The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer

Schwede, M.; Waldron, L.; Mok, S. C.; Wei, W.; Basunia, A.; Merritt, M. A.; Parmigiani, G.; Harrington, D.; Quackenbush, J.; Birrer, M. J.; Culhane, A.

doi:10.1101/496406

bioRxiv · 10.1101/496406

The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer

Schwede, M.·Waldron, L.·Mok, S. C.·Wei, W.·Basunia, A.·Merritt, M. A.·Parmigiani, G.·Harrington, D.·Quackenbush, J.·Birrer, M. J.·Culhane, A.

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Abstract

PurposeRecent efforts to improve outcomes for high-grade serous ovarian cancer, a leading cause of cancer death in women, have focused on identifying molecular subtypes and prognostic gene signatures, but existing subtypes have poor cross-study robustness. We tested the contribution of cell admixture in published ovarian cancer molecular subtypes and prognostic gene signatures.\n\nExperimental DesignPublic gene expression data, two molecular subtype classifications, and 61 published gene signatures of ovarian cancer were examined. Using microdissected data, we developed gene signatures of ovarian tumor and stroma. Computational simulations of increasing stromal cell proportion were performed by mixing gene expression profiles of paired microdissected ovarian tumor and stroma.\n\nResultsEstablished ovarian cancer molecular subtypes are strongly associated with the cell admixture. Tumors were classified as different molecular subtypes in simulations, when the percentage of stromal cells increased. Stromal gene expression in bulk tumor was weakly prognostic, and in one dataset, increased stroma was associated with anatomic sampling location. Five published prognostic gene signatures were no longer prognostic in a multivariate model that adjusted for stromal content alone.\n\nConclusionsThe discovery that molecular subtypes of high grade serous ovarian cancer is influenced by cell admixture, and stromal cell gene expression is crucial for interpretation and reproduction of ovarian cancer molecular subtypes and gene signatures derived from bulk tissue. Single cell analysis may be required to refine the molecular subtypes of high grade serous ovarian cancer. Because stroma proportion was weakly prognostic, elucidating the role of the tumor microenvironments components will be important.\n\nTranslational relevanceOvarian cancer is a leading cause of cancer death in women in the United States. Although the tumor responds to standard therapy for the majority of patients, it frequently recurs and becomes drug-resistant. Recent efforts have focused on identifying molecular subtypes and prognostic gene signatures of ovarian cancer in order to tailor therapy and improve outcomes. This study demonstrates that molecular subtype identification depends on the ratio of tumor to stroma within the specimen. We show that the specific anatomic location of the biopsy may influence the proportion of stromal involvement and potentially the resulting gene expression pattern. It will be crucial for these factors to be taken into consideration when interpreting and reproducing ovarian cancer molecular subtypes and gene signatures derived using bulk tissue and single cells. Furthermore, it will be important to define the relative proportions of stromal cells and model their prognostic importance in the tumor microenvironment.

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Schwede, M., Waldron, L., Mok, S. C., Wei, W., Basunia, A., Merritt, M. A., Parmigiani, G., Harrington, D., Quackenbush, J., Birrer, M. J., Culhane, A.. 2018-12-13. The impact of stroma on the discovery of molecular subtypes and prognostic gene signatures in serous ovarian cancer. https://doi.org/10.1101/496406

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