Transcriptional consequences of 16p11.2 microdeletion/microduplication syndrome in human lymphoblasts and mouse cortex. I. Blumenthal1, A. Ragavendran1, S. Erdin1, L. Klei2, J. Guide1, M. Stone1, C. Ernst1, J. Levin3, V. Wheeler1, K. Roeder4, B. Devlin2, J. F. Gusella1,3,5, M. E. Talkowski1,3,5 1) Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA; 2) Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA; 3) Broad Institute of MIT and Harvard, Cambridge, MA; 4) Department of Statistics, Carnegie Mellon University, Pittsburgh, PA; 5) Department of Neurology, Harvard Medical School, Boston, MA.

   Autism spectrum disorder (ASD) is a heterogeneous developmental disorder affecting 1-2% of the population, with recurrent reciprocal copy number variants (CNVs) representing one of the largest known risk factors. We evaluated the global transcriptional consequences of one of these recurrent CNV regions, 16p11.2, which accounts for ~1% of all ASD cases, but also confers risk to diverse phenotypic outcomes despite recurrent breakpoints mediated by non-allelic homologous recombination, suggesting modifying factors that affect penetrance and expressivity. We performed a customized strand-specific RNA sequencing protocol (dUTP) on lymphoblasts from 7 multiplex ASD families (n=35 individuals), each harboring a segregating 16p11.2 CNV and displaying heterogeneity of both genotype (ASD individuals discordant for CNV) and phenotype (subjects with CNV without phenotype). We also sequenced RNA from the cortex of 8 mice with deletion or duplication of the 16p11.2 syntenic region (7qF3) and 8 gender-matched wild type littermates. For genes within the CNV region, we observed a highly significant and consistent effect in both human and mouse datasets associated with reduced expression in deletions and increased expression in duplications. We also detected presumed positional effects in the CNVs proximity as well as dysregulation of genes elsewhere in the genome. In the humans, 27 genes associated with ASD (from SFARIgene and AutismKB) were nominally significant and 9 appeared in a protein interaction network (generated with DAPPLE) connecting them to 3 genes in the CNV. Gene ontology of these results identified pathways important to chromatin structure and remodeling. The mouse cortex data identified 42 ASD associated loci among the nominal results, and a DAPPLE interaction network revealed a sub-network connecting seven of the CNV region genes to 16 ASD loci outside the region. Gene ontology analysis of the sub-network highlighted WNT signaling, MAPK signaling, and melanogenesis. Interestingly, there were 126 genes differentially expressed in the same direction as a consequence of both deletion and duplication. Our findings reveal interconnected networks of genes whose expression is disrupted by 16p11.2 dosage imbalance, suggesting potential convergence on common ASD pathways due to different mutational mechanisms, as well as a potential common mechanism of ASD risk conferred by both deletion and duplication through genes that require tight dosage control.

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