Investigating the role of AP-1 in the transcriptional regulation of hypoxic cell adaptation

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The majority of hypoxic research has focused on HIF1alpha and HIF2alpha, transcription factors (TFs) which are stabilised in hypoxia. Data suggests that the transcriptomic changes that occur are regulated by a number of TFs and epigenetic regulators. Our evidence suggests that the AP-1 transcription factors (a heterodimer of proteins from c-FOS, c-JUN and ATF proteins) are key regulators of hypoxic molecular adaptation.We plan to test the hypothesis that novel downstream targets of the AP-1 transcription factor are activated in response to hypoxia and regulate key aspects of molecular adaptation to hypoxia. We will:1. Identify novel targets of AP-1 in hypoxia based on in-house RNA-SEQ data and ChIP-SEQ.2. Validate the activation of targets in hypoxia and confirm direct activation by AP-1.3. Identify the role of novel AP-1 targetas in molecular adaptation to hypoxia.4. Investigate phenotypic effects of novel AP-1 pathways in cancer cells.5. Identify HIF-independent hypoxic regulation of novel AP-1 targets using CRISPR-generated knockout lines.Further to the skills developed in the lab rotation the student will utilise lentiviral-shRNA/CRISPR to analyse the phenotypic effects on cancer cells including stem cell capacity angiogenesis, proliferation, 3 Dimensional culture and immunohistochemistry. The student will with support undertake bioinformatics analyses of in house RNA-SEQ data and publically available data from The Cancer Genome Atlas.