We analyzed the expression signatures of 14 tumor biopsies from children affected by alveolar rhabdomyosarcoma (ARMS) to identify genes correlating to biological features of this tumor. Seven of these patients were positive for the PAX3-FKHR fusion gene and 7 were negative. We used a cDNA platform containing a large majority of probes derived from muscle tissues. The comparison of transcription profiles of tumor samples with fetal skeletal muscle identified 171 differentially expressed genes common to all ARMS patients. The functional classification analysis of altered genes led to the identification of a group of transcripts (LGALS1, BIN1) that may be relevant for the tumorigenic processes. The muscle-specific microarray platform was able to distinguish PAX3-FKHR positive and negative ARMS through the expression pattern of a limited number of genes (RAC1, CFL1, CCND1, IGFBP2) that might be biologically relevant for the different clinical behavior and aggressiveness of the 2 ARMS subtypes. Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR. ' 2005 Wiley-Liss, Inc.Key words: alveolar rhabdomyosarcoma; microarray; gene expression profiling; PAX3-FKHR Rhabdomyosarcomas (RMS) are rare but very aggressive tumors of childhood. It is generally hypothesized that these tumors arise as a consequence of regulatory disruption of the growth and differentiation pathways of myogenic precursor cells, but the actual identity of this precursor is still a matter of debate and research. 1,2 Based on morphology, 2 major RMS subtypes can be identified: embryonal RMS (ERMS) and alveolar RMS (ARMS). The embryonal RMS includes also the botryoid, anaplastic and spindle-cell variants. An additional subtype is the pleomorphic RMS, which is exceptionally found in childhood. 3 ARMS represents approximately 25-30% of RMS and has a worse prognosis than ERMS. Cytogenetic and molecular analyses have demonstrated that ARMS frequently harbor the reciprocal chromosomal translocation t(2;13)(q35;q14), in which the PAX3 and FKHR genes are juxtaposed; also the less frequent variant translocation t(1;13)(p36;q14) has been associated to ARMS. The PAX3-FKHR chimeric protein binds regulatory sequences of genes involved in growth, differentiation, apoptosis and in vivo migration of rhabdomyoblasts, including c-met, IGF-1, PDGF-R, BCL-X, SDF-1 and CXCR4. [4][5][6][7][8] Moreover, retrospective analysis of PAX3-FKHR positive and negative ARMS 9-11 suggested that the translocation positive ARMS patients fared worse than the negative counterpart. Thus, the presence of the t(2;13) reciprocal translocation should be considered one of the main features affecting the biology of ARMS cells and might represent an adverse prognostic factor.Recently, the genomic approach based on global gene expression profiling by DNA microarrays has seen an explosive number of applications for cancer classification, prognosis and functional analysis of gene networks implicated in cancer biology. [12][13][14] Among a num...