Characterization of sarcomas by means of gene expression

Sarcomas represent a heterogeneous group of diseases of a variety of recognized histologic types. Among these subtypes is malignant fibrous histiocytoma (MFH), a diagnosis no longer recognized as a specific diagnosis at some institutions. In this study, gene expression in 38 histologically well-defined sarcoma samples, 17 MFH samples, 12 samples of sarcomas classified simply as high-grade sarcoma (NOS, standing for "not otherwise specified"), and 26 other mesenchymal tumors was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 known genes and expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic Gene Express® Software System. Differences in gene expression were quantified as the fold change in gene expression between the various sets of well-defined sarcomas. A set of genes was then identified that could be used to distinguish the well-defined sets of 11 liposarcomas, 9 leiomyosarcomas, 4 synovial sarcomas, 8 schwannomas, and 12 cases of aggressive fibromatosis through the use of Eisen clustering. Eisen clustering was then repeated with the same set of gene fragments with the sample set of 38 histologically well-defined sarcomas, the 17 sarcomas classified as MFH, 12 sarcomas classified as high-grade sarcoma (NOS), and 26 other mesenchymal tumors. Under these conditions, each of the samples of well-defined sarcoma formed distinct clusters that contained some of the MFH and NOS samples. In addition, distinct clusters were observed that contained only MFH and NOS samples. We conclude that gene-expression patterns may be useful in helping further classify subtypes of sarcomas.