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Connective Tissue Oncology Society |
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| 2001 CTOS Annual Meeting Posters— Biology CLASSIFICATION OF
GENE EXPRESSION PROFILES IN ADULT SOFT TISSUE SARCOMA USING OLIGONUCLEOTIDE
ARRAY ANALYSIS OBJECTIVE: Adult soft tissue sarcoma (STS) represents a diverse group of neoplastic diseases that are grouped together because of shared biological characteristics and clinical responses [1]. This study was undertaken to identify the differential gene expression profile obtained from various histological categories of STS. Large scale gene expression data could be used to validate the current classification system for STS, investigate an alternative gene expression based classification system, and furthermore identify genes that differentiate between tumors of varying clinical outcome. Gene expression profiles may offer more information than classic morphology and provide an alternative to morphology-based tumor classification systems. METHODS: Total RNA was isolated from 30 cases of high grade STS, including leiomyosarcoma, fibrosarcoma, liposarcoma, synovial sarcoma, GIST, MFH and clear cell sarcoma. cRNA was prepared according to the Affymetrix® protocol and hybridized to the U95A GeneChip® array. An average difference (AD) value was generated that corresponds to the level of gene expression. Expression data was scaled to 2500 using the 96% mean-centered method. Absent calls and negative values were set to an overall average background value. Gene lists by tumor type were generated by ranking of F-statistic values. Multi-dimensional scaling was also applied to the original data in an unsupervised analysis to demonstrate inherent similarity of STS tumors. RESULTS: Expression data was determined for ~12 500 genes previously reported in terms of function or disease association (Affymetrix®). Individual tumors showed distinct patterns of gene expression. The top 100 genes were selected by rank of F-statistic to discriminate the test group of STS. 21 genes were shown to discriminate synovial sarcoma. PRAME, a cancer-testis antigen recognized by autologous T cells in melanoma [2], was shown to be expressed in synovial sarcoma and to a lesser extent in fibrosarcoma. 40 genes were shown to discriminate GIST, including c-kit. 39 genes were shown to discriminate clear cell sarcoma. Using unsupervised multidimensional scaling, across ~10 500 genes, synovial sarcoma, GIST and clear cell sarcomas emerge as distinct clusters. The remaining specimens did not appear to separate into histological or distinct genetic groups (figure). CONCLUSION: We identified several potentially important genes in the diagnosis and biology of STS. We have shown that synovial sarcoma, GIST and clear cell sarcoma are genetically distinct within themselves and relative to the more homogeneous group of high grade leiomyosarcoma, fibrosarcoma and MFH. The liposarcoma group is as yet inconclusive, being comprised of dedifferentiated and pleomorphic liposarcomas. MFH and fibrosarcomas grouped together. These data indicate that MFH may represent pleomorphic fibroblastic tumors rather than tumors with a distinct histiocytic histogenesis. GISTs, previously considered as gastro-intestinal leiomyosarcomas, stand out as a separate group characterized by abnormalities in c-kit. Research in progress aims to identify gene lists that may discriminate between the latter group of tumors, and to characterize selected transcripts that may provide insight into the pathology and clinical behavior of STS. 1. Mann, G.B. et al. Aust N Z J Surg, 1999. 69(5): p. 336–43. 2. Ikeda, H., et al. Immunity, 1997. 6(2): p. 199–208.
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