Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value

Abstract

BackgroundColon cancer (CC) pathological staging fails to accurately predict recurrence, and to date, no gene expression signature has proven reliable for prognosis stratification in clinical practice, perhaps because CC is a heterogeneous disease. The aim of this study was to establish a comprehensive molecular classification of CC based on mRNA expression profile analyses.Methods and FindingsFresh-frozen primary tumor samples from a large multicenter cohort of 750 patients with stage I to IV CC who underwent surgery between 1987 and 2007 in seven centers were characterized for common DNA alterations, including BRAF, KRAS, and TP53 mutations, CpG island methylator phenotype, mismatch repair status, and chromosomal instability status, and were screened with whole genome and transcriptome arrays. 566 samples fulfilled RNA quality requirements. Unsupervised consensus hierarchical clustering applied to gene expression data from a discovery subset of 443 CC samples identified six molecular subtypes. These subtypes were associated with distinct clinicopathological characteristics, molecular alterations, specific enrichments of supervised gene expression signatures (stem cell phenotype–like, normal-like, serrated CC phenotype–like), and deregulated signaling pathways. Based on their main biological characteristics, we distinguished a deficient mismatch repair subtype, a KRAS mutant subtype, a cancer stem cell subtype, and three chromosomal instability subtypes, including one associated with down-regulated immune pathways, one with up-regulation of the Wnt pathway, and one displaying a normal-like gene expression profile. The classification was validated in the remaining 123 samples plus an independent set of 1,058 CC samples, including eight public datasets. Furthermore, prognosis was analyzed in the subset of stage II–III CC samples. The subtypes C4 and C6, but not the subtypes C1, C2, C3, and C5, were independently associated with shorter relapse-free survival, even after adjusting for age, sex, stage, and the emerging prognostic classifier Oncotype DX Colon Cancer Assay recurrence score (hazard ratio 1.5, 95% CI 1.1–2.1, p = 0.0097). However, a limitation of this study is that information on tumor grade and number of nodes examined was not available.ConclusionsWe describe the first, to our knowledge, robust transcriptome-based classification of CC that improves the current disease stratification based on clinicopathological variables and common DNA markers. The biological relevance of these subtypes is illustrated by significant differences in prognosis. This analysis provides possibilities for improving prognostic models and therapeutic strategies. In conclusion, we report a new classification of CC into six molecular subtypes that arise through distinct biological pathways. Please see later in the article for the Editors' Summary

The molecular landscape of colorectal cancer cell lines unveils clinically actionable kinase targets

“…Colorectal tumours can be classified in up to six unique subtypes with diverse clinical features according to the genes they express [8][9][10][11][12] .…”

“…Expression profiles were therefore used to assign each cell line to a molecular subtype [8][9][10][11][12] by the Nearest Template Prediction (NTP) algorithm, which also estimates the classification false discovery rate (FDR) 23 . Each of the five classifiers was able to assign (FDRo0.2) the large majority of the cell lines to a subtype.…”

“…We conclude that genetic and pharmacological profiling CRC lines can successfully nominate clinically-relevant molecular determinants of response to targeted therapies. In addition to the mutation-based categories described above, CRC can be subdivided in up to six transcriptional subtypes with distinct molecular and clinical features [8][9][10][11][12] , which we found to be robustly maintained in cells grown in vitro. This observation, along with the evidence that independent cell lines derived from the same patient consistently co-cluster transcriptionally, suggests that the transcriptional profile is stable and predominantly controlled by the genome in the absence of environmental inputs.…”

“…Transcriptional profiling has been recently used to identify distinct CRC subtypes [8][9][10][11][12] . The subtypes are associated with biological and clinical features such as cell of origin, MSI, prognosis and response to treatments.…”

Precision Oncology: The UC San Diego Moores Cancer Center PREDICT Experience

“…NGS permits rapid testing of multiple cancerrelated genes, and its price has dropped precipitously over the last decade (1). Furthermore, our understanding of targetable gene alterations has also expanded at a remarkable pace (2)(3)(4)(5)(6). As examples, EGFR and ALK alterations in lung cancer (7)(8)(9), KRAS in colorectal cancer (as a marker of resistance; ref.…”