Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models.

Chromosome 16p11.2 reciprocal genomic disorder due to recurrent copy number variants (CNVs) involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue, cell-type, and dosage specific, though more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2163 differentially expressed genes) and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated/loss-of-function constraint/FMRP gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, while single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Both neuronal ratios and gene expression changes in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption in 16p11.2 carriers that may contribute to changes in neurodevelopmental and cognitive function. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes, with relative impacts that are context-specific. Overall design: bulk RNAseq based transcriptomic analyses of six tissues from 16p11.2 deletion and duplication as well as control mouse models; single cell RNAseq based transcriptomic analyses of human iPSC-derived 16p11.2 deletion and duplication as well as control organoids.