An interaction-based model for neuropsychiatric features of copy-number variants

Abstract

18Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic 19 heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for 20 these phenotypes within each CNV have not been successful. Here, we posit using multiple lines 21 of evidence, including pathogenicity metrics, functional assays of model organisms, and gene 22 expression data, that multiple genes within each CNV region are likely responsible for the 23 observed phenotypes. We propose that candidate genes within each region likely interact with 24 each other through shared pathways to modulate the individual gene phenotypes, emphasizing 25 the genetic complexity of CNV-associated neuropsychiatric features. 26 27 28A case for a multi-genic model of CNV pathogenicity 29 Since the advent of large-scale sequencing studies, the number of genes associated with 30 neurodevelopmental disorders such as autism, intellectual disability, and schizophrenia has 31 increased dramatically. For example, nearly 200 genes have been identified with recurrent de 32 novo mutations in both individuals with autism and intellectual disability (1-8). In fact, complex 33 human disease phenotypes can be influenced by variation in both a small number of core genes 34 with large effect size and a large number of modifier genes with small effect size, accounting for 35 the large number of candidate neurodevelopmental genes (9,10). The application of a multi-genic 36 model for disease pathogenicity has not been fully expanded to cover copy-number variants 37 (CNVs), or large duplications and deletions in the genome. The prevailing notion of single 38 causative genes for CNV disorders is due to the paradigm of gene discoveries for CNVs 39 associated with genetic syndromes in individuals with specific constellations of clinical features, 40 such as Smith-Magenis syndrome (SMS). Although some variability in phenotypic expression 41 has been documented, these disorders usually occur de novo and are characterized by high 42 penetrance for the observed phenotypes (11,12) (Figure 1). In these cases, individuals 43 manifesting the characteristic features of the syndrome but with either atypical breakpoints or 44 mutations in individual genes within the CNV region were used to identify causative genes for 45 the major phenotypes (13-15). These causative genes, such as RAI1 for SMS, were then 46 confirmed by recapitulating conserved phenotypes of the deletion using functional evaluations in 47 animal models (16,17). 48 In contrast, another category of CNVs has been identified in individuals with 49 neurodevelopmental disorders, including duplications and deletions at proximal 16p11.2, 3q29, 50 distal 16p11.2, and 1q21.1 (18-21). Although these CNVs are enriched in affected individuals 51 compared to population controls, they are primarily characterized by variable expressivity of 52 clinical features (12,22-26) (Figure 1B). For example, the 16p11.2 deletion has been implicated 53 in 1% of individuals with idiopathic autism (...

Functional assessment of the “two-hit” model for neurodevelopmental defects inDrosophilaandX. laevis

“…We previously described multiple models for how genes within CNVs contribute towards neurodevelopmental phenotypes (20,21,48). Here, we analyzed neurodevelopmental defects and cellular and molecular mechanisms due to individual and pairwise knockdown of conserved 16p12.1 homologs in Drosophila and X. laevis, and evaluated how these defects are modulated by homologs of "second-hit" genes.…”

“…Our previous functional studies of genes within CNV regions identified several potential models for how genes within CNVs interact with each other to influence neurodevelopmental phenotypes (20,21,48). As multiple homologs of 16p12.1 genes contribute towards developmental, neuronal, and cellular phenotypes, we used the sensitive fly eye system to assess for genetic interactions among the 16p12.1 fly homologs.…”

“…Furthermore, we identified a synergistic interaction between homologs of MOSMO and SETD5, which led to more with the 16p12.1 deletion. The ultimate nature of these interactions depends on the role of the individual CNV genes towards specific phenotypes, as well as the molecular complexity associated with each phenotypic domain(48).The high inheritance rate of the 16p12.1 deletion(8,9) suggests that while it confers risk for several phenotypes, the CNV can be transmitted through multiple generations until additional variants accumulate and cumulatively surpass the threshold for severe disease(7). In contrast,other CNVs associated with neurodevelopmental disease, such as the autism-associated 16p11.2 deletion and the 17p11.2 deletion that causes Smith-Magenis syndrome, occur mostly de novo and are less likely to co-occur with another "second-hit", suggesting a higher pathogenicity on their own (11).…”