Frequent alterations in gene expression in colon tumor cells of the microsatellite mutator phenotype

Tumors of the microsatellite mutator phenotype (MMP) are characterized by the accumulation of many thousands of somatic mutations in tracts of simple repeated sequences or microsatellites. Using arbitrarily primed PCR fingerprinting of RNA (RAP-PCR), we have comparatively analyzed the overall gene expression patterns of several colorectal tumor cell lines with and without the MMP. A reproducible pattern of 30-40 main products was obtained for each fingerprint with a total of about 200 cell transcripts analyzed. Differences in RAP-PCR fingerprints were detected between these tumor cell lines. Some of these expression polymorphisms appeared to be specific for tumor cells of the MMP because they were present in two or more different MMP+ cell lines but absent in all MMP- cell lines analyzed. We also analyzed RNAs prepared from single cell clones isolated from these tumor cell lines. Reproducible differences in the fingerprints were detected between single cell clones from each of the cell lines analyzed. Examples of single cell clone-specific fingerprint differences from one of the MMP tumor cell lines were cloned and sequenced. Differential expression of some of these sequences was confirmed by Northern analysis using the cloned fragments as probes. Similar fingerprint alterations were also observed among single cell clones derived from single cell clones from mutator tumor cell lines, which appeared to exhibit higher clonal variation in gene expression compared with MMP- cells. The detection of inter- and intra-tumor alterations in gene expression by unbiased RAP-PCR show that these fluctuations occur with high frequency in tumor cells of the MMP. These results indicate that the profound genomic instability of tumor cells of the MMP is also reflected in a high incidence of alterations in their patterns of gene expression.