The spectrum of EWSR1-rearranged neoplasms at a tertiary sarcoma centre; assessing 772 tumour specimens and the value of current ancillary molecular diagnostic modalities

Abstract

Background:EWSR1 rearrangements were first identified in Ewing sarcoma, but the spectrum of EWSR1-rearranged neoplasms now includes many soft tissue tumour subtypes including desmoplastic small round cell tumour (DSRCT), myxoid liposarcoma (MLPS), extraskeletal myxoid chondrosarcoma (EMC), angiomatoid fibrous histiocytoma (AFH), clear cell sarcoma (CCS) and myoepithelial neoplasms. We analysed the spectrum of EWSR1-rearranged soft tissue neoplasms at our tertiary sarcoma centre, by assessing ancillary molecular diagnostic modalities identifying EWSR1-rearranged tumours and reviewing the results in light of our current knowledge of these and other Ewing sarcoma-like neoplasms.Methods:We retrospectively analysed all specimens tested for EWSR1 rearrangements by fluorescence in situ hybridisation (FISH) and/or reverse transcription–PCR (RT–PCR) over a 7-year period.Results:There was a total of 772 specimens. FISH was performed more often than RT–PCR (n=753, 97.5% vs n=445, 57.6%). In total, 210 (27.9%) specimens were FISH-positive for EWSR1 rearrangement compared to 111 (14.4%) that showed EWSR1 fusion transcripts with RT–PCR. Failure rates for FISH and RT–PCR were 2.5% and 18.0%. Of 109 round cell tumours with pathology consistent with Ewing sarcoma, 15 (13.8 %) cases were FISH-positive without an identifiable EWSR1 fusion transcript, 4 (3.7%) were FISH-negative but RT–PCR positive and 4 (3.7%) were negative for both. FISH positivity for DSRCT, MLPS, EMC, AFH and CCS was 86.3%, 4.3%, 58.5%, 60.0% and 87.9%, respectively. A positive FISH result led to diagnostic change in 40 (19.0%) EWSR1-rearranged cases. 13 FISH-positive cases remained unclassifiable.Conclusions:FISH is more sensitive for identifying EWSR1 rearrangements than RT–PCR. However, there can be significant morphologic and immunohistochemical overlap between groups of EWSR1-rearranged neoplasms, with important prognostic and therapeutic implications. FISH and RT–PCR should be used as complementary modalities in diagnosing EWSR1-rearranged neoplasms, but as tumour groups harbouring EWSR1 rearrangements are increasingly characterised and because given translocations involving EWSR1 and its partner genes are not always specific for tumour types, it is critical that these are evaluated by specialist soft tissue surgical pathologists noting the morphologic and immunohistochemical context. As RT–PCR using commercial primers is limited to only the most prevalent EWSR1 fusion transcripts, the incorporation of high-throughput sequencing technologies into the standard diagnostic repertoire to assess for multiple molecular abnormalities of soft tissue tumours in parallel (including detection of newly characterised Ewing sarcoma-like tumours) might be the most effective and efficient means of ancillary diagnosis in future.

A novel next generation sequencing approach to improve sarcoma diagnosis

“…RT-PCR on the other hand can be more sensitive than FISH in specimens with lower tumor content [38,39,40]. RT-PCR however may not detect rare fusion genes or those with unusual breakpoints and cannot easily detect copy number variation, for example MDM2 amplification, making FISH a continual requirement for comprehensive sarcoma testing [41].…”

Molecular Analysis of Gene Fusions in Bone and Soft Tissue Tumors by Anchored Multiplex PCR–Based Targeted Next-Generation Sequencing

“…24 In these cases, AMP-based targeted NGS cannot be used, and one can consider the use of FISH, which shows a lower failure rate. 25 In addition, although in most cases, both exact fusion partners will be revealed with AMP-based targeted NGS, one should be aware that the technique uses relatively small amplicons, and in the case of highly homologous genes being involved, for example, SSX1, SSX2, SSX4 in synovial sarcoma (Case 43), a certain distinction cannot be made. Thus, none of the molecular assays used in the current study was able to provide a 100% of certainty with respect to false-positive and false-negative results.…”

EWSR1 Rearrangement and CD99 Expression as Diagnostic Biomarkers for Ewing/PNET Sarcomas in a Moroccan Population

“…While the FISH break-apart method provided some clear advantages, its main disadvantage is that the translocation partner is not identified, which is important in predicting tumor behavior. As EWSR1 rearrangement may be found in other tumors such as desmoplastic small round cell tumors [ 16 ], a detection of fusion types ( EWSR1/FLI-1 and EWSR1/ERG ) from RNA is necessary to confirm the diagnosis using reverse transcription polymerase chain reaction (RT-PCR), which is a highly specific method [ 3 , 17 ]. Prognosis of this entity also depends on several factors including the location and volume of the tumor, the stage, the age, and the response to chemotherapy [ 18 ].…”