The PAX8 cistrome in epithelial ovarian cancer

// Emily K. Adler 1,* , Rosario I. Corona 2,3,* , Janet M. Lee 2 , Norma Rodriguez-Malave 2 , Paulette Mhawech-Fauceglia 4 , Heidi Sowter 5 , Dennis J. Hazelett 2,** , Kate Lawrenson 2,3,** and Simon A. Gayther 2,3,** 1 Department of Preventive Medicine, University of Southern California/Keck School of Medicine, Los Angeles, California, USA 2 Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA 3 Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA 4 Departments of Medicine and Pathology, University of Southern California/Keck School of Medicine, Los Angeles, California, USA 5 Department of Biomedical Science and Public Health, University of Derby, Derby, UK * These authors have contributed equally to this study ** Jointly lead the study Correspondence to: Kate Lawrenson, email: // Simon A. Gayther, email: // Keywords : PAX8, transcription factor, ovarian cancer, chromatin immunoprecipitation, ChIP-seq Received : August 24, 2017 Accepted : September 30, 2017 Published : November 27, 2017 Abstract PAX8 is a lineage-restricted transcription factor that is expressed in epithelial ovarian cancer (EOC) precursor tissues, and in the major EOC histotypes. Frequent overexpression of PAX8 in primary EOCs suggests this factor functions as an oncogene during tumorigenesis, however, the biological role of PAX8 in EOC development is poorly understood. We found that stable knockdown of PAX8 in EOC models significantly reduced cell proliferation and anchorage dependent growth in vitro, and attenuated tumorigenicity in vivo . Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and transcriptional profiling were used to create genome-wide maps of PAX8 binding and putative target genes. PAX8 binding sites were significantly enriched in promoter regions ( p < 0.05) and superenhancers ( p < 0.05). MEME-ChIP analysis revealed that PAX8 binding sites overlapping superenhancers or enhancers, but not promoters, were enriched for JUND/B and ARNT/AHR motifs. Integrating PAX8 ChIP-seq and gene expression data identified PAX8 target genes through their associations within shared topological association domains. Across two EOC models we identified 62 direct regulatory targets based on PAX8 binding in promoters and 1,330 putative enhancer regulatory targets . SEPW1, which isinvolved inoxidation-reduction,was identified as a PAX8 target gene in both cell line models. While the PAX8 cistrome exhibits a high degree of cell-type specificity, analyses of PAX8 target genes and putative cofactors identified common molecular targets and partners as candidate therapeutic targets for EOC.