Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition

Tanis, S.; Lixandrao, M.; Ivich, A.; Grieshober, L.; Lawson-Michod, K. A.; Collin, L. J.; Peres, L. C.; Salas, L. A.; Marks, J. R.; Bitler, B. G.; Greene, C. S.; Schildkraut, J. M.; Doherty, J. A.; Davidson, N. R.

doi:10.64898/2026.04.16.719000

bioRxiv · 10.64898/2026.04.16.719000

Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition

Tanis, S.·Lixandrao, M.·Ivich, A.·Grieshober, L.·Lawson-Michod, K. A.·Collin, L. J.·Peres, L. C.·Salas, L. A.·Marks, J. R.·Bitler, B. G.·Greene, C. S.·Schildkraut, J. M.·Doherty, J. A.·Davidson, N. R.

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Abstract

High-grade serous ovarian carcinoma (HGSC) is an aggressive malignancy for which bulk transcriptomic subtypes are used to stratify tumors, interpret biology, and guide biomarker development. The four TCGA-derived subtypes, mesenchymal (C1.MES), immunoreactive (C2.IMM), proliferative (C5.PRO), and differentiated (C4.DIF), are consistently observed across cohorts. However, despite their prominence, these subtypes have not translated into therapeutic utility, and their biological basis remains unresolved. Here, we show that HGSC transcriptomic subtypes are largely determined by tumor cellular composition rather than intrinsic malignant transcriptional programs. By integrating controlled single-cell-derived pseudobulk simulations with deconvolution-based analysis of 1,834 primary HGSC tumors across RNA-seq and microarray cohorts, we demonstrate that subtype probabilities align along a composition-driven axis of stromal and immune variation. Cellular composition alone predicted subtype labels with high accuracy (ROC-AUC = 0.81-0.95) and explained a substantial fraction of subtype-associated transcriptomic variation, with the mesenchymal (C1.MES) subtype representing the most robust and reproducible example of composition-driven signal. Although a secondary, composition-independent expression signal is detectable, it does not define the dominant structure of subtype classification. These findings redefine HGSC transcriptomic subtypes as features of the tumor ecosystem rather than discrete malignant states. This reinterpretation has immediate implications for studies that use subtype labels to infer tumor-intrinsic biology and provides a generalizable framework for separating composition-driven and intrinsic signals in bulk tumor data. Significance StatementHGSC transcriptomic subtypes lack consistent clinical utility and remain biologically ambiguous. We show subtype assignments are largely driven by tumor cellular composition, and less so by distinct intrinsic tumor states.

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Tanis, S., Lixandrao, M., Ivich, A., Grieshober, L., Lawson-Michod, K. A., Collin, L. J., Peres, L. C., Salas, L. A., Marks, J. R., Bitler, B. G., Greene, C. S., Schildkraut, J. M., Doherty, J. A., Davidson, N. R.. 2026-04-21. Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition. https://doi.org/10.64898/2026.04.16.719000

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