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A Better Early Blood Test for Autism

Genetic signatures point to disrupted neuroimmune pathways



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Researchers have developed a blood test for autism spectrum disorders (ASDs) that outperforms existing genetic tests while presenting evidence that abnormal immunologic activity affecting brain development may help explain some of  autism’s origins.

 The findings also suggest a new direction for genetic research on autism and the search for treatments.

The blood test, described December 5 in the online open-access journal PLOS ONE and based on the largest gene-chip investigation ever done in autism, could enable early diagnosis of autism in about two-thirds of patients before clear symptoms start to appear (the average age of diagnosis in the U.S. is 5 years).

Researchers led by Sek Won Kong, HMS instructor of pediatrics at Boston Children’s Hospital, and also a member of the hospital’s Informatics Program (CHIP), analyzed blood samples from 66 male patients with ASDs (from Boston Children’s and several other hospitals in collaboration with the Autism Consortium of Boston) and compared them with 33 age-matched boys without ASDs. Using microarrays, they looked for RNA signatures reflecting differences in gene activity, or expression, between the two groups.



Isaac Kohane. Rose Lincoln/Harvard Staff Photographer“Since brain biopsy isn’t a viable option for research, we asked whether blood could serve as a proxy for gene expression in the brain,” said Isaac Kohane, HMS professor of pediatrics at Boston Children’s and director of CHIP. “We found that it could, though we and others were initially skeptical.”



Analyzing the blood samples, Kong and colleagues flagged 489 genes as having distinct expression patterns in the ASD group, then narrowed this to a group of 55 genes that correctly identified or ruled out autism in 76 percent of samples. They validated their findings in a second group of 104 male and female patients with ASDs and 82 controls, achieving an overall classification accuracy of 68 percent (73 percent for males and 64 percent for females).



The gene signature approach, which Boston Children’s has licensed exclusively to SynapDx (Southborough, Mass.), can potentially diagnose autism far more often than the genetic tests currently available. Those tests look for a variety of autism-related mutations—from small “spelling” changes to lost or extra copies of a gene or genes (known as copy number variants) to wholesale chromosome abnormalities—but together, the known mutations account for fewer than 20 percent of autism cases.



“It’s clear that no single mutation or even a single pathway is responsible for all cases,” said Kohane, who is also senior investigator on both studies. “By looking at this 55-gene signature, which can capture disruptions in multiple pathways at once, we can say with about 70 percent accuracy that ‘this child does not have autism,’ or ‘this child could be at risk,’ putting him at the head of the queue for early intervention and evaluation. And we can do it relatively inexpensively and quickly.”



Previous gene-expression studies on blood samples have been limited by study size and by the challenge of obtaining well-matched control groups, Kohane noted. 



The 55 genes whose expression was altered also suggest more than one path to what we know as autism. Based on their genetic signatures, subjects with ASDs clustered into four subgroups marked by changes in different biological pathways:

•    Synaptic pathways, specifically long-term potentiation pathways (essential for memory and learning), and neurotrophic pathways (signaling neurons to survive, develop and grow)

•    Immune/inflammatory pathways

“In our sample, about half of the autism cases had some sort of alteration on immune pathways, synaptic pathways or both,” said Kong.



Adding to the neuroimmune theory of autism



Most current theories of autism focus on disordered synapses (connections between brain cells). But, citing previous studies in the medical literature, Kohane speculates that brain development in autism may be impaired by abnormal immune responses to infections and other stressors during infancy or prenatally. For example, chemokines (inflammatory chemical messengers that recruit immune cells to fight infections) have been found to be overexpressed in some neurocognitive disorders, and animal studies have found that prenatal infections are associated with autism-like features in offspring.

“We know that if a mother has rheumatoid arthritis or the father has type 1 diabetes, there is an increased risk of autism in the child,” said Kohane. “Studies have also noted an increase in autoimmune disease, just as autism is increasing.”

Previous studies of brain tissue from patients with autism have found significant activation of immune cells in the cerebral cortex and cerebellum, and recent research at Boston Children's has shown that the same molecules used by the immune system also play a role in the development and functioning of the brain. “One can imagine that an infectious assault during pregnancy could increase chemokines into the brain,” Kohane said. “Or there may be something intrinsic to the brain that causes it to generate an inflammatory reaction. Genetic makeup may set up vulnerability in a subgroup of infants, but there may be some environmental factor that triggers the disease in that subgroup.”



Previous studies of brain tissue from patients with autism have found significant activation of immune cells in the cerebral cortex and cerebellum, and recent research at Boston Children's has shown that the same molecules used by the immune system also play a role in the development and functioning of the brain.



This work was funded in part by the CTSA award (National Institutes of Health/National Center for Research Resources NIH/NCRR 1UL1RR025758-01) and the i2b2 National Center for Biomedical Computing (NIH/NLM U54 LM008748) and the Conte Center for Computational System Genomics of Neuropsychiatric Phenotypes (NIH P50MH94267).

This story was adapted from a Boston Children’s Hospital news release.