Transcription site profiling reveals predictive markers in colon cancer

Abstract

Gene expression profiling studies have identified marker signatures predictive of tumor phenotypes, such as drug sensitivity and invasive or metastatic potential. However, the application of such information to the evaluation of tumors in the clinic is limited by cell heterogeneity in the tumor. We have developed a novel method of fluorescence in situ hybridization (FISH) that detects the transcriptional activation of individual genes in single cells. Here, we have applied this method to both predict response of colon cancer cells to chemotherapy and to define the spatial-temporal organization of gene expression along the small intestinal crypt-villus axis.;A major obstacle in the treatment of colorectal cancer patients is relative insensitivity to 5-Fluorouracil (5-FU), the agent most commonly used, usually in combination, for treatment of the disease. To define a set of genes predictive of relative sensitivity to 5-FU in colon cancer cells, we used FISH with probes targeted to nascent mRNAs and measured the number of individual cells with active transcription sites for a panel of candidate genes. These results reveal that the transcriptional status of four key genes, MRGX, TYMS, BAK and ATP7B can accurately predict response to 5-FU. We then demonstrated that this transcriptional profile was predictive of response to 5-FU in patient colon tumor tissues. This approach provides a novel ability to identify and characterize unique minor cell populations in the tumor that may exhibit relative resistance to chemotherapy.;In order to characterize the initial events in colorectal cancer development, we used FISH in paraffin-embedded mouse duodenum tissue to analyze the spatial-temporal distribution of key Wnt and Notch target genes involved in cell maturation and lineage-specific differentiation as cells migrate along the crypt-villus axis. Further, to define gene expression patterns in pre-malignant intestinal tissues, we examined the spatial-temporal expression of Wnt and Notch target genes along the crypt-villus axis in Apc+/- mice, a model for human colon cancer development. Our analysis indicates that the Wnt and Notch signaling pathways may interact in the development of intestinal tumors and reveals a disruption in the spatial-temporal organization of target genes that may be predictive of intestinal tumor development.