Target choice and exon skipping regulate CRISPR-directed gene editing of NRF2 in head/neck and esophageal cancer cells

Head and neck cancer (HNC) is the seventh most diagnosed cancer, with a predicted 30% increase annually by 2030. Conventional treatment is often combinatorial involving chemotherapy and radiation therapy, immunotherapy, and surgery, but over time, therapy becomes ineffective as treatment resistance develops. Our laboratory has been advancing a CRISPR-directed gene editing platform as an augmentative therapeutic strategy for squamous cell carcinoma. Our genetic target is <i>NRF2</i>, a global transcription regulator involved in response to cellular stress and drug resistance among other cellular functions. In this study, we disable specific endpoints of NRF2 in an attempt to restore chemo-sensitivity in head/neck and esophageal cancer cells. We identify two targeting characteristics that regulate the effectiveness of this approach. The first is the choice of the targeting site reflecting the importance of disabling specific protein domains that achieve specific phenotypic endpoints. The second involves the induction of a molecular rearrangement known as exon skipping that can counterbalance the desired functional outcome even when significant levels of gene disruption are achieved. By considering these experimental parameters, we achieved high levels of gene disruption at the genotypic, phenotypic, and most importantly, functional levels to restore chemosensitivity and significantly reduce tumor cell proliferation.