We previously found that an epithelial-to-mesenchymal transition (EMT)-based gene expression signature was highly correlated to the first principal component (PC1) of 326 colorectal cancer (CRC) tumors and was prognostic. This study was designed to improve these signatures for better prediction of metastasis and outcome.

468 CRC tumors including all stages (I-IV) and metastatic lesions were used to develop a new prognostic score (ΔPC1.EMT) by subtracting the EMT signature score from its correlated PC1 signature score. The score was validated on six other independent datasets with total 3697 tumors.

ΔPC1.EMT was found to be far more predictive of metastasis and outcome than its parent scores. It performed well in Stages I-III, amongst MSI subtypes, and across multiple mutation-based subclasses, demonstrating a refined capacity to predict distant metastatic potential in tumors even with a "good" prognosis. For example, in the PETACC-3 clinical trial dataset it predicted worse overall survival in an adjusted multivariable model for Stage III patients (HR by IQR=1.50, 95%CI=1.25-1.81, P=0.000016, N=644). The improved performance of ΔPC1.EMT was related to its propensity of identifying epithelial-like subpopulations as well as mesenchymal-like subpopulations. Biologically, the signature was correlated positively with RAS signaling but negatively with mitochondrial metabolism. ΔPC1.EMT was a "best of assessed" prognostic score when compared to ten other known prognostic signatures.

The study developed a prognostic signature score with a propensity of detecting non-EMT features, including epithelial cancer stem cell-related properties, thereby improving its potential to predict metastasis and poorer outcome in Stages I-III patients.