Research Papers:

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

Annalisa Astolfi _, Fraia Melchionda, Daniela Perotti, Maura Fois, Valentina Indio, Milena Urbini, Chiara Giusy Genovese, Paola Collini, Nunzio Salfi, Marilina Nantron, Paolo D’Angelo, Filippo Spreafico and Andrea Pession

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Oncotarget. 2015; 6:40934-40939. https://doi.org/10.18632/oncotarget.5882

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Annalisa Astolfi1,2, Fraia Melchionda2, Daniela Perotti3, Maura Fois2, Valentina Indio1, Milena Urbini1,2, Chiara Giusy Genovese1, Paola Collini4, Nunzio Salfi5, Marilina Nantron6, Paolo D’Angelo7, Filippo Spreafico8, Andrea Pession2

1“Giorgio Prodi” Cancer Research Center, University of Bologna, Bologna, Italy

2Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy

3Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy

4Soft Tissue and Bone Pathology, Histopathology, and Pediatric Pathology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy

5Pathology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy

6Department of Pediatric Hematology and Oncology, Istituto G. Gaslini, Genova, Italy

7Pediatric Hematology and Oncology Unit, A.R.N.A.S. Civico, Di Cristina and Benfratelli Hospital, Palermo, Italy

8Pediatric Oncology Unit, Department of Hematology and Pediatric Onco-Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy

Correspondence to:

Fraia Melchionda, e-mail: [email protected]

Keywords: CCSK, whole transcriptome sequencing, BCOR

Received: August 10, 2015     Accepted: September 28, 2015     Published: October 22, 2015


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.

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