Multiplexed single-cell autism modeling reveals convergent mechanisms altering neuronal differentiation

We coupled dCas9-based transcriptional repression of autism and neurodevelopmental disease genes to single-cell RNA-sequencing in the context of human neuron differentiation to identify the unique and shared consequences of these perturbations in a pooled experimental format. We infected LUHMES cells with a library of sgRNAs targeting 14 ASD-relevant genes or non-targeting guides (47 unique guideRNAs total), selected cells at a low MOI to enrich for cells with only 1 perturbation, and then differentiated these cells for 8 days. After 8 days, we performed single cell RNA-sequencing using the 10X Chromium platform to identify the effects of ASD-gene knockdown on neuron differentiation. We used the CROP-seq method to recover the sgRNA sequences from polyA RNA.