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Bolis M, Bossi D, Vallerga A, Ceserani V, Cavalli M, Impellizzieri D, Di Rito L, Zoni E, Mosole S, Elia AR, Rinaldi A, Pereira Mestre R, D’Antonio E, Ferrari M, Stoffel F, Jermini F, Gillessen S, Bubendorf L, Schraml P, Calcinotto A, Corey E, Moch H, Spahn M, Thalmann G, Kruithof-de Julio M, Rubin MA, Theurillat JPP. Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Nat Commun 2021; 12:7033. [PMID: 34857732 PMCID: PMC8640014 DOI: 10.1038/s41467-021-26840-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Marco Bolis
- 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. .,Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI, 6500, Bellinzona, Switzerland.
| | - Daniela Bossi
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Arianna Vallerga
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland ,grid.419765.80000 0001 2223 3006Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI 6500 Bellinzona, Switzerland
| | - Valentina Ceserani
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Manuela Cavalli
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Daniela Impellizzieri
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Laura Di Rito
- grid.4527.40000000106678902Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche ‘Mario Negri’ IRCCS, 20156 Milano, Italy
| | - Eugenio Zoni
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Simone Mosole
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Angela Rita Elia
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Andrea Rinaldi
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Ricardo Pereira Mestre
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland
| | - Eugenia D’Antonio
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland
| | - Matteo Ferrari
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Flavio Stoffel
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Fernando Jermini
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Silke Gillessen
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland ,grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, University of Southern Switzerland (USI), TI 6900 Lugano, Switzerland
| | - Lukas Bubendorf
- grid.410567.1Institute of Surgical Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Peter Schraml
- grid.412004.30000 0004 0478 9977Department of Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Arianna Calcinotto
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Eva Corey
- grid.34477.330000000122986657Department of Urology, University of Washington, Seattle, WA 98195 USA
| | - Holger Moch
- grid.412004.30000 0004 0478 9977Department of Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Martin Spahn
- grid.415941.c0000 0004 0509 4333Lindenhofspital Bern, Prostate Center Bern, 3012 Bern, Switzerland
| | - George Thalmann
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Urology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Urology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland
| | - Mark A. Rubin
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Bern Center for Precision Medicine, University of Bern and Inselspital, 3012 Bern, Switzerland
| | - Jean-Philippe P. Theurillat
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
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Theurillat JPP, Udeshi ND, Errington WJ, Svinkina T, Baca SC, Pop M, Wild PJ, Blattner M, Groner AC, Rubin MA, Moch H, Prive GG, Carr SA, Garraway LA. Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer. Science 2014; 346:85-89. [PMID: 25278611 PMCID: PMC4257137 DOI: 10.1126/science.1250255] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cancer genome characterization has revealed driver mutations in genes that govern ubiquitylation; however, the mechanisms by which these alterations promote tumorigenesis remain incompletely characterized. Here, we analyzed changes in the ubiquitin landscape induced by prostate cancer-associated mutations of SPOP, an E3 ubiquitin ligase substrate-binding protein. SPOP mutants impaired ubiquitylation of a subset of proteins in a dominant-negative fashion. Of these, DEK and TRIM24 emerged as effector substrates consistently up-regulated by SPOP mutants. We highlight DEK as a SPOP substrate that exhibited decreases in ubiquitylation and proteasomal degradation resulting from heteromeric complexes of wild-type and mutant SPOP protein. DEK stabilization promoted prostate epithelial cell invasion, which implicated DEK as an oncogenic effector. More generally, these results provide a framework to decipher tumorigenic mechanisms linked to dysregulated ubiquitylation.
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Affiliation(s)
- Jean-Philippe P. Theurillat
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Wesley J. Errington
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2M9. Canada
| | - Tanya Svinkina
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sylvan C. Baca
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Marius Pop
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Peter J. Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, ZH 8091, Switzerland
| | - Mirjam Blattner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Anna C. Groner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mark A. Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA
- Institute for Precision Medicine of Weill Cornell and New York Presbyterian Hospital, New York, NY 10065
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, ZH 8091, Switzerland
| | - Gilbert G. Prive
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2M9. Canada
| | - Steven A. Carr
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Levi A. Garraway
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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