Abstract
BackgroundReciprocal genomic disorders (RGDs) represent a unique class of recurrent genomic variation that offer insight into highly dosage sensitive regions of the morbid human genome. However, the genomic architecture mediating RGDs, namely non-allelic homologous recombination (NAHR) of flanking segmental duplications, has rendered these genomic segments recalcitrant to conventional model studies. We recently developed a novel CRISPR method that leverages the homology of segmental duplications and efficiently generates large microdeletions and microduplications that mimic NAHR in humans, including ablation or duplication of one copy equivalent of the segmental duplications. Here, we explore the functional consequences of 16p11.2 RGD in iPS derived neuronal models and across mouse tissues.MethodsWe generated CRISPR-engineered 16p11.2 RGD models against an isogenic iPSC background and performed transcriptome profiling in iPSC-derived neural stem cells (NSCs) and induced neurons (iN) (n = 10 isogenic deletions, 10 duplications, 6 controls). We then integrated these data with RNAseq from 306 libraries from multiple tissues in 70 mouse models of reciprocal deletion and duplication of the syntenic 7qf3 region (cortex, striatum, cerebellum, liver, white fat, brown fat in 16 mice; and replication from cortex, striatum, cerebellum in 54 mice).ResultsIn ongoing analyses, weighted-gene correlation network analysis (WGCNA) identified co-expression modules that were significantly enriched for 16p11.2 genes, evolutionarily constrained genes, genes robustly associated with autism spectrum disorder (ASD; TADA q < 0.1) and developmental disorders (DDD). Pathway analyses within modules discovered enrichment of genes critical to synaptic formation and neural connectivity as well as the protocadherin gene family. Network analyses specific to brain tissues within modules further identified a convergence on highly connected, or ‘hub’ genes, on Wnt signaling, including Ctnnb1 and Ctnnd1. The module was also again enriched for ASD loci (TADA, FDR < 0.1), constrained genes (ExAC, pLI ≥ 0.9) and brain specific genes from the Human Protein Atlas.DiscussionThese studies suggest the functional consequences of 16p11.2 RGD across models converge on transcriptional signatures associated with critical neurodevelopmental pathways and individual genes implicated in a spectrum of developmental and neuropsychiatric disorders.
Highlights
Reciprocal genomic disorders (RGDs) represent a unique class of recurrent genomic variation that offer insight into highly dosage sensitive regions of the morbid human genome
Our overall objective is to consider the role of human induced pluripotent stem cell (hiPSC)-based studies in dissecting the genetic origins of schizophrenia, validating causal variants identified through ongoing genetic analyses, and serving as a personalized medicine approach to screen for novel therapeutics with which to prevent or reverse disease course
We recently developed a novel CRISPR method that leverages the homology of segmental duplications and efficiently generates large microdeletions and microduplications that mimic non-allelic homologous recombination (NAHR) in humans, including ablation or duplication of one copy equivalent of the segmental duplications
Summary
S33 that we unravel how these risk factors interact within and between the diverse cell types populating the brain. The lack of human post-mortem tissue, coupled with the inability to conduct functional experiments in patient cells, has to date left us with a very limited understanding of how rare and common variants impact gene expression or cellular function. Given the heterogeneity of schizophrenia and the limited cohort sizes feasible with hiPSC-based cohorts, our panelists will share their successes and struggles in developing cohorts defined by shared clinical or genetic features. They will discuss both the molecular and phenotypic insights they have uncovered, in neurons and glia, from case/control and geneticallyedited isogenic cohorts. Our overall objective is to consider the role of hiPSC-based studies in dissecting the genetic origins of schizophrenia, validating causal variants identified through ongoing genetic analyses, and serving as a personalized medicine approach to screen for novel therapeutics with which to prevent or reverse disease course
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