title: A taxonomy of epithelial human cancer and their metastases.
abstract: BACKGROUND
  Microarray technology has allowed to molecularly characterize many different cancer sites. This technology has the potential to individualize therapy and to discover new drug targets. However, due to technological differences and issues in standardized sample collection no study has evaluated the molecular profile of epithelial human cancer in a large number of samples and tissues. Additionally, it has not yet been extensively investigated whether metastases resemble their tissue of origin or tissue of destination.
  
  
  METHODS
  We studied the expression profiles of a series of 1566 primary and 178 metastases by unsupervised hierarchical clustering. The clustering profile was subsequently investigated and correlated with clinico-pathological data. Statistical enrichment of clinico-pathological annotations of groups of samples was investigated using Fisher exact test. Gene set enrichment analysis (GSEA) and DAVID functional enrichment analysis were used to investigate the molecular pathways. Kaplan-Meier survival analysis and log-rank tests were used to investigate prognostic significance of gene signatures.
  
  
  RESULTS
  Large clusters corresponding to breast, gastrointestinal, ovarian and kidney primary tissues emerged from the data. Chromophobe renal cell carcinoma clustered together with follicular differentiated thyroid carcinoma, which supports recent morphological descriptions of thyroid follicular carcinoma-like tumors in the kidney and suggests that they represent a subtype of chromophobe carcinoma. We also found an expression signature identifying primary tumors of squamous cell histology in multiple tissues. Next, a subset of ovarian tumors enriched with endometrioid histology clustered together with endometrium tumors, confirming that they share their etiopathogenesis, which strongly differs from serous ovarian tumors. In addition, the clustering of colon and breast tumors correlated with clinico-pathological characteristics. Moreover, a signature was developed based on our unsupervised clustering of breast tumors and this was predictive for disease-specific survival in three independent studies. Next, the metastases from ovarian, breast, lung and vulva cluster with their tissue of origin while metastases from colon showed a bimodal distribution. A significant part clusters with tissue of origin while the remaining tumors cluster with the tissue of destination.
  
  
  CONCLUSIONS
  Our molecular taxonomy of epithelial human cancer indicates surprising correlations over tissues. This may have a significant impact on the classification of many cancer sites and may guide pathologists, both in research and daily practice. Moreover, these results based on unsupervised analysis yielded a signature predictive of clinical outcome in breast cancer. Additionally, we hypothesize that metastases from gastrointestinal origin either remember their tissue of origin or adapt to the tissue of destination. More specifically, colon metastases in the liver show strong evidence for such a bimodal tissue specific profile.
authors.affiliation: Bioinformatics, Department of Electrical Engineering (ESAT/SCD), Katholieke Universiteit Leuven, Belgium. olivier.gevaert@esat.kuleuven.be
authors.forename: Olivier
authors.initials: O
authors.lastname: Gevaert
authors.forename: Anneleen
authors.initials: A
authors.lastname: Daemen
authors.forename: Bart
authors.initials: B
authors.lastname: De Moor
authors.forename: Louis
authors.initials: L
authors.lastname: Libbrecht
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D038622:Internationality; D009362:Neoplasm Metastasis / Q000235:genetics / Q000473:pathology; D009375:Neoplasms, Glandular and Epithelial / Q000145:classification* / Q000188:drug therapy / Q000235:genetics / Q000473:pathology*; D009382:Neoplasms, Unknown Primary / Q000628:therapy; D020411:Oligonucleotide Array Sequence Analysis; D049490:Systems Biology