title: Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value.
abstract: BACKGROUND
  Colon 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.
  
  
  RESULTS
  Fresh-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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre Cancer, Paris, France.
authors.forename: Laetitia
authors.initials: L
authors.lastname: Marisa
authors.forename: Aurélien
authors.initials: A
authors.lastname: de Reyniès
authors.forename: Alex
authors.initials: A
authors.lastname: Duval
authors.forename: Janick
authors.initials: J
authors.lastname: Selves
authors.forename: Marie Pierre
authors.initials: MP
authors.lastname: Gaub
authors.forename: Laure
authors.initials: L
authors.lastname: Vescovo
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Etienne-Grimaldi
authors.forename: Renaud
authors.initials: R
authors.lastname: Schiappa
authors.forename: Dominique
authors.initials: D
authors.lastname: Guenot
authors.forename: Mira
authors.initials: M
authors.lastname: Ayadi
authors.forename: Sylvain
authors.initials: S
authors.lastname: Kirzin
authors.forename: Maurice
authors.initials: M
authors.lastname: Chazal
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Fléjou
authors.forename: Daniel
authors.initials: D
authors.lastname: Benchimol
authors.forename: Anne
authors.initials: A
authors.lastname: Berger
authors.forename: Arnaud
authors.initials: A
authors.lastname: Lagarde
authors.forename: Erwan
authors.initials: E
authors.lastname: Pencreach
authors.forename: Françoise
authors.initials: F
authors.lastname: Piard
authors.forename: Dominique
authors.initials: D
authors.lastname: Elias
authors.forename: Yann
authors.initials: Y
authors.lastname: Parc
authors.forename: Sylviane
authors.initials: S
authors.lastname: Olschwang
authors.forename: Gérard
authors.initials: G
authors.lastname: Milano
authors.forename: Pierre
authors.initials: P
authors.lastname: Laurent-Puig
authors.forename: Valérie
authors.initials: V
authors.lastname: Boige
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D016009:Chi-Square Distribution; D016000:Cluster Analysis; D003110:Colonic Neoplasms / Q000145:classification / Q000235:genetics* / Q000401:mortality / Q000473:pathology / Q000601:surgery; D005260:Female; D005602:France; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D053208:Kaplan-Meier Estimate; D016015:Logistic Models; D008207:Lymphatic Metastasis; D008297:Male; D008875:Middle Aged; D015999:Multivariate Analysis; D009367:Neoplasm Staging; D010641:Phenotype; D057285:Precision Medicine; D011237:Predictive Value of Tests; D011379:Prognosis; D016016:Proportional Hazards Models; D012333:RNA, Messenger / Q000032:analysis; D015203:Reproducibility of Results; D018570:Risk Assessment; D012307:Risk Factors; D013997:Time Factors; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger