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Background & aims Staging inadequately predicts metastatic risk in patients with colon cancer. We used a gene expression profile derived from invasive, murine colon cancer cells that were highly metastatic in an immunocompetent mouse model to identify patients with colon cancer at risk of recurrence. Methods This phase 1, exploratory biomarker study used 55 patients with colorectal cancer from Vanderbilt Medical Center (VMC) as the training dataset and 177 patients from the Moffitt Cancer Center as the independent dataset. The metastasis-associated gene expression profile developed from the mouse model was refined with comparative functional genomics in the VMC gene expression profiles to identify a 34-gene classifier associated with high risk of metastasis and death from colon cancer. A metastasis score derived from the biologically based classifier was tested in the Moffitt dataset. Results A high score was significantly associated with increased risk of metastasis and death from colon cancer across all pathologic stages and specifically in stage II and stage III patients. The metastasis score was shown to independently predict risk of cancer recurrence and death in univariate and multivariate models. For example, among stage III patients, a high score translated to increased relative risk of cancer recurrence (hazard ratio, 4.7; 95% confidence interval, 1.566–14.05). Furthermore, the metastasis score identified patients with stage III disease whose 5-year recurrence-free survival was >88% and for whom adjuvant chemotherapy did not increase survival time. Conclusion A gene expression profile identified from an experimental model of colon cancer metastasis predicted cancer recurrence and death, independently of conventional measures, in patients with colon cancer.

Several genes such as Cdx2 and HoxD ase known to be expressed ditterentially during colonic developmem; however, mechanisms regulating remodeling of colon after early organogenesis are poorly understood. In order to study changes in gene expression during this remodeling, we compared RNA kvels usmg eDNA microarrays made from a set ot 20,114 cDNA clones (Research Genetics and National Institute of Aging) containing approximately" 14,723 different murine genes. We made eDNA probes from total RNA that had been twice amplified. RNA samples were obtained from embryonic colons of CD-1 and C57BU6j inbred mice at six dflterent embryonic stages between 13.5 and 18.5 days. Comrol probe was prepared from Wtmle 17.5 day" embryos. Ten [housand eighty nine genes exhibited consistent patterns of expression intensity in [hree rephcations using two sets of probes made from each embrymxic stage of colon in both strains Gene expression in the six embryonic stages clustered into two main groups (13.5 to 155 day versus 16.5 to 18.5 day) according to hierarchical chistering. These clusters corresponded to major changes in morphological remodeling, as determined by light and electron microscopy. We observed, for instance, that tf~e colon developed a central lumen and stromal invagination by day 16.5. Most of the genes (91.8% (CD-1) and 93.6% (C57BU6J)) did not show sigmficant changes in expression during this period However, 530 (5.3%) genes in both strains exhibited at least two-fold diflerences in expression leveI. By a pair-wlse comparison of expression levels of these genes between 13.5 and 18.5 days, we identified ibur difterent expression patterns (figure) A complete characterizatmn, atong with validation of selected genes by RT-PCR and in situ hybridization, will be presented.