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Background  Clear cell sarcoma of soft tissue (CCSST) and clear cell sarcoma-like gastrointestinal tumor (CCSLGT) are malignant mesenchymal tumors that share some pathological features, but they also have several different characteristics. They are well known to express chimeric fusions of Ewing sarcoma breakpoint region 1 ( EWSR1 ) and cAMP response element-binding protein ( CREB ) family members; namely,  EWSR1- activating transcription factor 1 ( ATF1 ) and  EWSR1-CREB1 . In addition, recent studies have suggested the presence of other fusions.    Methods  We used fluorescence  in situ  hybridization to detect specific rearrangements including  EWSR1 ,  ATF1 ,  CREB1 , and cAMP response element modulator ( CREM ) in 16 CCSST and 6 CCSLGT cases. We also used reverse transcription polymerase chain reaction (RT-PCR) to detect specific chimeric fusions of  EWSR1-ATF1  and  EWSR1-CREB1  using fresh tumor samples in available cases.    Results  A total of 15 of 16 CCSST cases (93.8%) had  EWSR1  rearrangement, of which 11 (68.8%) also had  ATF1  rearrangement, suggestive of the presence of  EWSR1-ATF1  fusions. One CCSST case (6.3%) was found to have  EWSR1  and  CREM  rearrangements, and 4 of 6 CCSLGT cases (66.7%) had  EWSR1  rearrangement, of which 2 (33.3%) showed  ATF1  rearrangement and the other 2 cases (33.3%) showed  CREB1  rearrangement. These cases most likely had  EWSR1-ATF1  and  EWSR1-CREB1  fusions, respectively. RT-PCR was performed in 8 available cases, including 6 CCSSTs and 2 CCSLGTs. All CCSSTs showed  EWSR1-ATF1  fusions. Among the 2 CCSLGT cases, one had  EWSR1-ATF1  fusion and the other had  EWSR1-CREB1  fusion.    Conclusions  Rearrangements of  EWSR1  and  ATF1  or  EWSR1-ATF1  fusion were predominantly found in CCSST, whereas those of  EWSR1  and  CREB1  or  EWSR1-CREB1  tended to be detected in CCSLGT. A novel  CREM  fusion was also detected in a few cases of CCSST and CCSLGT. The cases in which  EWSR1  rearrangement was detected without definitive partner genes should be considered for the presence of  CREM  rearrangement.

diagnostic pathology

Detection of specific gene rearrangements by fluorescence in situ hybridization in 16 cases of clear cell sarcoma of soft tissue and 6 cases of clear cell sarcoma-like gastrointestinal tumor