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

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

doi:10.18632/oncotarget.5882

Abstract

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. 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). 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. 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.

Highlights

Clear cell sarcoma of the kidney (CCSK) is a rare pediatric renal tumor that represents 3–5% of all childhood renal tumors, being the second most common malignant neoplasia of the kidney after Wilms tumor in the 0–14 age range [1]
The t(10;17) involving the YWHAE-NUTM2 fusion has been recognized as a recurrent genetic event in CCSK, though identified in just 12% of cases [7]
A series of 8 patients among 14 cases diagnosed with CCSK from 2003 to 2013, for whom fresh frozen tumor samples were available, were enrolled in the study

Summary

Introduction

Clear cell sarcoma of the kidney (CCSK) is a rare pediatric renal tumor that represents 3–5% of all childhood renal tumors, being the second most common malignant neoplasia of the kidney after Wilms tumor in the 0–14 age range [1]. Outcome was markedly affected by the improvement in chemo-radiotherapy protocols, with a current 5-year overall survival rate of 86% and a 5-year event-free survival rate of 78% [5]. Relapses occur in about 15% of the patients, with a 5-year event-free survival after relapse of 18%, and 5-year overall survival of 26% [6]. The absence of distinguishing clinical, histological and genetic features is at the basis of the frequent misdiagnosis of this tumor type, that requires different and intensified therapeutic protocols than other pediatric renal tumors. The t(10;17) involving the YWHAE-NUTM2 fusion has been recognized as a recurrent genetic event in CCSK, though identified in just 12% of cases [7]. Very recently new molecular features emerged, as the internal tandem duplication of BCOR [10], and the recurrent hypermethylation of TCF21 [11]

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