Dissection of a metastatic gene expression signature into distinct components.
BACKGROUND
Metastasis, the process whereby cancer cells spread, is in part caused by an incompletely understood interplay between cancer cells and the surrounding stroma. Gene expression studies typically analyze samples containing tumor cells and stroma. Samples with less than 50% tumor cells are generally excluded, thereby reducing the number of patients that can benefit from clinically relevant signatures.


RESULTS
For a head-neck squamous cell carcinoma (HNSCC) primary tumor expression signature that predicts the presence of lymph node metastasis, we first show that reduced proportions of tumor cells results in decreased predictive accuracy. To determine the influence of stroma on the predictive signature and to investigate the interaction between tumor cells and the surrounding microenvironment, we used laser capture microdissection to divide the metastatic signature into six distinct components based on tumor versus stroma expression and on association with the metastatic phenotype. A strikingly skewed distribution of metastasis associated genes is revealed.


CONCLUSIONS
Dissection of predictive signatures into different components has implications for design of expression signatures and for our understanding of the metastatic process. Compared to primary tumors that have not formed metastases, primary HNSCC tumors that have metastasized are characterized by predominant down-regulation of tumor cell specific genes and exclusive up-regulation of stromal cell specific genes. The skewed distribution agrees with poor signature performance on samples that contain less than 50% tumor cells. Methods for reducing tumor composition bias that lead to greater predictive accuracy and an increase in the types of samples that can be included are presented.
Roepman
Paul
P
Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg, Utrecht, The Netherlands.
de Koning
Erica
E
van Leenen
Dik
D
de Weger
Roel A
RA
Kummer
J Alain
JA
Slootweg
Piet J
PJ
Holstege
Frank C P
FC
D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000473:pathology*; D015870:Gene Expression; D006258:Head and Neck Neoplasms / Q000235:genetics / Q000473:pathology*; D006801:Humans; D009362:Neoplasm Metastasis / Q000235:genetics*