Investigating Transcriptional Elongation and Nuclear RNA Surveillance in Melanoma

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Project Summary Metastatic melanoma, a cancer derived from pigment-producing melanocytes, is the deadliest type of skin cancer. Metastatic melanoma that is refractory or resistant to current therapies has a poor prognosis. Melanoma growth and therapy resistance is dependent on dysregulated gene expression, and gene expression in melanoma remains poorly understood. The transcriptional cyclin dependent kinases (CDKs) are a phylogenetically distinct group of kinases that directly regulate transcriptional subprocesses. I found that CDK13 is mutated in melanoma; these mutations are kinase-dead and act by interfering with WT CDK13 function (dominant negative). Downregulation or mutation in CDK13 is associated with poor prognosis in metastatic melanoma patients, expression of mutant CDK13 in a zebrafish model expedites melanoma onset, and expression of mutant CDK13 in human melanoma cells causes the cells to be more proliferative. Mutant CDK13 fails to phosphorylate a protein that activates nuclear degradation of prematurely truncated ‘junk’ RNAs (ptRNAs). Subsequently, ptRNAs accumulate, are exported to the cytoplasm, and are translated into short proteins. This work is newly published on BioRxiv. I have also recently identified recurrent truncations in two nuclear RNA surveillance members: ZFC3H1 and ZC3H18. Here, I propose to further investigate the mechanism of mutant-CDK13 oncogenesis and nuclear RNA surveillance in melanoma. In Aim1, I plan to a) determine how protein stress pathways are affected in CDK13-mutant cells and b) to test whether truncated protein expression is sufficient to recapitulate the CDK13-mutant phenotype in zebrafish melanoma. In Aim 2, I will investigate whether recurrent truncating mutations in two nuclear surveillance complex members (ZFC3H1 and/or ZC3H18) cause more aggressive melanoma and if so, how nuclear RNA surveillance is impacted using proteomics and 3’ transcriptomics. This work has the potential to open a new cancer biology field and to lead to therapeutic strategies for cancers with deficient nuclear RNA surveillance. This research will be conducted in the laboratory of Dr. Leonard Zon, a renowned hematologist/oncologist and cancer biologist who has developed the zebrafish into a mainstream model organism for melanoma research. Under the guidance of Dr. Zon and an exceptional mentoring committee, that is personally invested in my growth into an independent investigator, this award will provide the necessary protected time to develop skills to study nuclear RNA surveillance in melanoma as an independent investigator. As recommended by this committee, I have developed a new collaboration with Dr. Steve Gygi in order to learn cutting-edge proteomic techniques. My rigorous training plan will help me build scientific and leadership skills necessary to succeed when I transition to independence. The research and clinical environment at Boston Children’s Hospital, Dana Farber Cancer Institute, and Harvard Medical School is the ideal environment to develop into a successful independent scientist who investigates nuclear RNA surveillance in melanoma.