Characterization of fusion genes in common and rare epithelial ovarian cancer histologic subtypes

// Madalene A. Earp 1 , Rama Raghavan 2 , Qian Li 2, 10 , Junqiang Dai 2 , Stacey J. Winham 1 , Julie M. Cunningham 3 , Yanina Natanzon 1 , Kimberly R. Kalli 4 , Xiaonan Hou 5 , S. John Weroha 5, 6 , Paul Haluska 5, 6 , Kate Lawrenson 7 , Simon A. Gayther 8, 9 , Chen Wang 1 , Ellen L. Goode 1, * and Brooke L. Fridley 2, 10, * 1 Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA 2 Department of Biostatistics, University of Kansas Medical Center, KS, USA 3 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA 4 Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA 5 Department of Oncology, Mayo Clinic, Rochester, MN, USA 6 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA 7 Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 8 Center for Cancer Prevention and Translational Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA 9 Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA 10 Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA * These authors contributed equally to this work Correspondence to: Brooke L. Fridley, email: Brooke.Fridley@moffitt.org Keywords: fusion gene, ovarian cancer, RNA-sequencing, histological subtypes, TCGA Received: August 08, 2016      Accepted: March 22, 2017      Published: April 01, 2017 ABSTRACT Gene fusions play a critical role in some cancers and can serve as important clinical targets. In epithelial ovarian cancer (EOC), the contribution of fusions, especially by histological type, is unclear. We therefore screened for recurrent fusions in a histologically diverse panel of 220 EOCs using RNA sequencing. The Pipeline for RNA-Sequencing Data Analysis (PRADA) was used to identify fusions and allow for comparison with The Cancer Genome Atlas (TCGA) tumors. Associations between fusions and clinical prognosis were evaluated using Cox proportional hazards regression models. Nine recurrent fusions, defined as occurring in two or more tumors, were observed. CRHR1-KANSL1 was the most frequently identified fusion, identified in 6 tumors (2.7% of all tumors). This fusion was not associated with survival; other recurrent fusions were too rare to warrant survival analyses. One recurrent in-frame fusion, UBAP1-TGM7 , was unique to clear cell (CC) EOC tumors (in 10%, or 2 of 20 CC tumors). We found some evidence that CC tumors harbor more fusions on average than any other EOC histological type, including high-grade serous (HGS) tumors. CC tumors harbored a mean of 7.4 fusions (standard deviation [sd] = 7.4, N = 20), compared to HGS EOC tumors mean of 2.0 fusions (sd = 3.3, N = 141). Few fusion genes were detected in endometrioid tumors (mean = 0.24, sd = 0.74, N = 55) or mucinous tumors (mean = 0.25, sd = 0.5, N = 4) tumors. To conclude, we identify one fusion at 10% frequency in the CC EOC subtype, but find little evidence for common (> 5% frequency) recurrent fusion genes in EOC overall, or in HGS subtype-specific EOC tumors.