Adaptation to chronic hypoxia in triple-negative breast cancer

Low levels of oxygen (i.e. hypoxia) are often observed in solid tumours. Hypoxia is able to drive several of the cancer hallmarks and promotes resistance to both radio and chemotherapy, resulting in its association with poor prognosis. Triple-negative breast cancer has the worst prognosis of all breast cancer subtypes with a 5 year survival rate of only 76.7%, and only 10.8% if the cancer has already metastasised. In line with this, triple-negative tumours often have higher levels of hypoxia than their hormone receptor expressing counterparts. The length and severity of hypoxia is heterogeneous both within and between tumours, meaning cells within the same tumour may experience both acute and chronic hypoxia. Acute hypoxia (⩽ 24 hours) is relatively well studied, whereas research into chronic hypoxia (⩾ 7 days) is lacking. This thesis therefore aimed to characterise the transcriptional response to chronic hypoxia using RNA sequencing. It also aimed to identify proteins or microRNAs which are necessary for adaptation to chronic hypoxia using genome-wide CRISPR screening. This method enables specific vulnerabilities in hypoxic cells to be identified, meaning drugs can be designed to target these “Achilles heels”. The major pathways altered under chronic hypoxia were related to epithelial-mesenchymal transition (EMT) and cell adhesion, with triple-negative breast cancer cells undergoing an atypical form of EMT. However, none of the genes which were upregulated in response to chronic hypoxia were found to be essential for their survival. Instead, hypoxic cells had a greater dependence on general control nonderepressible 2 (GCN2), an instigator of the integrated stress response usually activated under amino acid starvation. GCN2 was found to be active under chronic hypoxia, and chemical inhibition of GCN2 reduced cell growth in vitro. Previous work has shown that GCN2 knockout mice are healthy unless fed a diet restricted in essential amino acids, meaning targeting GCN2 is unlikely to result in severe toxicities. Together, this means GCN2 constitutes a promising therapeutic target for hypoxic tumours. No microRNAs essential for survival under hypoxia were identified in this study.