More evidence for a genetic basis for autism

ResearchBlogging.orgI wonder what the loons at Age of Autism will say about this.

Actually, I know what they’ll say. Whenever a scientific study like the one just published earlier this week the top tier journal Nature, which examines genetic variations (CNVs) associated with autism and autism spectrum disorders (ASDs), comes out, they have a standard reply. Even though, as of this writing, I haven’t seen yet seen a reply on the anti-vaccine crank blog Age of Autism to the study I’m about to describe, I’m sure it’s coming and I’m sure it will look something like this article from a year ago by Mark “Not A Scientist Not a Doctor” Blaxill entitled Latest Autism Gene Studies Find….Not Very Much:

There’s a familiar rhythm to the most prominent autism gene hunt publications. Their authors hype their newly minted study aggressively in the media. The prestigious journals that publish them lend their imprimatur to press releases that say, “this study is a big deal.” The findings sound impressive in the press release (and the authors get plenty of time on camera and in leading newspapers to tell us how truly impressive they are). In the meantime–in papers that are so densely written that making sense of what they really say requires far more reflection than the media hype cycle permits–skillfully concealed evidence reveals the truly important news in the findings: the authors whisper quietly (if at all) that the new analysis negates the most important findings of some of the most prominent previous gene hunts, while crucial detail on their new findings is often relegated to “supplementary material” that’s not available on the publication date.

Such a declaration is then almost inevitably followed by rants against scientists for concentrating on genes rather than vaccines as a cause of autism, claims of “conflicts of interest,” and an “analysis” of the findings of the study that betray an incredible lack of understanding of molecular biology, genetics, and developmental biology. I expect that the response to this study will be no different and may well appear on AoA by tomorrow morning, quite possibly written by Mark “Not a Scientist Not a Doctor” Blaxill. The study by Pinto et al, looks at the functional impact of global rare copy number variation in autism spectrum disorders.

Before you can understand what this paper found, you need to know what copy number variation is. In basic genetics and biology classes, many of you probably learned, depending on how long ago you took the courses, that we have two copies of each gene, one on each chromosome, one inherited from the father and one inherited from the mother. The exception is that men have a Y-chromosome instead of a second X chromosome and therefore have only one copy of genes on the X and Y chromosome, the X-linked genes inherited from the mother, the Y-linked genes inherited from the father. Of course, nature is seldom quite so neat, and now that we have powerful tools for sequencing the entire genome and probing its entire DNA looking for anomalies, we’re finding that things aren’t quite so simple. It turns out that there is considerable variation in the copy numbers of some genes. This is due to the rare duplication or deletion of a stretch of chromosome during replication. Such errors can leave a person with, for example, one copy on one chromosome and two on another. Although these events are rare for individual stretches of chromosomal DNA, over time and over many generations they can lead to some genes having several. Moreover, there appear to be “hot spots” in various chromosomes that are more prone to duplications or deletions.

Because I’m a cancer surgeon and biologist, I’m mostly familiar with variations in gene copy number associated with cancer, and there are many of these. Duplications and amplifications of stretches of DNA are practically the sine qua non of cancer. Often in cancer the amount of gene product in the form of protein that a given gene makes is proportional to the copy number. For instance, in breast cancer, there is a stretch of DNA known as the 8p11-12 amplicon. Basically, it’s a stretch of DNA on the p arm of chromosome 8 that is commonly amplified in breast cancer. This region of chromosome 8 is under active study, and there appear to be a number of candidate oncogenes there. One consequence of our learning about such amplified regions is that a formerly popular (about 30 years ago) and somewhat simplistic idea that single oncogenes would explain carcinogenesis, an idea that was later supplanted by a less simplistic but still too simple idea of multistage carcinogenesis in which a series of mutations in key oncogenes led to cancer. Now we understand that it is many genes that cause cancer. Whole networks of genes are perturbed.

Cancer is one extreme, though. Although CNVs are associated with many diseases and conditions, the abnormalities in are not as dramatic or numerous as they are in cancer. In the study under discussion, Pinto et al undertook an a survey of as many CNVs as they could identify in autistic children. Basically, they genotyped 1,275 children with ASD and 1,981 neurotypical controls and compared the frequency of single nucleotide polymorphisms (SNPs) according to the following scheme:


It’s not necessary for you to understand what SNPs are, only that by examining them scientists can estimate CNVs. Using a technique that can look for SNPs in 1.2 million loci per sample. This allows the performance of what is known as a genome wide association study (GWAS), which can look at genetic variation over the entire genome. Genetic variations that are more common in people with a disease are said to be associated with that disease. GWAS can be very powerful, but, like much of modern genomic medicine, these studies produce incredible amounts of data, with all the attendant difficulties, both computational and scientific, in interpreting what all the associations that are found may or may not mean.
As the authors note in their introduction, previous attempts at GWAS for autism have identified candidate genetic loci at 5p14.1 and 5p15.2. However, variations in these loci can only account for a relatively small percentage of the heritibility of ASD, hence the desire to examine the entire genome in a large number of children with ASD.

What Pinto et al found was this:

The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours1. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability2. Although ASDs are known to be highly heritable (~90%)3, the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 × 10-4). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.

One interesting finding was that 5.7% of the CNVs discovered appeared not to be inherited; i.e., they were de novo, meaning, basically, new CNVs. More important, though, was the bioinformatic and systems biology analysis of the CNVs. This led to the identification of potential new pathways whose function in ASDs may be abnormal compared to the control group. This is mapped out in the following illustration:


Candidate pathways for ASD identified by this method included genes involved with the cytoskeleton and microtubules, as well as genes involved in cell projection and motility, all of which are involved in cell migration. Other candidate pathways included genes involved in cell adhesion. It is not difficult to imagine how defective or altered migration and adhesion of neurons might result in the creation of abnormal neural pathways and thus result in the differences in cognition and behavior observed in ASDs. Of course, I’m putting things very simply. Even if this is true and these pathways are involved in ASDs, we know so little about how neural networks result in cognition and behavior that it will take a very long time and a lot of work to figure out excactly why and how abnormalities in these pathways result in ASDs. The same is true of other potential pathways implicated by these studies. These include GTPase and ras signaling pathways, as well as other kinase pathways. It’s not necessary to understand the significance of these pathways, just to know that they are involved in the transmission of signals from protein receptors on the cell surface into the cell, with the result being a number of processes, such as proliferation, migration, and the transmission of signals between neurons, among others.

Almost as important as the candidate pathways implicated by this study that clearly need further study to validate whether they are truly involved in the pathogenesis of ASDs or not are the pathways that were not implicated. One of the major claims of the “autism biomed” movement, the group of quacks who claim that they can treat autism with all manner of woo ranging from chelation therapy to various antioxidants and supplements, is that there are significant defects in pathways involved in countering the effects of oxidative stress, particularly pathways that result in glutathione production. (Glutathione is one of the major scavengers of reactive oxygen species–a.k.a. free radicals–in the cell.) Such claims were prominently featured by the lawyers for the complainants in the Autism Omnibus. Treatments allegedly targeting “detoxification” pathways involving “Glutathione, Cystathionine, Homocysteine, Methionine” figure prominently on the website of many a quack and are a favorite among the “vaccines cause autism” crowd. Don’t ask me how “vaccine injury” somehow causes oxidative stress sufficient to “cause autism.” Anti-vaccine “scientists” have long and convoluted pseudoscientific explanations that are implausible and unconvincing.

None of these “detoxification” pathways showed up in the analysis of Pinto et al. Big surprise, there. Well, not really. Of course, the fact that Pinto et al failed to find any of these pathways in ASDs in their analysis will no doubt be seized upon as “proof” that their analysis is hopelessly flawed. Just you wait. It’s coming. Because everything old is new again when it comes to the anti-vaccine movement, also coming will be another turd from Mark “Not a Scientist Not a Doctor” Blaxill that will go something like this one from a year ago:

But if the de novo CNV theory was plausible at one level, it was absurd at another. The genetic mutations the theory proposed (because this was the best the available evidence could support) were completely non-specific. The copy variants were spread widely (even randomly) over the genome, the theory went. No individual mutation was responsible for autism, just the unhappy presence of the wrong one. And these non-specific mutations were not only widely spread, they were virtually undetectable in the infant: no dysmorphic features; generally normal birth and (in many cases development); and the beautiful children we so often see affected by autism.

In other words these CNVs were a case of immaculate mutations.

And it was the perfect new project for the genetics research community. A wide open field of research opportunities. Lots of new money. And a chance to explain past failure away as part of the inexorable march towards genetic understanding.

If there’s one thing that annoys the crap out of me, as regular readers know, is likening science to religion. It’s a favorite canard of cranks of all stripes, be they anti-vaccinationists, creationists, alt-med promoters, 9/11 Truthers, and Holocaust deniers. I’ve heard anti-vaccine loons refer to “Vaccinianity“; creationists refer to the “church of Darwin”; and Holocaust deniers refer to “Holocaustianity,” among others. The intent is obvious: Try to paint the science detested as being faith-based rather than science-based.

No doubt when Blaxill or whoever at AoA decides to attack Pinto et al shows up to do it, he’ll also parrot the same breathtaking combination of ignorance and binary thinking. P.Z. Myers put it well when he pointed out that these things are very complicated. So did Pinto et al:

Our findings provide strong support for the involvement of multiple rare genic CNVs, both genome-wide and at specific loci, in ASD. These findings, similar to those recently described in schizophrenia, suggest that at least some of these ASD CNVs (and the genes that they affect) are under purifying selection. Genes previously implicated in ASD by rare variant findings have pointed to functional themes in ASD pathophysiology. Molecules such as NRXN1, NLGN3/4X and SHANK3, localized presynaptically or at the post-synaptic density (PSD), highlight maturation and function of glutamatergic synapses. Our data reveal that SHANK2, SYNGAP1 and DLGAP2 are new ASD loci that also encode proteins in the PSD. We also found intellectual disability genes to be important in ASD. Furthermore, our functional enrichment map identifies new groups such as GTPase/Ras, effectively expanding both the number and connectivity of modules that may be involved in ASD. The next step will be to relate defects or patterns of alterations in these groups to ASD endophenotypes. The combined identification of higher-penetrance rare variants and new biological pathways, including those identified in this study, may broaden the targets amenable to genetic testing and therapeutic intervention.

The problem is that none of this is easy, and none of it is likely to result in effective treatments for ASDs soon. Autism quacks and anti-vaccine zealots, however, can’t accept this. Again, like Blaxill, they demonstrate binary thinking. If a study doesn’t find a single, clear-cut gene causing autism or ASDs, then the study is crap. They also seem completely oblivious to developmental biology. It bothers them that a child with ASD appears normal at birth and then only manifests symptoms between the ages of 2 and 4. Development proceeds, however, according to predictable, sequential steps that are under genetic control, and genetic variations and abnormalities can have a profound impact on development that may not manifest itself until previous parts of the developmental program are complete. They also seem unable to understand that most chronic diseases and conditions with a strong genetic component are multifactorial and due to differences multiple genes. Due to functional redundancy in our cells, there are also often multiple abnormalities that can produce similar phenotypes; it is therefore not surprising that there might be many different gene abnormalities that contribute to ASDs. Systems biology gives us the tools to start to understand these exceedingly complex processes.

While it is possible–even likely–that there is an environmental component to ASDs, the evidence to date has not convincingly implicated any, except for, ironically enough, given how anti-vaccine zealots believe that the MMR vaccine causes autism, maternal rubella infection while the fetus is in the uterus, as a cause of autism. Moreover, as P.Z. pointed out, no transient exposure or exposures to an external agent (such as a vaccine) is known to be able to produce such a consistent pattern of gene duplications and deletions in human cells like the sets detected in Pinto et al. Thus far, the preponderance of evidence points to primarily a genetic cause for autism and ASDs, and Pinto et al is another solid study supporting a genetic basis for autism. It also suggests potential cell signaling pathways that might be abnormal in autism and thus targets for therapeutic intervention. That’s all we can ask of such a study.

Now remains the hard work of validating and replicating these findings and then figuring out which pathways can be targeted for therapy. What I’m afraid of now is that the quacks will look at the pathways identified by Pinto et al and try to come up with new pseudoscientific “biomed treatments” for autism based on these results, after (of course) “showing” how vaccine “injury” can create these same CNVs in children.

That’s coming, too. Just you wait. It wouldn’t surprise me if I were to see this sort of “science” presented at Autism One next year.


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