An integrated, transcript-resolution atlas of prostate cancer progression unmasks associations with oncogenic pathways

Zhang, J.; Lorenzi, C.; Bossi, D.; Nicastri, S.; Corpetti, M.; Formaggio, N.; Sgrignani, J.; Cavalli, A.; Bolis, M.; Theurillat, J.-P.

doi:10.64898/2026.09.18.752617

bioRxiv · 10.64898/2026.09.18.752617

An integrated, transcript-resolution atlas of prostate cancer progression unmasks associations with oncogenic pathways

Zhang, J.·Lorenzi, C.·Bossi, D.·Nicastri, S.·Corpetti, M.·Formaggio, N.·Sgrignani, J.·Cavalli, A.·Bolis, M.·Theurillat, J.-P.

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Abstract

Most genes produce multiple non-coding and coding RNA transcripts with potentially divergent biological functions, yet their contribution to cancer remains largely unexplored. Here, we built an integrated, transcript-resolution RNA sequencing atlas of prostate cancer spanning 1,140 clinical samples from 10 independent studies, covering the full range of disease progression from normal tissue to primary, hormone-sensitive, and castration-resistant disease. Cross-study integration removes technical batch effects while retaining the biological heterogeneity that distinguishes these disease states, a property we validate against long-read sequencing and leverage to place newly incorporated external cohorts within this disease-progression context. We describe transcript patterns of oncogenic and tumor-suppressive long non-coding RNAs along disease progression and identify 41 protein-coding genes with significant isoform switches in cancer-relevant pathways, including WNT2B, RNF43, RELA, BRCA1, ROCK2, and TRIM11. Finally, we provide the Prostate Cancer Atlas (www.prostatecanceratlas.org), an interactive web resource that lets researchers contextualize their own transcriptomic data against this atlas.

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Zhang, J., Lorenzi, C., Bossi, D., Nicastri, S., Corpetti, M., Formaggio, N., Sgrignani, J., Cavalli, A., Bolis, M., Theurillat, J.-P.. 2026-09-22. An integrated, transcript-resolution atlas of prostate cancer progression unmasks associations with oncogenic pathways. https://doi.org/10.64898/2026.09.18.752617

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