Finally, several pathway analyses have been performed using either genetic or transcriptome data to gain insight into the biological functions associated with ASD candidate genes. For instance, O’Roak et al. analyzed protein-interaction networks among genes implicated in ASD via whole-exome sequencing studies, and identified that de novo mutations in ASD patients are overrepresented among proteins involved in a chromatin remodeling network (O’Roak et al. 2012). Similarly, Gilman et al. demonstrated that CNVs identified in autistic patients are enriched for genes involved in a molecular network related to synaptogenesis,
axon guidance, and neuronal motility (Gilman et al. 2011). Only two studies have attempted to integrate autism candidate genes with known human brain gene expression patterns. Ben- David and Shifman attempted to assess for differences between rare and common ASD candidate genes by studying their co-expression relationships in adult human brain. They discovered these genes were both related to modules involved with synaptogenesis and neuronal plasticity, and that they are expressed in areas associated with learning, memory, and sensory perception (Ben-David and Shifman, 2012). The same authors also recently analyzed the neurodevelopmental expression of ASD candidate genes that had been discovered in cohorts as de novo mutations, and demonstrated that these genes appear to relate to networks involved in transcription regulation and chromatin remodeling processes (Ben-David and Shifman 2013).
Summary
In summary, while the number of investigations attempting to integrate genetic findings in ASD lags far behind gene discovery studies, there is evidence that through integrative functional genomics analysis, common pathways and mechanisms underlying ASD may be discovered. This thesis describes some of the first studies that have attempted to integrate large sets of ASD candidate genes to assess for common pathways, and to understand ncRNA regulation of gene expression in autistic brain.
1.4 Major Unanswered Questions and Motivations for this Work
The work described in Chapters 1.1 through 1.3 catalogs prior studies that have identified genetic mutations in individuals with ASD, explored the functional genomics of human brain development, and have attempted to integrate what is known about autism genetics with human neurodevelopmental functional genomics. These bodies of work make clear a number of important observations:
(i) Autism spectrum disorders have a significant hereditary/genetic component (ii) The genetic etiology of ASD is extremely heterogeneous
(iii) Gene expression in the human developing brain is unique from other human tissues and brain gene expression in other model organisms
(iv) Regulation of human neurodevelopmental gene expression is exquisitely regulated through a number of mechanisms including ncRNAs
(v) Autistic brain tissue displays disrupted gene expression patterns
However, there remain a number of fundamental questions about the functional genomics underlying autism spectrum disorders that serve as the main motivations for the studies described in Chapters 2 and 3 of this work:
(i) Are there common developmental gene expression properties/patterns among the genes implicated in autism that may be informative of their role in ASD?
(ii) Do these patterns provide insight into how so many genes with different functions can all relate to the same clinical phenotype?
(iii) Are there inherent gene expression differences between the developing male and female brain that may be informative of the significant bias in ASD seen in males? (iv) Can studies of non-coding regions of the genome in ASD help explain some of the
‘missing heritability’ by regulating genes involved in ASD pathogenesis?
These four questions served as the theoretical basis for the work that I performed for this thesis, as is described in the following chapters.
Chapter 2. Characterizing ASD Candidate Genes
During Human Neurodevelopment
Hundreds of genes have been implicated in autism spectrum disorders through many different approaches. However, most of these studies failed to also assess these genes for expression in human brain tissue, and in early human neurodevelopment in particular. Furthermore, as has already been discussed, it is important to consider the genetic interaction among various autism candidate genes, as their relation to each other throughout human brain development may provide additional layers of information regarding the pathogenesis of ASD.
In this chapter, I describe a set of studies that explored the expression of autism candidate genes throughout human brain development, in order to provide relevant insight into the functional genomics of this complex syndrome. In the first study, I performed the first comprehensive analysis to date of individual ASD candidate gene expression patterns spanning human neurodevelopment. Then, I performed (in collaboration) a study of autism candidate gene co-expression relationships. These two projects represent a comprehensive functional genomics assessment of ASD candidate genes during human brain development, and provide unique insight into common pathways that may underlie ASD pathogenesis.
Next, I performed two analyses on aspects of normal human neurodevelopmental genomics that have important implications for ASD. First, I assessed for sex-specific differences in human brain gene expression during development, as autism spectrum disorders are known to affect a preponderance of males. Then, I describe results of miRNA differential expression analysis across human brain development, and evaluated their relationship to known ASD candidate genes.
The work in this chapter provides critical insight into the functional roles of ASD candidate genes during normal human brain development, and how sex-specific gene expression and miRNA regulation of gene expression may relate to the functional genomics of ASD.