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BCOR internal tandem duplications in clear cell sarcoma of the kidney

A recurrent somatic internal tandem duplication (ITD) in the BCOR gene affecting the 30 part of the exon 16 coding sequence has recently been discovered in clear cell sarcoma of the kidney (CCSK), a renal tumor responsible for 3% of all pediatric renal tumors (Ueno-Yokohata et al., 2015). Soon after this report, an additional three confirmatory studies reported the same mutation in a combined total of 71/77 CCSKs tested (Astolfi et al., 2015; Roy et al., 2015; Ueno-Yokohata et al., 2015; Karlsson et al., 2016). Another recurrent genetic aberration previously described in 10% of CCSKs is t(10;17)(q22;p13), which leads to the fusion of YWHAE and NUTM2B/E (O’Meara et al., 2012). Karlsson et al. (2016) analyzed two CCSKs with the YWHAENUTM2B/E fusion for BCOR ITDs and demonstrated these to be negative, suggesting that these two events may be mutually exclusive. We report the absence of BCOR ITDs in an additional CCSK case bearing the YWHAE-NUTM2B/E fusion transcript, which provides further support that these events are mutually exclusive in CCSK. This case was previously included in the CCSK TARGET initiative as a validation sample (USI CCSKPAJPCZ) (Gooskens et al., 2015). Methods utilized for RT-PCR of BCOR and YWHAE-NUTM2B/E have been described previously by Ueno-Yokohata et al. (2015) and Gooskens et al. (2015), respectively. The patient with the fusion transcript we report was male and 9 months of age at diagnosis. This patient had Stage II disease, relapsed in 15 months, and was alive 14 years after the initial diagnosis. The BCOR ITDs identified in CCSKs involve the PUFD domain of the BCOR protein, which is important for functioning of BCOR as an epigenetic modifier. We recently reported the presence of hypermethylation and decreased expression of the tumor suppressor gene TCF21 in the majority of CCSKs (Gooskens et al., 2015). Examining this feature in TARGET CCSK cases bearing the BCOR ITD mutation (n 5 7) and two TARGET CCSK cases bearing the YWHAE-NUTM2B/E transcript (USI CCSK-PAJPCZ and USIPAKWMM, which was also described in the report by Karlsson et al. (2016)) illustrates that CCSKs bearing the BCOR ITDs show hypermethylation of TCF21, while CCSKs bearing the YWHAENUTM2B/E show significant lower methylation of TCF21 (Fig. 1). This suggests that the BCOR ITD mutations may be directly or indirectly responsible for the TCF21 hypermethylation.