Molecular diagnosis applied to Ewing’s sarcoma and alveolar rhabdomyosarcoma biopsies: experience at the “Dr. Ricardo Gutiérrez” Children’s Hospital, Buenos Aires, Argentina

Abstract

Introduction: In Argentina, soft tissue tumors represent about 6% of the annual pediatric cancer cases (Registro Oncopediátrico Hospitalario Argentino). Chromosomal translocations described for Ewing’s sarcoma (ES) and rhabdomyosarcoma (RMS) can be applied to molecular classification and differential diagnosis and/or prognosis. Aims: To confirm diagnosis of pediatric ES and RMS by means of molecular classification and to evaluate the impact of the biopsy preservation procedure on the integrity of nucleic acids.
Materials and methods: Children younger than 18 years with ES (n=13) and RMS (n=4) were enrolled. Seventeen primary tumor biopsies [(7 stored at –70° C and 12 formalin-fixed paraffin-embedded (FFEP)] and two bone marrow aspirates were studied. RNA was isolated by Trizol or RecoverAll™ Total Nucleic Acid Isolation. EWS-FLI1[t(11;22)(q24;q12)]/EWS-ERG[t(21;22)(q22;q12)] in ES and PAX3-FOXO1[t(2;13)(q35;q14)]/PAX7-FOXO1[t(1;13)(p36;q14)] in RMS were assessed by fluorescent in situ hybridization (FISH) and RT-PCR followed by sequencing.
Results: The rearrangement of EWRS1 was detected by FISH in 9/13 ES, whereas that of FOXO1 was detected in 3/4 RMS. PGK amplification by RT-PCR was positive in 8/12 FFEP and 7/7 frozen samples (five biopsies and two bone marrow aspirates). In ES, EWS-FLI1 was detected by RT-PCR in 7/8 samples (two type 1, three type 2, one type 4 and one EWS exon 7/FLI1 exon 4 translocation). In RMS, FOXO1-PAX3 was present in 1/3 and FOXO1-PAX7 in 0/3 samples. One RMS was diagnosed as embryonic subtype by RT-PCR, but FISH failed to accurately classify the case. In 2/2 samples, the absence of BM infiltration was confirmed.