The 16p11.2 microdeletion enhances gene expression variability between human IPSC derived forebrain interneuron progenitor cells in culture

The 574 kilobase pair 16p11.2 microdeletion raises a person’s odds for neurodevelopmental and energy balance conditions, particularly autism and obesity. There is considerable clinical heterogeneity and how much this reflects genetic versus environmental or stochastic factors is unclear. Forebrain interneurons originate from progenitors residing in the ventricular zone of the foetal ventral telencephalon and their perturbation is implicated in a number of 16p11.2 phenotypes prompting investigation of how the 16p11.2 microdeletion impacts their development. We differentiate human induced pluripotent stem cells (IPSCs), isogenic except for heterozygous 16p11.2 microdeletion to minimise confounding effects of genetic background, to ventral telencephalic interneuron progenitor fate in 2D culture and use single cell RNA sequencing to obtain single cell transcriptome populations for comparative bioinformatics. Hundreds of transcripts are differentially expressed and many associate with cell signalling, chromatin, neurodevelopmental conditions including autism, and obesity. Pertinently, we find that transcript level variation is significantly greater in 16p11.2 heterozygous progenitors than their isogenic wild type counterparts and this holds for sets of genes comprising regulons, gene-sets functionally connected by transcription factor regulation, and for randomly selected gene-sets indicating that the 16p11.2 locus itself has a genome-wide property in stabilising transcription between cells. Regulons with greatest increased variation in 16p11.2 heterozygous progenitors exhibit strong enrichment for cell cycle related genes, resonating with our earlier finding of increased cell cycle variability between 16p11.2 heterozygous organoids, and many are regulated by transcription factors associated with autism and/or obesity enforcing the idea that unusual transcriptional variation itself contributes to phenotypes.