Detection of EWSR1 fusions in CCOC by targeted RNA-seq

Abstract

To describe the application of a targeted RNA sequencing assay to detect fusion transcripts in formalin-fixed paraffin-embedded (FFPE), non-decalcified samples of clear cell odontogenic carcinoma (CCOC) and related tumors, and to add to knowledge of the genetic drivers of CCOC. Five FFPE tissues, including intraosseous CCOC (n=3), clear cell carcinoma of the salivary gland (CCC, n=1), and Ewing sarcoma (ES, n=1), were analyzed by targeted RNA-seq to detect fusions. The 3 intraosseous CCOC samples harbored EWSR1 translocations: EWSR1-ATF1 (n=2) and EWSR1-CREM (n=1); the CCC sample contained an EWSR1-ATF1 fusion; and the ES sample contained an EWSR1-FLI1 fusion detected by RNA-seq. These results demonstrate that targeted RNA-seq is a valuable tool to detect fusions in FFPE samples of rare tumors such as CCOC and CCC. The results also confirm the observations that CCOC is driven by fusions between EWSR1 and CREB family transcription factors, including ATF1 and CREM. To our knowledge, this is the second report of CCOC with an EWSR1-CREM translocation.