Production of a synthetic superenhancer to monitor SOX2 transcriptional activity in glioblastoma
Item statusRestricted Access
Embargo end date31/07/2023
Glioblastoma (GBM) is the most common adult brain cancer and one of the most lethal human cancers. SOX2-expressing GBM cells drive tumour growth and have a neural stem cell-like identity. Here, we developed novel synthetic superenhancers that inform some of the gene regulatory circuits operating in GBM stem cells (GSCs). Individual SOX2 enhancers that are active within the GSC, but not in their differentiated progeny, were identified from published ChIP-seq datasets. High throughput functional screening was performed for 4579 on individual plasmids. Interestingly, the validated functional enhancer fragments shared a SOX dimer motif, suggesting that SOX9 may be an important regulator that cooperates with SOX2 at key enhancers to drive expression of oncogenic genes in GBM. By creating tandem arrays of the functional enhancer fragments we created ‘synthetic superenhancers’. These had significantly increased activity compared to individual enhancer fragments, but retained cell type selectivity. We show that SOX2 and SOX9 physically bind to these enhancer fragments, and that loss of the SOX dimer motif reduced activity significantly. These synthetic superenhancers provide valuable new experimental tools for reporting SOX activity in GBM applications (e.g. small molecule phenotypic screening). Our findings suggest that SOX9 is a key regulator of GSCs that likely cooperates with SOX2 at shared target genes. These findings may be of broader significance, as many solid cancers co-express SOX2 and SOX9 at high levels.