Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression.

Comprehensive genomic studies have delineated key driver mutations linked to disease progression for most cancers. However, corresponding transcriptional changes remain largely elusive because of the bias associated with cross-study analysis. Here, we overcome these hurdles and generate a comprehensive prostate cancer transcriptome atlas that describes the roadmap to tumor progression in a qualitative and quantitative manner. Most cancers follow a uniform trajectory characterized by upregulation of polycomb-repressive-complex-2, G2-M checkpoints, and M2 macrophage polarization. Using patient-derived xenograft models, we functionally validate our observations and add single-cell resolution. Thereby, we show that tumor progression occurs through transcriptional adaption rather than a selection of pre-existing cancer cell clusters. Moreover, we determine at the single-cell level how inhibition of EZH2 - the top upregulated gene along the trajectory - reverts tumor progression and macrophage polarization. Finally, a user-friendly web-resource is provided enabling the investigation of dynamic transcriptional perturbations linked to disease progression.

Nature communications. 2021 Dec 02*** epublish ***

Marco Bolis, Daniela Bossi, Arianna Vallerga, Valentina Ceserani, Manuela Cavalli, Daniela Impellizzieri, Laura Di Rito, Eugenio Zoni, Simone Mosole, Angela Rita Elia, Andrea Rinaldi, Ricardo Pereira Mestre, Eugenia D'Antonio, Matteo Ferrari, Flavio Stoffel, Fernando Jermini, Silke Gillessen, Lukas Bubendorf, Peter Schraml, Arianna Calcinotto, Eva Corey, Holger Moch, Martin Spahn, George Thalmann, Marianna Kruithof-de Julio, Mark A Rubin, Jean-Philippe P Theurillat

Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI, 6500, Switzerland. ., Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI, 6500, Switzerland., Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, 20156, Milano, Italy., Department of Biomedical Research, University of Bern, 3008, Bern, Switzerland., Oncology Institute of Southern Switzerland, Bellinzona, TI, 6500, Switzerland., Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI, Switzerland., Institute of Surgical Pathology, University Hospital Basel, 4031, Basel, Switzerland., Department of Pathology, University Hospital Zurich, 8091, Zurich, Switzerland., Department of Urology, University of Washington, Seattle, WA, 98195, USA., Lindenhofspital Bern, Prostate Center Bern, 3012, Bern, Switzerland., Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI, 6500, Switzerland. .

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