Blood-Based Gene Expression In Infants and Toddlers with ASD

Background: Autism Spectrum Disorder (ASD) is a genetically complex neurodevelopmental disorder characterized by deficits in communication, social reciprocity, and patterns of repetitive or stereotypic behaviors that emerge during the first three years of life.  Previous gene expression studies of lymphoblastoid cell lines implicate genes involved in circadian rhythm, nervous system development, inflammation, cytoskeletal organization, steroid biosynthesis, and ASD-specific physiological symptoms (i.e. gastrointestinal symptoms), while analysis of peripheral blood gene expression profiles point to the involvement of NK cells in ASD susceptibility. These studies demonstrate the utility of whole genome gene expression profiling in identifying genes associated with ASD.   

Objectives: Few, if any, studies of blood or lymphocyte gene expression have been done at young ages in ASD, while most studies have been pursued with a small sample size. Gene expression profiles from older ASD subjects may only reflect secondary perturbations of ASD. Evaluation of infants and toddlers with ASD may be beneficial in identifying the primary genetic effects that lead to early developmental abnormalities, thus being more relevant to the development of the ASD prognostic and diagnostic biomarkers. Our objective was to identify genetic pathways, networks, and processes altered in autism at the age of first clinical signs. 

Methods: Gene expression profiles of peripheral blood mononuclear cells (PBMCs) from 73 young male subjects (12 months to 45 months of age; ASD = 41, typically developing = 32) were assessed via direct hybridization to Illumina Human Ref-8 bead-arrays. Linear regression analysis on probes filtered for average intensity less than background (n=14921) was performed to identify differentially expressed genes between ASD and typical subjects. Significantly identified genes (n=461; p < .01, FDR = .26) were imported into MetaCore for enrichment analysis in GeneGO Pathway Maps, GeneGO Process Networks, and GO Processes. 

Results: Genes involved in prenatal neural developmental functions were represented among the networks that were significantly differentially expressed in ASD infants and toddlers. Specifically, significant differences between ASD and typical subjects were found in cell cycle regulation, DNA damage response, apoptosis and survival, and cytoskeleton pathways, as well as in several neurophysiological processes. 

Conclusions: These findings suggest that PBMC-based gene expression profiling of ASD may reveal unique and possibly fundamental dysregulated gene expression patterns that may be of use as  clinically significant biomarkers of ASD. Moreover, the dysregulated expression profile detected in living ASD infants and toddlers maps remarkably well onto profiles derived for CNV analyses of large autism samples (Pinto et al., 2010), and new CNV and gene expression profiles derived from prefrontal cortex brain tissue of young autistic postmortem cases. In each of these very different types of genetic analyses (brain, blood, CNV, RNA), the strongest signals were dysregulation of proliferation, cell cycle, cell differentiation and cyctosketelon mitosis- and migration-relevant pathways. We theorize these processes reflect the first prenatal steps of maldevelopment that lead to autism. They underlie early brain overgrowth, migration defects, defects in cortical lamina and aberrant connectivity.