Molecular diagnosis of clear cell sarcoma: detection of EWS-ATF1 and MITF-M transcripts and histopathological and ultrastructural analysis of 12 cases

J Mol Diagn. 2002 Feb;4(1):44-52. doi: 10.1016/S1525-1578(10)60679-4.


Clear cell sarcoma (CCS), also known as melanoma of soft parts, is an uncommon deep soft tissue tumor presenting typically in the lower extremities of young adults. Previous cytogenetic studies have established the specificity of the recurrent t(12;22)(q13;q12), resulting in a EWS-ATF1 fusion, for CCS. The prevalence of the EWS-ATF1 fusion in CCS remains unclear, since most genetically confirmed CCS have been reported as isolated cytogenetic or molecular diagnostic case reports. We therefore studied histologically confirmed CCS from 12 patients for the presence of EWS-ATF1 by reverse-transcriptase polymerase chain reaction (RT-PCR), using RNA extracted from either frozen (four cases) or formalin-fixed paraffin-embedded (eight cases) material. All primary tumors were located in the deep soft tissues of the extremities. Histologically, 10 cases had a typical epithelioid nested appearance. Most or all cases showed immunostaining for HMB45 (12 of 12), S-100 protein (10 of 12), and MITF (12 of 12). Ultrastructural analysis showed melanosomes in six of seven cases. The presence of an EWS-ATF1 fusion transcript was identified by RT-PCR in 11 of 12 cases (91%), all of which showed the same fusion transcript structure, namely the previously described in-frame fusion of EWS exon 8 to ATF1 codon 65. RT-PCR analysis for the melanocyte-specific splice form of the MITF transcript was positive in all cases tested (4 of 4). These data confirm that EWS-ATF1 detection can be used as a highly sensitive diagnostic test for CCS and that CCS expresses the melanocyte-specific form of the MITF transcript, further supporting its genuine melanocytic differentiation.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adult
  • Aged
  • Antigens, Neoplasm
  • Cell Differentiation
  • Chromosomes, Human, Pair 12
  • Chromosomes, Human, Pair 22
  • DNA Primers
  • DNA-Binding Proteins / genetics*
  • Female
  • Humans
  • Male
  • Melanocytes / metabolism
  • Melanoma-Specific Antigens
  • Microphthalmia-Associated Transcription Factor
  • Middle Aged
  • Neoplasm Proteins / genetics
  • Oncogene Proteins, Fusion / genetics*
  • Prospective Studies
  • RNA, Neoplasm / analysis
  • Reverse Transcriptase Polymerase Chain Reaction
  • S100 Proteins / genetics
  • Sarcoma / genetics*
  • Sarcoma / pathology*
  • Sarcoma / ultrastructure
  • Sarcoma, Clear Cell / genetics*
  • Sarcoma, Clear Cell / pathology*
  • Sarcoma, Clear Cell / ultrastructure
  • Transcription Factors / genetics
  • Translocation, Genetic


  • Antigens, Neoplasm
  • DNA Primers
  • DNA-Binding Proteins
  • EWS-ATF1 fusion protein, human
  • MITF protein, human
  • Melanoma-Specific Antigens
  • Microphthalmia-Associated Transcription Factor
  • Neoplasm Proteins
  • Oncogene Proteins, Fusion
  • RNA, Neoplasm
  • S100 Proteins
  • S100A1 protein
  • Transcription Factors