Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric soft tissue tumor with striated muscle differentiation. Chromosomal studies of these tumors identified 2;13 and 1;13 translocations. Using physical mapping and cloning strategies, we determined that t(2;13) and t(1;13) rearrange PAX3 and PAX7, which encode members of the paired box transcription factor family, and juxtapose these genes with FKHR, which encodes a novel member of the fork head transcription factor family. These translocations result in chimeric transcripts consisting of 5′ PAX3 or PAX7 exons fused to 3′ FKHR exons, which encode fusion proteins containing the PAX3 or PAX7 DNA-binding domain and the COOH-terminal FKHR transcriptional activation domain. In transfection studies, the PAX3-FKHR fusion activates transcription of reporter genes containing PAX DNA-binding sites, and is 10–100-fold more potent as a transcriptional activator than is wild-type PAX3. This increased function results from the insensitivity of the COOH-terminal FKHR activation domain to the inhibitory effects of NH2-terminal PAX3 domains. In addition to functional alterations, our studies demonstrated PAX3-FKHR and PAX7-FKHR overexpression resulting from two distinct mechanisms, increased transcription of PAX3-FKHR by a copy number-independent mechanism, and gene amplification of PAX7-FKHR. These findings indicate that the genetic changes in these tumors result in high levels of chimeric transcription factors that are hypothesized to inappropriately activate transcription of genes with PAX DNA-binding sites and thereby induce tumorigenic behavior. The differences in overexpression strategies suggest important differences between the mechanisms for regulating PAX3 and PAX7 expression. These differences extend to the phenotypic level, at which clinical differences have been found between the two ARMS subtypes: PAX7-FKHR tumors more often occur as localized lesions in the extremities of younger patients and are associated with longer event-free survival as compared to PAX3-FKHR tumors. Therefore, the clinical heterogeneity within the ARMS category is associated with genetic heterogeneity. Further analysis of the transcriptional function, regulation of expression, and phenotypic effects will help to elucidate the action of these fusion products and the biological basis of the clinical heterogeneity.

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Presented at the “General Motors Cancer Research Foundation Twentieth Annual Scientific Conference: Developmental Biology and Cancer,” June 9–10, 1998, Bethesda, MD. This work was supported in part by NIH Grants CA64202 and CA71838.

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