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Astolfi A, Melchionda F, Perotti D, Fois M, Indio V, Urbini M, Genovese CG, Collini P, Salfi N, Nantron M, D'Angelo P, Spreafico F, Pession A. Whole transcriptome sequencing identifies BCOR internal tandem duplication as a common feature of clear cell sarcoma of the kidney. Oncotarget 2016; 6:40934-9. [PMID: 26516930 PMCID: PMC4747379 DOI: 10.18632/oncotarget.5882] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/28/2015] [Indexed: 01/23/2023] Open
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.
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Affiliation(s)
- Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy.,Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Fraia Melchionda
- Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Daniela Perotti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Maura Fois
- Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Valentina Indio
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Milena Urbini
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy.,Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | | | - Paola Collini
- Soft Tissue and Bone Pathology, Histopathology, and Pediatric Pathology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Nunzio Salfi
- Pathology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Marilina Nantron
- Department of Pediatric Hematology and Oncology, Istituto G. Gaslini, Genova, Italy
| | - Paolo D'Angelo
- Pediatric Hematology and Oncology Unit, A.R.N.A.S. Civico, Di Cristina and Benfratelli Hospital, Palermo, Italy
| | - Filippo Spreafico
- Pediatric Oncology Unit, Department of Hematology and Pediatric Onco-Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Andrea Pession
- Pediatric Hematology and Oncology Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
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