Is there an abnormal regulation of the immune response in autism?

One month ago the online journal Nature Communication published a study claiming that inflammation is a hallmark of autism. The study, a conjoint effort between Johns Hopkins and the University of Alabama, analyzed the expression of RNA molecules (i.e., substances that are essential for protein synthesis) in the brains of autistic and neurotypical subjects. Until present, similar attempts had been hampered by the limited availability of tissue. Autopsied brain tissue is scarce, but this study was able to acquire 104 samples matched for brain region (i.e., BA19, BA10, and BA44) that allowed comparisons between 40 neurotypicals and 32 autistic individuals.


The study analyzed 13,262 genes with only 2 (!) transcribed genes being differentially expressed between the brains of autistic and neurotypical individuals. These genes were Myelin And Lymphocyte protein (MAL), and C11orf30. MAL is a myelination gene that has been implicated in other psychiatric disorders and C11orf30 has a role in DNA repair, inflammation and malignant disease. From here on findings were stretched by using computer programs to perform a “gene correlation network analysis” that could identify differentially expressed groups or modules of genes between autistic and neurotypicals. One of these modules was enriched with genes involved in how certain cells called microglia worked and others that were involved in viral infections. Contrary to previous studies implicating a role for cells involved in repairing brain injury (cells called astrocytes), no significant differences were found in the present study. The authors further noted a negative correlation between their microglia module and others involved in transmission of signals among neurons (those involved in “synaptic” transmission).

Overall, I thought the study was weak and incapable of supporting any of their conclusions. Some basic criticisms of the study are as follows:

1) The authors claimed that the study groups were matched for cause of death. This was not the case! The autistics were a mismatch of cases that included some with chromosomal abnormalities (n=3, not enough to make them a group on their own) and others who died specifically from seizures (n=7, including those with chromosomal abnormalities). None of the controls had seizures as a cause of death. The most common cause of death among controls was accidental with multiple injuries. One could suspect that these multiple injured individuals were motor vehicle accidents whose brains were obtained through the medical examiners. Some of these patients even died of their head injuries.

A) Brains of people who die in car accidents, as in the control series for this study, make for poor postmortem controls. Over half of all reported traumatic brain injuries are the result of car accidents, e.g., as when the skull hits the steering wheel or windshield. Depending on how long the individual survives the accident the brain may undergo reactive changes to the incurred injury.
B) The large number of cases who died from seizures in the autism group could by itself explain the reported findings. There is a large body of literature indicating that seizures and the engendered hypoxia can activate the innate immune response of the brain and associated inflammatory changes. This large body of literature was either unknown to the authors or simply ignored. Also be aware that even though some of the autism patients died from seizures, many others within the series, could have had convulsions during life without having had a diagnosis for the same. In effect some convulsions can be totally missed (e.g., nocturnal seizures).
C) Although there were drowning victims in both the autism and control series, the important thing is who was resuscitated and survived for a period of time (so-called “near drowning” victims). Near drowning procreates a type of injury (ischemia-reperfusion) that causes a prolific inflammatory response. The affects of the same can be noticed even in those who survive drowning for a couple of hours

2) Using samples from at least 2 sources of tissue offers a major confound that may be difficult or impossible to resolve. It appears that the authors obtained the brain tissue for autistic individuals from the Autism Tissue Program (ATP) and their controls from the NICHD Brain and Tissue Bank at the University of Maryland. These two brain banks differ markedly among themselves in regards to tissue quality and collection methods. Many of the samples of the ATP are slow frozen and those from the NICHD are quick or snap frozen.

3) Although the authors claim that autism is a neurodevelopmental condition their study design took a snap shot of a process that was happening at the time the persons died. There is no way to extrapolate the data to the time of brain development.

4) The inflammatory response in the brain is not restricted to one cell as the authors seemingly imply in the article. The microglia acts in conjunction with astrocytes to wall off and contain the injury in damaged areas. In this study there was “evidence” for microglia activation but not for the activation of supporting astrocytes.

5) Even if the microglia were activated in the brains of autistic individuals this does not mean that they are involved in an inflammatory response. Microglia act in other capacities, including synaptic remodeling, which may be more appropriate considering other findings in autism. Aslo as an aside, as microglia and inflammatory reactions are not restricted to the gray matter the study design should have also included sampling of the white matter.

6) There are many other limitations to the study including the small number of brain regions sampled and no histological criteria being specified or who performed the neuropathological screening of the samples used. Why were these brain areas selected? Did they relate in any way to symptomatology? Other areas of the brain that could have acted as control (e.g., visual cortex) are usually selected in postmortem studies. Maybe the authors should have considered a similar strategy.

It is a pity that this and other genetic studies offer only confusion to the field without really adding anything constructive. If the idea is to study inflammation, do a properly controlled postmortem study. See whether there is a breach in the blood brain barrier. Do immunocytochemistry and examine whether there is truly activation of microglia. There are much better ways to broach the subject than with genetics.

A few months ago a good friend Paul Patterson died. He was a stellar researcher within the field of autism. Probably the last thing Paul penned as he died was an opinion piece for a book I was editing. In those few paragraphs Paul expressed a certain amount of indignation at the overstated importance and biased funding that genetic research receives from the NIH and other organizations like the Simons Foundation (see ). I certainly join Paul in expressing due frustration.

For related blogs see:

1) Brain donations and research in autism: the good, the bad and the ugly
2) Autism: banking on the future of our children
3) The importance of postmortem research in autism


Gupta S, et al. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nature Communications 5, article number 5748, December 2014. See

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