Human Cancer Biology High-Resolution Array CGH and Gene Expression Pro fi ling of Alveolar Soft Part Sarcoma

Purpose: Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis, and little molecular evidence exists for its origin, initiation, and progression. The aim of this study was to elucidate candidate molecular pathways involved in tumor pathogenesis. Experimental Design: We employed high-throughput array comparative genomic hybridization (aCGH) and cDNA-Mediated Annealing, Selection, Ligation, and Extension Assay to profile the genomic and expression signatures of primary andmetastatic ASPS from17 tumors derived from11patients.Weused an integrative bioinformatics approach to elucidate the molecular pathways associated with ASPS progression. FISH was performed to validate the presence of the t(X;17)(p11.2;q25) ASPL–TFE3 fusion and, hence, confirm the aCGH observations. Results: FISH analysis identified the ASPL–TFE3 fusion in all cases. aCGH revealed a higher number of numerical aberrations inmetastatic tumors relative to primaries, but failed to identify consistent alterations in either group. Gene expression analysis highlighted 1,063 genes thatwere differentially expressed between the two groups. Gene set enrichment analysis identified 16 enriched gene sets (P < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6was upregulated in the primary tumors, along with several genes whosemouse orthologs have previously been implicated in Pax6 DNA binding during neural stem cell differentiation. Conclusion: In addition to suggesting a tentative neural line of differentiation for ASPS, these results implicate transcriptional deregulation from fusion genes in thepathogenesis of ASPS.ClinCancer Res; 20(6);