Combining Two Genome Analysis Approaches Supports Immune System Contribution to Autism
ScienceDaily (Dec. 6, 2012) — Researchers using novel approaches and methodologies of identifying genes that contribute to the development of autism have found evidence that disturbances in several immune-system-related pathways contribute to development of autism spectrum disorders.
The report published December 4 in the open-access journal PLOS ONE powerfully supports a role for the immune function in autism by integrating analysis of autism-associated DNA sequence variations with that of markers identified in studies of families affected by autism.
“Others have talked about immune function contributions to autism, but in our study immune involvement has been identified through a completely nonbiased approach,” says Vishal Saxena, PhD, of the Massachusetts General Hospital (MGH) Department of Neurology, first, corresponding and co-senior author of the PLOS ONE paper. “We let the data tell us what was most important; and most tellingly, viral infection pathways were most important in this immune-related mechanism behind autism.”
Genetic studies of families including individuals with autism have identified linkages with different locations in the genome. Since traditional interpretation methods implicate the gene closest to a marker site as the cause of a condition, those studies appeared to point to different genes affecting different families. However, Saxena’s team realized that, since autism has typical symptoms and affects the same biological processes, a common molecular physiology must be affecting the different families studied.
To search for genetic pathways incorporating these autism-associated sites, they developed a methodology called Linkage-ordered Gene Sets (LoGS) that analyzes all of the genes within a particular distance from marker sites and ranks them according to their distance from the marker.
Saxena’s team first analyzed previously identified copy-number variants (CNVs) — deletions or duplications of large DNA segments — linked to autism, and identified associated pathways for the first time. After finding that the two pathways most frequently affected by CNVs in autism were related to immune function, they went on to identify three additional immune-related pathways among the top 20 sets of genes with autism-associated CNVs.
They then conducted LoGS analysis on the five CNV-identified pathways, which they called iCNV-5, along with 186 other pathways involved in a range of biologic functions, ranking them according to their distance from marker sites identified in family studies. Four of the five iCNV-5 pathways received the top four rankings in the LoGS analysis, strongly supporting an immune function role in autism.
Additional pathways involved in neurodevelopment were highly ranked in both the CNV and LoGS analyses.
“The idea behind LoGS is akin to viewing a digital photograph,” says Saxena, an instructor in Neurology at Harvard Medical School.
“When one looks at a digital image from very close up, one only sees a few pixels and is unable to recognize the picture. Zooming out however, makes the picture understandable. In the same way, looking at single genes may lead to a disorganized view of a disease, but zooming out to the pathway level clarifies and unifies the mechanism.”
The immune system genes included in the iCNV-5 pathways code for two different types of proteins — interferons, in which DNA segments were reduced or absent in the iCNV-5 pathways, and chemokines, which showed duplication of DNA segments.
Interferons help control viral infections, so reduced production of interferons could delay control of a viral infection in a pregnant woman and her fetus.
Viral infections also induce the production of chemokines, which have an additional role in fetal brain development. A combination of reduced interferon levels, which would prolong the course of a viral infection, and elevated chemokine levels could potentially alter brain development in an infected fetus.
The researchers are continuing to investigate how these and other immune pathways may be involved in the development of autism.
The co-senior author of the PLOS ONE report is Isaac Kohane, MD, PhD, Boston Children’s Hospital. Additional co-authors are Shweta Ramdas, University of Michigan; Courtney Rothrock Ochoa, University of South Alabama College of Medicine; David Wallace, PhD, Massachusetts Institute of Technology; and Pradeep Bhide, PhD, Florida State University. The study was supported by National Institutes of Health grant P50MH94267 and the Nancy Lurie Marks Foundation.
Structural, Genetic, and Functional Signatures of Disordered Neuro-Immunological Development in Autism Spectrum Disorder.
Full article at Link
Numerous linkage studies have been performed in pedigrees of Autism Spectrum Disorders, and these studies point to diverse loci and etiologies of autism in different pedigrees. The underlying pattern may be identified by an integrative approach, especially since ASD is a complex disorder manifested through many loci.
Autism spectrum disorder (ASD) was studied through two different and independent genome-scale measurement modalities. We analyzed the results of copy number variation in autism and triangulated these with linkage studies.
Consistently across both genome-scale measurements, the same two molecular themes emerged: immune/chemokine pathways and developmental pathways.
Linkage studies in aggregate do indeed share a thematic consistency, one which structural analyses recapitulate with high significance. These results also show for the first time that genomic profiling of pathways using a recombination distance metric can capture pathways that are consistent with those obtained from copy number variations (CNV).
“…it is striking that of the genes implicated by LoGS, there is a loss of genomic copies in the interferon alphas (IFNA10, IFNA14, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA8, IFNA17) and gain of copies in the “C-C” motif chemokine ligands (CCL1, CCL11, CCL13, CCL2, CCL7, CCL8) as summarized in Table 1. Several of these chemokines have been found to be overexpressed in inflammatory diseases such as ulcerative colitis , atopic dermatitis , rheumatoid arthritis , and in neurocognitive disorders .
This suggests an etiological basis for the disordered innate immunity response found in autism , particularly as mediated by monocytes  and the histologically related microglia , , .
The loss of interferon alpha copies, usually implicated in the response to viral infection and another component of innate immunity, could also account for a dysregulated, secondary or compensatory response of interferons and chemokines. Several of these messengers “…are produced by neurons and glia in the adult brain, and that they can acutely influence synaptic transmission.” . Certain neurotrophins (which are also released by immune cells  cause activity-dependent changes in neural circuits in development .”
The above could be suggestive of a link between in utero infections and brain development in the child. Thus, the genetic background by itself would not be enough via this view to cause a deranged developmental process which would rather only occur in the presence of relevant infections.
Interferons are important in the control of viral infections via the induced expression of interferon-stimulated genes .
The loss of copy number in the interferon genes suggests a possible reduced expression of such genes when stimulated.
Thus, a viral infection would last longer under such a genetic background.
There would therefore be a longer generation of chemokines and other cytokines that could interfere with normal brain development. Further, gain in copy number in chemokines may lead to higher levels of these chemokines and would thus exacerbate the derangement in brain development.