacts that I think has salience towards this discussion.
Here is the abstract:
Gene by environment interactions (G × E) are thought to underlie neurodevelopmental disorder, etiology, neurodegenerative disorders, including the multiple forms of autism spectrum disorder. However, there is limited biological information, indicating an interaction between specific genes and environmental components. The present study focuses on a major component of airborne pollutants, polycyclic aromatic hydrocarbons (PAHs), such as benzo(a)pyrene [B(a)P], which negatively impacts cognitive development in children who have been exposed in utero. In our study, prenatal exposure of Cpr(lox/lox) timed-pregnant dams to B(a)P (0, 150, 300, and 600 μg/kg body weight via oral gavage) on embryonic day (E14-E17) consistent with our susceptibility-exposure paradigm was combined with the analysis of a replicated autism risk gene, the receptor tyrosine kinase, Met. The results demonstrate a dose-dependent increase in B(a)P metabolite generation in B(a)P-exposed Cpr(lox/lox) offspring. Additionally, a sustained persistence of hydroxy metabolites during the onset of synapse formation was noted, corresponding to the peak of Met expression. Prenatal B(a)P exposure also downregulated Met RNA and protein levels and dysregulated normal temporal patterns of expression during synaptogenesis (!). Consistent with these data, transcriptional cell-based assays demonstrated that B(a)P exposure directly reduces human MET promoter activity. Furthermore, a functional readout of in utero B(a)P exposure showed a robust reduction in novel object discrimination in B(a)P-exposed Cpr(lox/lox) offspring. These results confirm the notion that common pollutants, such as the PAH B(a)P, can have a direct negative impact on the regulated developmental expression of an autism risk gene with associated negative behavioral learning and memory outcomes.
(my emphasis)
I have to say, finding this paper was a bit of tragic humor for me; it was published in December 2010, with zero fanfare from the press, as opposed to the confounder heavy, Residential Proximity to Freeways and Autism in the CHARGE study, study, which had a thousand similar articles in Google News. But here we find a superb example of what gets bandied around a lot when in quick passing but rarely with any meat behind the discussion; a real life, experimentally sound version of a gene environment interaction that integrates biologically plausible mechanisms that is able to describe what is observed physiologically in autism with dose responses. Beautiful. But, it gets even better. It just so happens, the classifications of agents in use in this study, polycyclic aromatic hydrocarbons, are generated, in some instances, by car exhaust. In fact, in Detection of polycyclic aromatic hydrocarbon exposure from automobile exhaust fumes using urinary 1-hydroxypyrene level as an index, the authors conclude in part that “Automobile exhaust fume exposed subjects have a higher risk to be exposed to PAHs than the non-exposed subjects”. Go figure.
Whatever the problems with the freeway CHARGE study, they pale in comparison to the problems that the notion that because we didn’t observe increases in autism when the Interstate system was constructed, the findings must be spurious. Similarly, genetic predisposition is an indisputable fact; and knowing which genes are implicated in autism can help us intelligently target environmental factors that might be changing our infants.
– 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
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
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
passionless Droning about autism 
