Whole transcriptome sequencing identifies BCOR internal tandem duplication as a common feature of clear cell sarcoma of the kidney

// Annalisa Astolfi 1, 2 , Fraia Melchionda 2 , Daniela Perotti 3 , Maura Fois 2 , Valentina Indio 1 , Milena Urbini 1, 2 , Chiara Giusy Genovese 1 , Paola Collini 4 , Nunzio Salfi 5 , Marilina Nantron 6 , Paolo D’Angelo 7 , Filippo Spreafico 8 , Andrea Pession 2 1 “Giorgio Prodi” Cancer Research Center, University of Bologna, Bologna, Italy 2 Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy 3 Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy 4 Soft Tissue and Bone Pathology, Histopathology, and Pediatric Pathology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy 5 Pathology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy 6 Department of Pediatric Hematology and Oncology, Istituto G. Gaslini, Genova, Italy 7 Pediatric Hematology and Oncology Unit, A.R.N.A.S. Civico, Di Cristina and Benfratelli Hospital, Palermo, Italy 8 Pediatric Oncology Unit, Department of Hematology and Pediatric Onco-Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy Correspondence to: Fraia Melchionda, e-mail: fraia.melchionda@aosp.bo.it Keywords: CCSK, whole transcriptome sequencing, BCOR Received: August 10, 2015 Accepted: September 28, 2015 Published: October 22, 2015 ABSTRACT Purpose: Clear cell sarcoma of the kidney (CCSK) is a rare pediatric renal tumor that is frequently difficult to distinguish among other childhood renal tumors due to its histological heterogeneity. This work evaluates genetic abnormalities carried by a series of CCSK samples by whole transcriptome sequencing (WTS), to identify molecular biomarkers that could improve the diagnostic process. Methods: WTS was performed on tumor RNA from 8 patients with CCSK. Bioinformatic analysis, with implementation of a pipeline for detection of intragenic rearrangements, was executed. Sanger sequencing and gene expression were evaluated to validate BCOR internal tandem duplication (ITD). Results: WTS did not identify any shared SNVs, Ins/Del or fusion event. Conversely, analysis of intragenic rearrangements enabled the detection of a breakpoint within BCOR transcript recurrent in all samples. Three different in-frame ITD in exon15 of BCOR, were detected. The presence of the ITD was confirmed on tumor DNA and cDNA, and resulted in overexpression of BCOR. Conclusion: WTS coupled with specific bioinformatic analysis is able to detect rare genetic events, as intragenic rearrangements. ITD in the last exon of BCOR is recurrent in all CCSK samples analyzed, representing a valuable molecular marker to improve diagnosis of this rare childhood renal tumor.