Chromosomal translocations identified in hematopoietic and solid tumors result in deregulated expression of protooncogenes or creation of chimeric proteins with tumorigenic potential. In the pediatric solid tumor alveolar rhabdomyosarcoma, a consistent t(2;13)(q35;q14) or variant t(1;13)(p36;q14) translocation generates PAX3-FKHR or PAX7-FKHR fusion proteins, respectively. In this report, we demonstrate that in addition to functional alterations these translocations are associated with fusion product overexpression. Furthermore, PAX3-FKHR and PAX7-FKHR overexpression occurs by distinct mechanisms. Transcription of PAX3-FKHR is increased relative to wild-type PAX3 by a copy number-independent process. In contrast, PAX7-FKHR overexpression results from fusion gene amplification. Thus, gene-specific mechanisms were selected to overexpress PAX3-FKHR and PAX7-FKHR in alveolar rhabdomyosarcoma, presumably due to differences in regulation between the wild-type loci. We postulate that these overexpression mechanisms ensure a critical level of gene product for the oncogenic effects of these fusions.Cytogenetics has demonstrated the presence of consistent chromosomal translocations in hematopoietic and solid malignancies (1). Molecular analysis of the consequences of these events has revealed two models for oncogene activation (1). Either protooncogene expression is deregulated by juxtaposition with strong regulatory elements or novel fusion proteins are created with altered function and tumorigenic potential.Alveolar rhabdomyosarcoma (ARMS) is a pediatric soft tissue tumor that is associated with either a t(2;13)(q35;q14) or variant t(1;13)(p36;q14) translocation (2, 3). These translocations fuse either PAX3 or PAX7 with FKHR to generate chimeric genes that express PAX3-FKHR or PAX7-FKHR fusion products, respectively (4-7). These fusion proteins consist of the N-terminal DNA-binding domains of PAX3 or PAX7 fused to the C-terminal transcriptional activation domain of FKHR. Transient transfection experiments indicate that PAX3-FKHR functions as a transcription factor (8, 9). Moreover, PAX3-FKHR exhibits increased transcriptional potency relative to PAX3 due to swapping of PAX3 and FKHR C-terminal transactivation domains. Cell culture experiments also have demonstrated that PAX3-FKHR can induce phenotypic changes, including cellular transformation (10) and inhibition of myogenic differentiation (11).While these studies of the ARMS translocations are consistent with the fusion protein model of oncogene activation, additional evidence indicates that altered expression of PAX3-FKHR and PAX7-FKHR is another fundamental characteristic of ARMS. Previous Northern blot analysis of a few ARMS cell lines demonstrated that while PAX3-FKHR RNA was readily detectable, PAX3 RNA was expressed at low or undetectable levels (4). Furthermore, amplification of the PAX3-FKHR and PAX7-FKHR fusion genes has been detected in tumor specimens (12). Finally, antisense oligonucleotide treatment of ARMS cells has shown that transient down-regu...