Gene expression profiling in pediatric and adolescent and young adult rhabdomyosarcomas

Adolescents and young adults (AYA) with rhabdomyosarcoma (RMS) form a subgroup of patients whose optimal clinical management and best possible access to care remain a challenge and survival lacks behind that of children while diagnosed with histologically similar tumors. Understanding the tumor biology that differentiate children from AYA-RMS could provide critical information and drive new initiatives to improve their final outcome. Gene expression profiling was evaluated in a RMS series of 48 tumor and 13 non-neoplastic tissues. GEP analysis detected 793 age-correlated genes in tumors. NOTCH2, FGFR1 were significantly down-modulated in AYA-RMS. GEP showed an increase in CD4 memory resting cells and a decrease in γδ T-cells in AYA-RMS. IHC analysis demonstrated an increase of infiltrated CD4, CD8 and neutrophils in AYA-RMS tumors. A cohort of 48 RMS FFPE (formalin fixed paraffin embedded) tissues (not pre-treated primary tumors) was carefully selected and retrieved from the archive of Fondazione IRCCS Istituto Nazionale dei Tumori and were re-evaluated by expert pathologists for abundance and adequacy of material. Non-neoplastic components were identified where possible for each age groups of RMS, so to use as controls in bioinformatic analyses. In details, RNA was successfully isolated from 27 pediatric RMS (0-14 years) and 21 AYA RMS (15-+30 years). Two samples (FF62 and FG07) were used as controls for adjacent normal tissues; the remaining 48 tumors and 13 normal counterpart were used for the analysis. Gene expression analysis was performed on ClariomS (Affymetrix) chips. When possible the normal tissue was obtained by a FFPE tissue block different from that of the tumor; otherwise, the pathologist selected a normal tissue area next to the tumor. The former was defined "normal", the latter "adjacent_normal".