Elucidating the role of an essential transcription factor in SWI/SNF -mutant rhabdoid tumors

St. Jude Children'S Research Hospital, Memphis TN

Investigators

Abstract

Abstract Mutations in genes that encode subunits of the SWI/SNF chromatin remodeling complex are observed in nearly 25% of all cancers. Because of this, understanding the mechanisms that lead to cancer progression following SWI/SNF perturbation has great relevance for our understanding of cancer. Rhabdoid tumors (RTs) provide an excellent model for the study of SWI/SNF loss as these genomically simple, but lethal cancers of early childhood are driven by the biallelic inactivation of a single SWI/SNF encoding tumor suppressor gene, SMARCB1. Through the Pediatric Cancer Dependency Project, 16 RT cell lines from various tissues of origin were submitted by our lab to the Broad Institute for genome-wide CRISPR-Cas9 knockout screening as a part of the Cancer Dependency Map (DepMap). Due to the unique nature of RTs as diploid cancers with relatively low mutational burdens that are driven by the specific loss of SMARCB1, CRISPR screening in these cancers can be leveraged as a highly powerful tool. By comparing genetic dependencies in these 16 RT cell lines to over 1100 other cancers in DepMap, dependencies that are unique to SMARCB1-deficient cells can be systematically identified and characterized. This proposal focuses on a transcription factor encoding gene which is a unique dependency in RT cell lines. I propose that studying the function of this poorly characterized transcription factor will provide critical insight into the dysregulated cellular environment that results from SMARCB1 loss. Whilst little studied, the available literature suggests that this transcription factor cooperates with a repressive chromatin-regulatory complex. I have confirmed that this factor is essential in RTs, interacts with this repressive complex, and co- localizes with this complex on chromatin. However, instead of repressing transcription, my preliminary work shows that this factor is a robust transcriptional activator, a previously undescribed function. I hypothesize that this transcription factor exerts a critical activating function in RTs by antagonizing the activity of its repressive binding partners. Further, I propose that this function is uniquely essential in cells that have lost the ability to activate genes through SMARCB1-containing SWI/SNF activity. Through two aims, I will investigate this transcription factor’s mechanism of function and the role of SMARCB1 loss in promoting cellular dependence on its expression. Using a targeted structure-function approach in conjunction with genome-wide approaches, I will uncover the relationship between this transcription factor and its binding partners and elucidate the effects of disrupting this relationship on chromatin and transcription. Additionally, using cell line models pioneered by our lab to efficiently add and remove SMARCB1, I will study this protein’s function with direct respect to SWI/SNF status. In pursuit of this project under the mentorship of Dr. Charles Roberts, I will build the necessary technical, computational, and professional skills to become an independent investigator focused on chromatin dysregulation in cancer by the end of my training period.