Gene switches and treatment resistance in cancer

Biology textbooks teach that the central dogma is that DNA is transcribed to mRNA and mRNA is translated to protein. This overlooks the complex processes that enable selective exon transcription and translation which are essential for normal cellular function and the deregulation of which are now known to contribute to cancer and other diseases. Indeed it is now known that both epigenetic (how DNA is packaged in chromatin) and epitranscriptomic (how RNAs are modified) mechanisms underpin transcriptional regulation. Your project will dissect how these mechanisms converge.
Prostate and breast cancers are the most common cancers affecting men and women. Prostate and many breast cancers are driven by the androgen and estrogen receptors. Both AR and ER are transcription factors that play a vital role in health and wellbeing. However cancers hijack androgen and estrogen signalling to enable malignant cells to proliferate and metastasize. For this reason treatments which block androgen and estrogen signalling are used to treat prostate and breast cancers respectively. Sadly, treatment resistance emerges frequently and rapidly. Our research seeks to prevent, delay or reverse such treatment resistance.
Our outstanding DTP students (Drs. Veronika Metzler, Daisy Haigh, Jennifer Lothion-Roy, Corinne Woodcock and Anna Harris) have identified novel epigenetic and epitranscriptomics regulatory loops whereby the expression of the androgen and estrogen receptors, are altered in cancer. We have found that epigenetic mechanisms involving histone lysine methylation and epitranscriptomic mechanisms involving RNA methylation appear to converge to (i) select which regions of DNA are actively transcribed and (ii) which exons within mRNAs are translated. Most importantly we have found that these mechanisms are disrupted in cancer cells as compared to non-malignant cells, enabling these cancer cells to selectively change isoform expression to evade current cancer treatments. This leads to the hypothesis that aberrant RNA methylation contributes to the pro-oncogenic alternatively spliced transcriptome found in cancer. To test this hypothesis you will study the mechanistic and clinical relevance of the ZFP217 component of the RNA methylation complex.
You will
1. use immunohistochemistry to assess ZFP217 protein expression in our human prostate and breast cancer specimens.
2. use CRISPR-Cas9 and/ or siRNA to target ZFP217 in breast and prostate cancer cell lines and determine the effect on androgen and estrogen regulated gene expression by qRTPCR
3. use RNAseq and western blotting to determine the relative role of ZFP217 and the m6A and histone lysine demethylases in alternative splicing and exon utilization of the AR protein
4. will compare the effects of functional depletion of ZFP217, and other components of the m6A regulating complex, with new pharmaco-inhibitors of RNA methyltransferases on the transcriptome, proliferation and in vitro invasion of cancer cells.
You will receive training in the following techniques
1. Cell culture, CRISPR-cas9, in vitro pharmacology, reporter assays
2. Basic molecular biology, cloning, qRTPCR, western blotting
3. Bioinformatics: our group has optimized pipelines and existing datasets already available for comparison
4. Clinical genomics and data interpretation: the student will learn how to complete immunohistochemistry and clinical correlations