Synergistic Interactions between Drosophila Orthologues of Genes Spanned by De Novo Human CNVs Support Multiple-Hit Models of Autism

Autism spectrum disorders (ASDs) are highly heritable and characterised by deficits in social interaction and communication, as well as restricted and repetitive behaviours. Although a number of highly penetrant ASD gene variants have been identified, there is growing evidence to support a causal role for combinatorial effects arising from the contributions of multiple loci. By examining synaptic and circadian neurological phenotypes resulting from the dosage variants of unique human:fly orthologues in Drosophila, we observe numerous synergistic interactions between pairs of informatically-identified candidate genes whose orthologues are jointly affected by large de novo copy number variants (CNVs). These CNVs were found in the genomes of individuals with autism, including a patient carrying a 22q11.2 deletion. We first demonstrate that dosage alterations of the unique Drosophila orthologues of candidate genes from de novo CNVs that harbour only a single candidate gene display neurological defects similar to those previously reported in Drosophila models of ASD-associated variants. We then considered pairwise dosage changes within the set of orthologues of candidate genes that were affected by the same single human de novo CNV. For three of four CNVs with complete orthologous relationships, we observed significant synergistic effects following the simultaneous dosage change of gene pairs drawn from a single CNV. The phenotypic variation observed at the Drosophila synapse that results from these interacting genetic variants supports a concordant phenotypic outcome across all interacting gene pairs following the direction of human gene copy number change. We observe both specificity and transitivity between interactors, both within and between CNV candidate gene sets, supporting shared and distinct genetic aetiologies. We then show that different interactions affect divergent synaptic processes, demonstrating distinct molecular aetiologies. Our study illustrates mechanisms through which synergistic effects resulting from large structural variation can contribute to human disease.

孤独症谱系障碍（Autism spectrum disorders, ASDs）具有高度遗传度，以社交互动与沟通缺陷、局限重复行为为核心特征。尽管已鉴定出多种高外显率的ASD基因变异，但越来越多的证据表明，多个基因位点的协同贡献所产生的组合效应在ASD发病中发挥因果作用。本研究通过分析果蝇（Drosophila）中独特人类-果蝇直向同源基因的剂量变异所引发的突触与昼夜节律神经表型，发现多对经信息学手段筛选获得的候选基因之间存在大量协同互作；这些候选基因的直向同源基因均受到大型新发拷贝数变异（copy number variants, CNVs）的共同影响，而此类CNV存在于自闭症患者的基因组中，其中包括一名携带22q11.2缺失的患者。我们首先证实，针对仅包含单个候选基因的新发CNV中的候选基因，其独特果蝇直向同源基因的剂量改变所表现出的神经功能缺陷，与此前在ASD相关变异的果蝇模型中报道的结果一致。随后我们针对受同一人类新发CNV影响的候选基因直向同源基因集合，探究了其成对剂量改变的效应。在4个具有完整直向同源关系的CNV中，有3个在同时改变来自单个CNV的基因对的剂量后，观察到了显著的协同效应。这些互作遗传变异在果蝇突触处引发的表型变异表明，按照人类基因拷贝数改变的方向，所有互作基因对均会产生一致的表型结果。我们在CNV候选基因集合内部及集合之间的互作因子中，均观察到了特异性与传递性，这支持ASD存在共同与独特的遗传病因。进一步研究发现，不同的互作会影响不同的突触过程，表明存在不同的分子病因。本研究阐明了大型结构变异所产生的协同效应如何促成人类疾病发生的分子机制。