Identification and characterisation of HNF1B as a pro-tumorigenic lineage factor in clear cell renal cell carcinoma

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Richardson, Emma Kay 

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer. ccRCCs exhibit considerable genetic intratumour heterogeneity, and current therapies lack long-term efficacy due to drug resistance. Novel therapeutic targets are thus required to combat this disease.

The most effective targets are likely to be factors essential for maintaining ccRCC cell phenotypes and survival across all tumour subclones. Transcription factors (TFs) are appealing candidates as they are key determinants of cellular phenotypes, including in cancer. There is growing evidence to suggest that lineage-specific TFs often play important roles in tumourigenesis and tumour progression. ccRCC phenotypes may also be fundamentally defined by tissue-specific core transcriptional networks. Thus, the aim of my PhD thesis was to identify novel TF dependencies in ccRCC, and characterise the mechanisms by which these essential TFs support these tumours.

I performed a CRISPR/Cas9-based genetic depletion screen in vitro with an sgRNA library targeting 50 TFs that are highly expressed in RCC. This highlighted HNF1B as a potential tumour dependency in ccRCC. I demonstrated that both HNF1B CRISPR knockout and CRISPRi knockdown conferred a strong selective disadvantage in vitro that was rescued by HNF1B restoration, suggesting that it was a specific effect of HNF1B loss. I also showed that HNF1B knockout impaired tumour initiation and growth in vivo.

I showed that HNF1B knockout led to a downregulation of MYC expression, along with a cell cycle defect in G1/S progression and an increase in cell death. HNF1B ChIP-seq in ccRCC cell lines revealed HNF1B binding peaks near the MYC gene, suggesting that HNF1B might directly regulate MYC in ccRCC. I subsequently found that MYC CRISPRi knockdown phenocopied the striking selective disadvantage associated with HNF1B depletion. Taken together, my data suggests that HNF1B-mediated regulation of MYC might be a key mechanism underlying the importance of HNF1B in ccRCC.

Vanharanta, Sakari
ccRCC, HNF1B, MYC, lineage, transcription, factor, transcription factor, hepatocyte nuclear factor, RCC, clear cell renal cell carcinoma, renal cell carcinoma, lineage transcription factor, kidney, renal
Doctor of Philosophy (PhD)
Awarding Institution
University of Cambridge
I received funding from the Medical Research Council (in the form of an MRC Research Studentship, administered by the MRC Cancer Unit). I also received stipend funding from the Funds for Women Graduates (FfWG) in my final year.