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Molecular Heterogeneity and Function of EWS-WT1 Fusion Transcripts in Desmoplastic Small Round Cell Tumors¹

Department of Medicine and Pharmacology, Yale Cancer Center, Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, Connecticut 06520 [J. L., E. C.], and Medicine Branch, Division of Clinical Science, National Cancer Institute, NIH, Bethesda, Maryland 20889 [M. M. N., J. C. Y., C. J. A., J. J. W.]

Desmoplastic small round cell tumor (DSRCT) is a primitive sarcoma with a consistent cytogenetic abnormality, t(11;22)(p13;q12). This chromosomal translocation generates a chimeric transcript that is formed by fusion of the 5' region of the Ewing’s sarcoma gene, EWS, with the 3' DNA-binding segment of WT1, the Wilms’ tumor suppressor gene. We collected 14 DSRCT tumor samples and examined the hybrid transcripts. We identified: (a) combinatorial heterogeneity of EWS exons fused to WT1 including use of EWS exons 7, 8, and 9; (b) subpopulations of variant transcripts in 6 of 14 tumors characterized by aberrant splicing resulting in loss of EWS exon 6 or WT1 exon 9; (c) multiple cDNA products with large internal deletions; and (d) insertion of small stretches of heterologous DNA at the fusion site or exon splice region in transcripts from two tumors. Most of the splice variants were in-frame, and in vitro translated fusion proteins with intact DNA-binding motifs formed complexes with a WT 1 response element in gel mobility assays. Each of the chimeric proteins retains the ability to bind to the GC and TC elements of the early transcription factor EGR-1 as well as WT1 consensus sequences. We present evidence that various EWS-WT1 proteins up-regulated EGR-1 promoter activity and that this up-regulation is specifically dependent upon the absence of the exon 9 KTS domain of WT1. The molecular diversity and functionality exhibited by these fusion transcripts may have significant biological implications for their transactivating and tumorigenic potential.

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