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Open Access Highly Accessed Research article

Colon cancer molecular subtypes identified by expression profiling and associated to stroma, mucinous type and different clinical behavior

Beatriz Perez Villamil1*, Alejandro Romera Lopez1, Susana Hernandez Prieto2, Guillermo Lopez Campos3, Antonio Calles1, Jose Antonio Lopez Asenjo2, Julian Sanz Ortega2, Cristina Fernandez Perez4, Javier Sastre1, Rosario Alfonso1, Trinidad Caldes1, Fernando Martin Sanchez35 and Eduardo Diaz Rubio1

Author affiliations

1 Molecular Oncology Laboratory, Medical Oncology Department, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria del Hospital Clinico San Carlos (IdISSC), C/ Martin Lagos s/n, Madrid, 28040, Spain

2 Department of Surgical Pathology, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria del Hospital Clinico San Carlos (IdISSC), C/ Martin Lagos s/n, Madrid, 28040, Spain

3 Medical Bioinformatics Department, National Institute of Health Carlos III, Ctra, Majadahonda a Pozuel, Km. 2 Majadahonda, 28220, Madrid, Spain

4 Department of Preventive Medicine, Hospital Clinico San Carlos, Instituto de Investigacion Sanitaria del Hospital Clinico San Carlos (IdISSC), C/ Martin Lagos s/n, Madrid, 28040, Spain

5 Health Informatics. Melbourne Medical School, Faculty of Medicine, Dentistry & Health Sciences. Health and Biomedical Informatics Research (HBIR) Unit IBES-Institute for the Broadband-Enabled Society, The University of Melbourne, Level 1, 202 Berkeley Street, 3010, Melbourne, VIC, Australia

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Citation and License

BMC Cancer 2012, 12:260  doi:10.1186/1471-2407-12-260

Published: 19 June 2012

Abstract

Background

Colon cancer patients with the same stage show diverse clinical behavior due to tumor heterogeneity. We aimed to discover distinct classes of tumors based on microarray expression patterns, to analyze whether the molecular classification correlated with the histopathological stages or other clinical parameters and to study differences in the survival.

Methods

Hierarchical clustering was performed for class discovery in 88 colon tumors (stages I to IV). Pathways analysis and correlations between clinical parameters and our classification were analyzed. Tumor subtypes were validated using an external set of 78 patients. A 167 gene signature associated to the main subtype was generated using the 3-Nearest-Neighbor method. Coincidences with other prognostic predictors were assesed.

Results

Hierarchical clustering identified four robust tumor subtypes with biologically and clinically distinct behavior. Stromal components (p < 0.001), nuclear β-catenin (p = 0.021), mucinous histology (p = 0.001), microsatellite-instability (p = 0.039) and BRAF mutations (p < 0.001) were associated to this classification but it was independent of Dukes stages (p = 0.646). Molecular subtypes were established from stage I. High-stroma-subtype showed increased levels of genes and altered pathways distinctive of tumour-associated-stroma and components of the extracellular matrix in contrast to Low-stroma-subtype. Mucinous-subtype was reflected by the increased expression of trefoil factors and mucins as well as by a higher proportion of MSI and BRAF mutations. Tumor subtypes were validated using an external set of 78 patients. A 167 gene signature associated to the Low-stroma-subtype distinguished low risk patients from high risk patients in the external cohort (Dukes B and C:HR = 8.56(2.53-29.01); Dukes B,C and D:HR = 1.87(1.07-3.25)). Eight different reported survival gene signatures segregated our tumors into two groups the Low-stroma-subtype and the other tumor subtypes.

Conclusions

We have identified novel molecular subtypes in colon cancer with distinct biological and clinical behavior that are established from the initiation of the tumor. Tumor microenvironment is important for the classification and for the malignant power of the tumor. Differential gene sets and biological pathways characterize each tumor subtype reflecting underlying mechanisms of carcinogenesis that may be used for the selection of targeted therapeutic procedures. This classification may contribute to an improvement in the management of the patients with CRC and to a more comprehensive prognosis.

Keywords:
Colon cancer; Microarray gene expression; Molecular classification; Stroma; Survival