DJ-1 deficiency in SH-SY5Y cells reveals dysregulated networks of genes and pathways involved in neuronal function and disease.

Parkinson's disease (PD) is the second most common neurodegenerative disorder. Although the etiology of idiopathic PD is unclear, recessive loss-of-function mutations in PARK7/DJ-1 cause familial early-onset PD, which mirrors key features of the idiopathic form. In this study, we ablate PARK7/DJ-1 via CRISPR-Cas9 from the human neuronal cell line, SH-SY5Y. Subsequently, RNA sequencing and the DESeq2 toolkit were utilized to identify 5468 differentially expressed genes (DEG) between PARK7/DJ-1 knockouts and control SH-SY5Y cells. Three genes from each of the top 10 upregulated and downregulated gene lists were selected and confirmed via RT-PCR. Differentially expressed gene lists were run through the WebGestalt functional enrichment analysis toolkit to identify enriched gene ontology (GO) terms. Among the top significantly enriched GO biological process terms include terms related to synaptic transmission (downrgulated DEG) and development (upregulated DEG). Differentially expressed genes were run through the STRING database to predict protein-protein interactions (PPI). A highly significant PPI enrichment was observed (p < 1.0e-16). To gain insight into what could potentially be driving the observed expression changes, we performed an iRegulon analysis within Cytoscape to identify potential upstream transcription factors. The top transcriptional factors identified for driving downregulated genes was REST, while EP300 was identified as the top candidate driving upregulated genes. Our results indicate that loss of DJ-1 in human neuronal cells leads to dysregulation of networks of connected genes and pathways that are implicated in neurodegenerative disease as well as neuronal function.