Epigenomic perturbation of novel EGFR enhancers reduces the proliferative and invasive capacity of glioblastoma and increases sensitivity to temozolomide

Glioblastoma (GB) is the most aggressive of all primary brain tumours. Patients typically rely on radiotherapy with concurrent temozolomide (TMZ) treatment and face a median survival of [~]14 months. Alterations in the Epidermal Growth Factor Receptor gene (EGFR) are common in GB tumours, but therapies targeting EGFR have not shown significant clinical efficacy. Here, we investigated the influence of the EGFR regulatory genome on GB cells, and identified novel EGFR enhancers located in an intronic region nearby the GB-associated SNP rs723527. Epigenomic perturbation of this regulatory region using CRISPR-based methods decreases EGFR expression and reduces the proliferative and invasive capacity of glioblastoma cells, while increasing their sensitivity to TMZ. The enhancer-perturbed GB cells also undergo a metabolic reprogramming in favour of mitochondrial respiration and present increased apoptosis. Our findings demonstrate how epigenomic perturbation of EGFR enhancers can ameliorate the aggressiveness of glioblastoma cells and enhance the efficacy of TMZ treatment. SIGNIFICANCEOur study demonstrates how CRISPR/Cas9-based perturbation of enhancers can be used to modulate the expression of key cancer genes, which can help improve the effectiveness of existing cancer treatments and potentially the prognosis of difficult-to-treat cancers such as glioblastoma.