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Parry MA, Grist E, Mendes L, Dutey-Magni P, Sachdeva A, Brawley C, Murphy L, Proudfoot J, Lall S, Liu Y, Friedrich S, Ismail M, Hoyle A, Ali A, Haran A, Wingate A, Zakka L, Wetterskog D, Amos CL, Atako NB, Wang V, Rush HL, Jones RJ, Leung H, Cross WR, Gillessen S, Parker CC, Chowdhury S, Lotan T, Marafioti T, Urbanucci A, Schaeffer EM, Spratt DE, Waugh D, Powles T, Berney DM, Sydes MR, Parmar MK, Hamid AA, Feng FY, Sweeney CJ, Davicioni E, Clarke NW, James ND, Brown LC, Attard G. Clinical testing of transcriptome-wide expression profiles in high-risk localized and metastatic prostate cancer starting androgen deprivation therapy: an ancillary study of the STAMPEDE abiraterone Phase 3 trial. Res Sq 2023:rs.3.rs-2488586. [PMID: 36798177 PMCID: PMC9934744 DOI: 10.21203/rs.3.rs-2488586/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Metastatic and high-risk localized prostate cancer respond to hormone therapy but outcomes vary. Following a pre-specified statistical plan, we used Cox models adjusted for clinical variables to test associations with survival of multi-gene expression-based classifiers from 781 patients randomized to androgen deprivation with or without abiraterone in the STAMPEDE trial. Decipher score was strongly prognostic (p<2×10-5) and identified clinically-relevant differences in absolute benefit, especially for localized cancers. In metastatic disease, classifiers of proliferation, PTEN or TP53 loss and treatment-persistent cells were prognostic. In localized disease, androgen receptor activity was protective whilst interferon signaling (that strongly associated with tumor lymphocyte infiltration) was detrimental. Post-Operative Radiation-Therapy Outcomes Score was prognostic in localized but not metastatic disease (interaction p=0.0001) suggesting the impact of tumor biology on clinical outcome is context-dependent on metastatic state. Transcriptome-wide testing has clinical utility for advanced prostate cancer and identified worse outcomes for localized cancers with tumor-promoting inflammation.
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Affiliation(s)
| | - Emily Grist
- Cancer Institute, University College London; London, UK
| | | | - Peter Dutey-Magni
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Ashwin Sachdeva
- Genito-Urinary Cancer Research Group, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester; Manchester, UK
| | - Christopher Brawley
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Laura Murphy
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | | | | | | | | | | | - Alex Hoyle
- Genito-Urinary Cancer Research Group, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester; Manchester, UK
- Department of Surgery, The Christie and Salford Royal Hospitals; Manchester, UK
| | - Adnan Ali
- Genito-Urinary Cancer Research Group, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester; Manchester, UK
| | - Aine Haran
- Genito-Urinary Cancer Research Group, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester; Manchester, UK
- Department of Surgery, The Christie and Salford Royal Hospitals; Manchester, UK
| | - Anna Wingate
- Cancer Institute, University College London; London, UK
| | - Leila Zakka
- Cancer Institute, University College London; London, UK
| | | | - Claire L. Amos
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Nafisah B. Atako
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute; Boston, USA
| | - Hannah L. Rush
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Robert J. Jones
- University of Glasgow, Beatson West of Scotland Cancer Centre; Glasgow, UK
| | - Hing Leung
- University of Glasgow, Beatson West of Scotland Cancer Centre; Glasgow, UK
| | | | - Silke Gillessen
- Istituto Oncologico della Svizzera Italiana, EOC; Bellinzona, Switzerland
- Università della Svizzera Italiana; Lugano, Switzerland
| | - Chris C. Parker
- Royal Marsden NHS Foundation Trust and Institute of Cancer Research; London, UK
| | | | | | - Tamara Lotan
- Johns Hopkins University School of Medicine; Baltimore, USA
| | | | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital; Oslo, Norway
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital; Tampere, Finland
| | - Edward M. Schaeffer
- Department of Urology, Northwestern University Feinberg School of Medicine; Chicago, USA
| | - Daniel E. Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Comprehensive Cancer Center; Cleveland, USA
| | - David Waugh
- Queensland University of Technology; Brisbane, Australia
| | - Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London; London, UK
| | - Daniel M. Berney
- Barts Cancer Institute, Queen Mary University of London; London, UK
| | - Matthew R. Sydes
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Mahesh K.B. Parmar
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
| | - Anis A. Hamid
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, USA
| | - Felix Y. Feng
- University of California San Francisco; San Francisco, USA
| | | | | | - Noel W. Clarke
- Genito-Urinary Cancer Research Group, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester; Manchester, UK
- Department of Surgery, The Christie and Salford Royal Hospitals; Manchester, UK
| | - Nicholas D. James
- Royal Marsden NHS Foundation Trust and Institute of Cancer Research; London, UK
| | - Louise C. Brown
- MRC Clinical Trials Unit at University College London, Institute of Clinical Trials and Methodology, University College London; London, UK
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Zajaczkowski EL, Zhao QY, Zhang ZH, Li X, Wei W, Marshall PR, Leighton LJ, Nainar S, Feng C, Spitale RC, Bredy TW. Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide Profiling. ACS Chem Neurosci 2018; 9:1858-1865. [PMID: 29874042 PMCID: PMC6272126 DOI: 10.1021/acschemneuro.8b00197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcriptome-wide expression profiling of neurons has provided important insights into the underlying molecular mechanisms and gene expression patterns that transpire during learning and memory formation. However, there is a paucity of tools for profiling stimulus-induced RNA within specific neuronal cell populations. A bioorthogonal method to chemically label nascent (i.e., newly transcribed) RNA in a cell-type-specific and temporally controlled manner, which is also amenable to bioconjugation via click chemistry, was recently developed and optimized within conventional immortalized cell lines. However, its value within a more fragile and complicated cellular system such as neurons, as well as for transcriptome-wide expression profiling, has yet to be demonstrated. Here, we report the visualization and sequencing of activity-dependent nascent RNA derived from neurons using this labeling method. This work has important implications for improving transcriptome-wide expression profiling and visualization of nascent RNA in neurons, which has the potential to provide valuable insights into the mechanisms underlying neural plasticity, learning, and memory.
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Affiliation(s)
- Esmi L. Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Qiong-Yi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zong Hong Zhang
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiang Li
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wei Wei
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul R. Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Laura J. Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Chao Feng
- Department of Pharmaceutical Sciences
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences
- Department of Chemistry, University of California, Irvine, Irvine, California, 92697, United States
| | - Timothy W. Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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