Analysis of the transcriptome of undifferentiated SH-SY5Y neuroblastoma cells following AS3MT knockout with CRISPR/Cas9.

Aims/Hypothesis: AS3MT is a risk gene for schizoprhenia and the role in neuronal cell lines has not been established. Using CRISPR/Cas9 generated two AS3MT knockout lines (B6/C6) and age matched wild type controls (D2/D3) in SH-SY5Y neuroblastoma cells and characterised the transcriptional response following knockout. We carried out two independent sequencing runs, including independent cell culturing, RNA extraction, library prep, and sequencing and identify considerable overlap of differentially expressed genes identifying a robust transcriptional response following AS3MT knockout. We identified a number of genes involved in cellular adhesions, ribosomal function, cell-cell contact, and neuronal development, as well as a significant enrichment of previously associated schizophrenia genes, including ZNF80a and DRD2. Knockout AS3MT SH-SY5Y and an age matched WT control line were cultured in 6 well plates until confluent and RNA extracted. Differential gene expression were performed with DESeq2, and ontology analysis with GOSeq.