Abstract
Simple SummaryA gene signature derived from the loss of CDKN1A (p21) gene, obtained in HCT116 p21-/- colorectal cancer cells, is identified in a large cohort of primary colorectal (CRC) tumors and is associated with the Consensus Molecular Subtype (CMS) of colon cancer that has a worse relapse-free and overall survival, that is, CMS4 (also called mesenchymal subtype). The presented gene signature can help to uncover the early molecular mechanisms of epithelial–mesenchymal transition (EMT), which is known to be associated with high stemness and drug resistance.The epithelial–mesenchymal transition (EMT) is associated with tumor aggressiveness and increased invasion, migration, metastasis, angiogenesis, and drug resistance. Although the HCT116 p21-/- cell line is well known for its EMT-associated phenotype, with high Vimentin and low E-cadherin protein levels, the gene signature of this rather intermediate EMT-like cell line has not been determined so far. In this work, we present a robust molecular and bioinformatics analysis, to reveal the associated gene expression profile and its correlation with different types of colorectal cancer tumors. We compared the quantitative signature obtained with the NanoString platform with the expression profiles of colorectal cancer (CRC) Consensus Molecular Subtypes (CMS) as identified, and validated the results in a large independent cohort of human tumor samples. The expression signature derived from the p21-/- cells showed consistent and reliable numbers of upregulated and downregulated genes, as evaluated with two machine learning methods against the four CRC subtypes (i.e., CMS1, 2, 3, and 4). High concordance was found between the upregulated gene signature of HCT116 p21-/- cells and the signature of the CMS4 mesenchymal subtype. At the same time, the upregulated gene signature of the native HCT116 cells was similar to that of CMS1. Using a multivariate Cox regression model to analyze the survival data in the CRC tumor cohort, we selected genes that have a predictive risk power (with a significant gene risk incidence score). A set of genes of the mesenchymal signature was proven to be significantly associated with poor survival, specifically in the CMS4 CRC human cohort. We suggest that the gene signature of HCT116 p21-/- cells could be a suitable metric for mechanistic studies regarding the CMS4 signature and its functional consequences in CRC. Moreover, this model could help to discover the molecular mechanisms of intermediate EMT, which is known to be associated with extraordinarily high stemness and drug resistance.
Highlights
Colorectal cancer (CRC) represents one of the leading causes of cancer-related deaths worldwide, mainly due to its high metastatic rate
The analysis revealed a clear separation of colorectal cancer (CRC) primary tumor samples, regarding survival when performing the risk prediction in the set of 167 CMS1 patients with the 40 upregulated genes in HCT116 p21−/− cells from our gene signature (Figure 5A–D)
We showed a strong separation of tumors with poor and good survival when performing the CRC patient risk prediction in the set of 246 CMS4 patients with the 27 genes upregulated in our proposed gene-signature in the HCT116 p21−/−
Summary
Colorectal cancer (CRC) represents one of the leading causes of cancer-related deaths worldwide, mainly due to its high metastatic rate. Metastasis formation is based on a multi-step process, that is known as the invasion–metastasis cascade. It starts with the dissemination of cancer cells from the primary tumor site, followed by invasion into the surrounding tissue, intravasation, survival in the circulatory system, extravasation, and recolonization at a distant organ site; eventually generating a secondary tumor [2]. Even though it is well known that the progression of the normal colon epithelium to an invasive and metastatic carcinoma is strongly associated with the process of EMT and the ability of tumor cells to survive under non-adherent conditions, the elucidation of the detailed mechanisms and regulators driving metastatic spread in patients remains a major focus for translational cancer research
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