1
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Kwan EM, Ng SWS, Tolmeijer SH, Emmett L, Sandhu S, Buteau JP, Iravani A, Joshua AM, Francis RJ, Subhash V, Lee ST, Scott AM, Martin AJ, Stockler MR, Donnellan G, Annala M, Herberts C, Davis ID, Hofman MS, Azad AA, Wyatt AW, TheraP Investigators and the ANZUP Cancer Trials Group. Lutetium-177-PSMA-617 or cabazitaxel in metastatic prostate cancer: circulating tumor DNA analysis of the randomized phase 2 TheraP trial. Nat Med 2025:10.1038/s41591-025-03704-9. [PMID: 40425844 DOI: 10.1038/s41591-025-03704-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Collaborators] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 04/07/2025] [Indexed: 05/29/2025]
Abstract
The prostate-specific membrane antigen (PSMA)-targeted radioligand [¹⁷⁷Lu]Lu-PSMA-617 is a new standard treatment for metastatic castration-resistant prostate cancer (mCRPC), but predictive genomic biomarkers informing its rational use are unknown. We performed detailed dissection of prostate cancer driver genes across 290 serial plasma cell-free DNA samples from 180 molecular imaging-selected patients with mCRPC from the randomized TheraP trial of [¹⁷⁷Lu]Lu-PSMA-617 (n = 97) versus cabazitaxel chemotherapy (n = 83). The primary endpoint was PSA50 biochemical response, with secondary endpoints of progression-free survival (PFS) and overall survival (OS). In this post-hoc biomarker analysis, a low pretreatment circulating tumor DNA (ctDNA) fraction predicted a superior biochemical response (100% versus 58%, P = 0.0067) and PFS (median 14.7 versus 6.0 months; hazard ratio 0.12, P = 2.5 × 10-4) on [¹⁷⁷Lu]Lu-PSMA-617 independent of predictive PSMA-positron emission tomography imaging parameters, although this benefit did not extend to OS. Deleterious PTEN alterations were associated with worse PFS and OS on cabazitaxel, whereas ATM defects were observed in select patients with favorable [¹⁷⁷Lu]Lu-PSMA-617 outcomes. Comparing pretreatment and progression ctDNA revealed population flux but no evidence that alterations in individual mCRPC genes (or FOLH1) are dominant causes of acquired [¹⁷⁷Lu]Lu-PSMA-617 or cabazitaxel resistance. Our results nominate new candidate biomarkers for [¹⁷⁷Lu]Lu-PSMA-617 selection and ultimately expand the mCRPC predictive biomarker repertoire. We anticipate our ctDNA fraction-aware analytical framework will aid future precision management strategies for [¹⁷⁷Lu]Lu-PSMA-617 and other PSMA-targeted therapeutics. ClinicalTrials.gov identifier: NCT03392428 .
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Affiliation(s)
- Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Eastern Health Clinical School, Monash University, Melbourne, Victoria, Australia
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sofie H Tolmeijer
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Louise Emmett
- Department of Theranostics and Nuclear Medicine, St Vincent's Hospital, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Shahneen Sandhu
- Prostate Cancer Theranostics and Imaging Centre of Excellence (ProsTIC), Molecular Imaging and Therapeutic Nuclear Medicine, Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - James P Buteau
- Prostate Cancer Theranostics and Imaging Centre of Excellence (ProsTIC), Molecular Imaging and Therapeutic Nuclear Medicine, Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amir Iravani
- Prostate Cancer Theranostics and Imaging Centre of Excellence (ProsTIC), Molecular Imaging and Therapeutic Nuclear Medicine, Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Division of Nuclear Medicine, Department of Radiology, University of Washington School of Medicine, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anthony M Joshua
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Medical Oncology, Kinghorn Cancer Centre, Sydney, New South Wales, Australia
| | - Roslyn J Francis
- Department of Nuclear Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Vinod Subhash
- Australian and New Zealand Urogenital and Prostate Cancer Trials Group (ANZUP), Sydney, New South Wales, Australia
| | - Sze-Ting Lee
- Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Andrew M Scott
- Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Andrew J Martin
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
- Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Martin R Stockler
- Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
- Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
| | - Gráinne Donnellan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Annala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ian D Davis
- Eastern Health Clinical School, Monash University, Melbourne, Victoria, Australia.
- Cancer Services, Eastern Health, Melbourne, Victoria, Australia.
| | - Michael S Hofman
- Prostate Cancer Theranostics and Imaging Centre of Excellence (ProsTIC), Molecular Imaging and Therapeutic Nuclear Medicine, Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Arun A Azad
- Prostate Cancer Theranostics and Imaging Centre of Excellence (ProsTIC), Molecular Imaging and Therapeutic Nuclear Medicine, Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
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Collaborators
Tim Akhurst, Ramin Alipour, Dale L Bailey, Patricia Banks, Alexis Beaulieu, Louise Campbell, Wei Chua, Megan Crumbaker, Nattakorn Dhiantravan, Kate Ford, Craig Gedye, Jeffrey C Goh, Alex D Guminski, Anis Hamid, Mohammad B Haskali, Rodney J Hicks, Edward Hsiao, Terry Hung, Ian D Kirkwood, Grace Kong, Ailsa Langford, Nicola Lawrence, Jeremy Lewin, Peter Lin, Michael McCarthy, Margaret M McJannett, William McDonald, Kate Moodie, Declan G Murphy, Siobhan Ng, Andrew Nguyen, David A Pattison, David Pook, Izabella Pokorski, Shakher Ramdave, Nisha Rana, Aravind S Ravi Kumar, Andrew D Redfern, Paul Roach, Peter Roselt, Natalie K Rutherford, Javad Saghebi, Geoffrey Schembri, Lavinia Spain, Shalini Subramaniam, Thean Hsiang Tan, Sue Ping Thang, Paul Thomas, Ben Tran, John A Violet, Roslyn Wallace, Andrew Weickhardt, Scott G Williams, Sonia Yip, Alison Y Zhang,
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2
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Lawrence MG, Keerthikumar S, Townley SL, Clark AK, Cuffe GB, Laven-Law G, Hanson AR, Shrestha RK, Knutson TP, Richards MG, Teng L, Choo N, Crumbaker M, Joshua AM, Corey E, Nelson PS, Dehm SM, Risbridger GP, Tilley WD, Hickey TE, Taylor RA, Selth LA. Reprogramming of Androgen Receptor Activity in Castration-resistant Prostate Cancer is Shaped by Truncated Variants. Eur Urol Focus 2025:S2405-4569(25)00073-2. [PMID: 40221372 DOI: 10.1016/j.euf.2025.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Accepted: 03/20/2025] [Indexed: 04/14/2025]
Abstract
BACKGROUND AND OBJECTIVE Under the selective pressure of treatment, prostate cancer cells express constitutively active androgen receptor (AR) variants. Whether AR variants mediate therapy resistance remains contested, because they are often coexpressed with abundant full-length AR. Therefore, we sought to determine how truncated variants shape AR chromatin occupancy and responses to treatments in both the presence and absence of full-length AR. METHODS We used a cohort of patient-derived xenografts of metastatic prostate cancer with diverse AR alterations. Chromatin immunoprecipitation and RNA sequencing were used to compare the landscape of AR binding and transcriptomic features. We assessed responses to castration by castrating host mice and evaluated responses to bipolar androgen therapy by administering testosterone cypionate. KEY FINDINGS AND LIMITATIONS By profiling the AR cistrome, we identified a distinct group of tumours defined by ARv567es expression, a variant arising due to structural rearrangements of the AR gene. ARv567es-positive tumours also had a distinct epigenomic profile and altered transcriptional features, including loss of canonical AR-regulated gene signatures and elevated expression of AR-repressed genes. ARv567es-positive tumours were resistant to castration and bipolar androgen therapy. In tumours that coexpress full-length AR, this involves dampened transcriptional responses and disruption of the autoregulatory loop that modulates AR levels. Study limitations include the need for additional models of AR-driven prostate cancer. CONCLUSIONS AND CLINICAL IMPLICATIONS The emergence of ARv567es via gene rearrangements causes transcriptional reprogramming and therapy resistance. This highlights ARv567es as a potential as a marker to guide treatment decisions.
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Affiliation(s)
- Mitchell G Lawrence
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia; Cabrini Institute, Cabrini Health, Malvern, Australia; Melbourne Urological Research Alliance, Monash University, Clayton, Australia.
| | - Shivakumar Keerthikumar
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Scott L Townley
- Flinders University College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, Australia
| | - Ashlee K Clark
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Georgia B Cuffe
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Geraldine Laven-Law
- Flinders University College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, Australia; Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Adrienne R Hanson
- Flinders University College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, Australia
| | - Raj K Shrestha
- Flinders University College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, Australia
| | - Todd P Knutson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Michelle G Richards
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Linda Teng
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Nicholas Choo
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Megan Crumbaker
- Garvan Institute of Medical Research, Sydney, Australia; St. Vincent's Clinical School, UNSW Australia, Sydney, Australia; The Kinghorn Cancer Centre, St. Vincent's Hospital, Sydney, Australia
| | - Anthony M Joshua
- Garvan Institute of Medical Research, Sydney, Australia; St. Vincent's Clinical School, UNSW Australia, Sydney, Australia; The Kinghorn Cancer Centre, St. Vincent's Hospital, Sydney, Australia
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Scott M Dehm
- Masonic Cancer Center and Departments of Laboratory Medicine and Pathology and of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Gail P Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia; Cabrini Institute, Cabrini Health, Malvern, Australia; Melbourne Urological Research Alliance, Monash University, Clayton, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Renea A Taylor
- Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia; Cabrini Institute, Cabrini Health, Malvern, Australia; Melbourne Urological Research Alliance, Monash University, Clayton, Australia; Department of Physiology, Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, Australia
| | - Luke A Selth
- Flinders University College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, Australia; Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia.
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3
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Nauseef JT, Chu TR, Hooper WF, Alonso A, Oku A, Geiger H, Goldstein ZR, Shah M, Sigouros M, Manohar J, Steinsnyder Z, Winterkorn L, Robinson BD, Sboner A, Beltran H, Elemento O, Hajirasouliha I, Imielinski M, Nanus DM, Tagawa ST, Robine N, Mosquera JM. A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer. NPJ Precis Oncol 2025; 9:91. [PMID: 40155466 PMCID: PMC11953479 DOI: 10.1038/s41698-025-00854-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 02/25/2025] [Indexed: 04/01/2025] Open
Abstract
Aggressive variant and androgen receptor (AR)-independent castration resistant prostate cancers (CRPC) represent the most significant diagnostic and therapeutic challenges in prostate cancer. This study examined a case of simultaneous progression of both adenocarcinoma and squamous tumors from the same common origin. Using whole-genome and transcriptome sequencing from 17 samples collected over >6 years, we established the clonal relationship of all samples, defined shared complex structural variants, and demonstrated both divergent and convergent evolution at AR. Squamous CRPC-associated circulating tumor DNA was identified at clinical progression prior to biopsy detection of any squamous differentiation. Dynamic changes in the detection rate of histology-specific clones in circulation reflected histology-specific sensitivity to treatment. This dataset serves as an illustration of non-neuroendocrine transdifferentiation and highlights the importance of serial sampling at progression in CRPC for the detection of emergent non-adenocarcinoma histologies with implications for the treatment of lineage plasticity and transdifferentiation in metastatic CRPC.
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Affiliation(s)
- Jones T Nauseef
- Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | | | | | - Alicia Alonso
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ali Oku
- New York Genome Center, New York, NY, USA
| | | | | | | | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Brian D Robinson
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrea Sboner
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Iman Hajirasouliha
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Marcin Imielinski
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David M Nanus
- Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott T Tagawa
- Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Juan Miguel Mosquera
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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4
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Van Goubergen J, Peřina M, Handle F, Morales E, Kremer A, Schmidt O, Kristiansen G, Cronauer MV, Santer FR. Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression. Mol Oncol 2025; 19:496-518. [PMID: 39258426 PMCID: PMC11792998 DOI: 10.1002/1878-0261.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/12/2024] Open
Abstract
In advanced prostate cancer (PC), in particular after acquisition of resistance to androgen receptor (AR) signaling inhibitors (ARSI), upregulation of AR splice variants compromises endocrine therapy efficiency. Androgen receptor splice variant-7 (ARV7) is clinically the most relevant and has a distinct 3' untranslated region (3'UTR) compared to the AR full-length variant, suggesting a unique post-transcriptional regulation. Here, we set out to evaluate the applicability of the ARV7 3'UTR as a therapy target. A common single nucleotide polymorphism, rs5918762, was found to affect the splicing rate and thus the expression of ARV7 in cellular models and patient specimens. Serine/arginine-rich splicing factor 9 (SRSF9) was found to bind to and increase the inclusion of the cryptic exon 3 of ARV7 during the splicing process in the alternative C allele of rs5918762. The dual specificity protein kinase CLK2 interferes with the activity of SRSF9 by regulating its expression. Inhibition of the Cdc2-like kinase (CLK) family by the small molecules cirtuvivint or lorecivivint results in the decreased expression of ARV7. Both inhibitors show potent anti-proliferative effects in enzalutamide-treated or -naive PC models. Thus, targeting aberrant alternative splicing at the 3'UTR of ARV7 by disturbing the CLK2/SRSF9 axis might be a valuable therapeutic approach in late stage, ARSI-resistant PC.
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Affiliation(s)
- Jasper Van Goubergen
- Division of Experimental Urology, Department of UrologyMedical University of InnsbruckAustria
| | - Miroslav Peřina
- Division of Experimental Urology, Department of UrologyMedical University of InnsbruckAustria
- Department of Experimental Biology, Faculty of SciencePalacký University OlomoucCzech Republic
| | - Florian Handle
- Institute of Pathology, Neuropathology & Molecular PathologyMedical University of InnsbruckAustria
| | - Elisa Morales
- Division of Experimental Urology, Department of UrologyMedical University of InnsbruckAustria
| | - Anika Kremer
- Institute of PathologyUniversity Hospital BonnGermany
| | - Oliver Schmidt
- Institute of Cell Biology, BiocenterMedical University of InnsbruckAustria
| | | | | | - Frédéric R. Santer
- Division of Experimental Urology, Department of UrologyMedical University of InnsbruckAustria
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5
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Raval H, Bhattacharya S. Early Detection, Precision Treatment, Recurrence Monitoring: Liquid Biopsy Transforms Colorectal Cancer Therapy. Curr Cancer Drug Targets 2025; 25:586-619. [PMID: 38623975 DOI: 10.2174/0115680096295070240318075023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 04/17/2024]
Abstract
Colorectal cancer (CRC) is a significant global health concern. We need ways to detect it early and determine the best treatments. One promising method is liquid biopsy, which uses cancer cells and other components in the blood to help diagnose and treat the disease. Liquid biopsies focus on three key elements: circulating tumor DNA (ctDNA), circulating microRNA (miRNA), and circulating tumor cells (CTC). By analyzing these elements, we can identify CRC in its early stages, predict how well a treatment will work, and even spot signs of cancer returning. This study investigates the world of liquid biopsy, a rapidly growing field. We want to understand how it can help us better recognize the molecular aspects of cancer, improve and diagnostics, tailor treatments to individual patients, and keep track of the disease over the long-term. We explored specific components of liquid biopsy, like extracellular vesicles and cell-free DNA, and how they are used to detect CRC. This review sheds light on the current state of knowledge and the many ways a liquid biopsy can be used in treating colorectal cancer. It can transform patient care, disease management, and clinical outcomes by offering non-invasive cancer-targeting solutions.
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Affiliation(s)
- Harshvardhan Raval
- Department of Pharmaceutics, School of Pharmacy and Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra, 425405, India
| | - Sankha Bhattacharya
- Department of Pharmaceutics, School of Pharmacy and Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra, 425405, India
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6
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Knutson TP, Luo B, Kobilka A, Lyman J, Guo S, Munro SA, Li Y, Heer R, Gaughan L, Morris MJ, Beltran H, Ryan CJ, Antonarakis ES, Armstrong AJ, Halabi S, Dehm SM. AR alterations inform circulating tumor DNA detection in metastatic castration resistant prostate cancer patients. Nat Commun 2024; 15:10648. [PMID: 39663356 PMCID: PMC11634963 DOI: 10.1038/s41467-024-54847-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 11/21/2024] [Indexed: 12/13/2024] Open
Abstract
Circulating tumor DNA (ctDNA) in plasma cell free DNA (cfDNA) of cancer patients is associated with poor prognosis, but is challenging to detect from low plasma volumes. In metastatic castration-resistant prostate cancer (mCRPC), ctDNA assays are needed to prognosticate outcomes of patients treated with androgen receptor (AR) inhibitors. We develop a custom targeted cfDNA sequencing assay, named AR-ctDETECT, to detect ctDNA in limiting plasma cfDNA available from mCRPC patients in the Alliance A031201 randomized phase 3 trial of enzalutamide with or without abiraterone. Of 776 patients, 59% are ctDNA-positive, with 26% having high ctDNA aneuploidy and 33% having low ctDNA aneuploidy but displaying AR gain or structural rearrangement, MYC/MYCN gain, or a pathogenic mutation. ctDNA-positive patients have significantly worse median overall survival than ctDNA-negative patients (29.0 months vs. 47.4 months, respectively). Here, we show that mCRPC patients identified as ctDNA-positive using the AR-ctDETECT assay have poor survival despite treatment with potent AR inhibitors in a phase 3 trial.
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Affiliation(s)
- Todd P Knutson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Bin Luo
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Anna Kobilka
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Jacqueline Lyman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Molecular, Cellular, and Developmental Biology and Genetics, University of Minnesota, Minneapolis, MN, USA
| | - Siyuan Guo
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Sarah A Munro
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Yingming Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Rakesh Heer
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Tyne and Wear, UK
- Translational and Clinical Research Institute, NU Cancer, Newcastle upon Tyne, Tyne and Wear, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, NU Cancer, Newcastle upon Tyne, Tyne and Wear, UK
| | - Michael J Morris
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Emmanuel S Antonarakis
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Andrew J Armstrong
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC, USA
| | - Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
- Department of Urology, University of Minnesota, Minneapolis, MN, USA.
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7
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De Laere B, Crippa A, Discacciati A, Larsson B, Persson M, Johansson S, D'hondt S, Bergström R, Chellappa V, Mayrhofer M, Banijamali M, Kotsalaynen A, Schelstraete C, Vanwelkenhuyzen JP, Hjälm-Eriksson M, Pettersson L, Ullén A, Lumen N, Enblad G, Thellenberg Karlsson C, Jänes E, Sandzén J, Schatteman P, Nyre Vigmostad M, Olsson M, Ghysel C, Sautois B, De Roock W, Van Bruwaene S, Anden M, Verbiene I, De Maeseneer D, Everaert E, Darras J, Aksnessether BY, Luyten D, Strijbos M, Mortezavi A, Oldenburg J, Ost P, Eklund M, Grönberg H, Lindberg J. Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial. Nat Med 2024; 30:3291-3302. [PMID: 39164518 PMCID: PMC11564108 DOI: 10.1038/s41591-024-03204-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
ProBio is the first outcome-adaptive platform trial in prostate cancer utilizing a Bayesian framework to evaluate efficacy within predefined biomarker signatures across systemic treatments. Prospective circulating tumor DNA and germline DNA analysis was performed in patients with metastatic castration-resistant prostate cancer before randomization to androgen receptor pathway inhibitors (ARPIs), taxanes or a physician's choice control arm. The primary endpoint was the time to no longer clinically benefitting (NLCB). Secondary endpoints included overall survival and (serious) adverse events. Upon reaching the time to NLCB, patients could be re-randomized. The primary endpoint was met after 218 randomizations. ARPIs demonstrated ~50% longer time to NLCB compared to taxanes (median, 11.1 versus 6.9 months) and the physician's choice arm (median, 11.1 versus 7.4 months) in the biomarker-unselected or 'all' patient population. ARPIs demonstrated longer overall survival (median, 38.7 versus 21.7 and 21.8 months for taxanes and physician's choice, respectively). Biomarker signature findings suggest that the largest increase in time to NLCB was observed in AR (single-nucleotide variant/genomic structural rearrangement)-negative and TP53 wild-type patients and TMPRSS2-ERG fusion-positive patients, whereas no difference between ARPIs and taxanes was observed in TP53-altered patients. In summary, ARPIs outperform taxanes and physician's choice treatment in patients with metastatic castration-resistant prostate cancer with detectable circulating tumor DNA. ClinicalTrials.gov registration: NCT03903835 .
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Affiliation(s)
- Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Alessio Crippa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Discacciati
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Berit Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Persson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Johansson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sanne D'hondt
- Health, Innovation and Research Institute (Clinical Trial Unit), University Hospital Ghent, Ghent, Belgium
| | - Rebecka Bergström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Markus Mayrhofer
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mahsan Banijamali
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anastasijia Kotsalaynen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Jan Pieter Vanwelkenhuyzen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | | | - Linn Pettersson
- Department of Oncology, Länssjukhuset Ryhov, Jönköping, Sweden
| | - Anders Ullén
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Nicolaas Lumen
- Department of Urology, University Hospital Ghent, Ghent, Belgium
| | - Gunilla Enblad
- Department of Oncology, Uppsala University Hospital, Uppsala, Sweden
| | | | - Elin Jänes
- Department of Oncology, Sundsvalls sjukhus, Sundsvall, Sweden
| | - Johan Sandzén
- Department of Oncology, Centralsjukhuset Karlstad, Karlstad, Sweden
| | - Peter Schatteman
- Department of Urology, Onze Lieve Vrouwziekenhuis, Aalst, Belgium
| | | | - Martha Olsson
- Department of Oncology, Centrallasarettet Växjö, Växjö, Sweden
| | | | - Brieuc Sautois
- Department of Oncology, CHU de Liège - site Sart Tilman, Liège, Belgium
| | - Wendy De Roock
- Department of Oncology, Ziekenhuis Oost- Limburg, Genk, Belgium
| | | | - Mats Anden
- Department of Oncology, Länssjukhuset i Kalmar, Kalmar, Sweden
| | | | | | - Els Everaert
- Department of Oncology, Vitaz campus Sint-Niklaas Lodewijk, Sint-Niklaas, Belgium
| | - Jochen Darras
- Department of Urology, AZ Damiaan, Oostende, Belgium
| | | | - Daisy Luyten
- Department of Oncology, Virga Jessa, Hasselt, Belgium
| | | | - Ashkan Mortezavi
- Department of Urology, Universitätsspital Basel, Basel, Switzerland
- Department of Urology, Universitätsspital Zürich, Zürich, Switzerland
| | - Jan Oldenburg
- Department of Oncology, Akershus University Hospital, Nordbyhagen, Norway
| | - Piet Ost
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Department of Radiation Oncology, GZA Sint-Augustinus, Antwerpen, Belgium
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Prostatacancer Centrum, Capio S:t Görans Sjukhus, Stockholm, Sweden.
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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8
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Liu S, Garcia-Marques FJ, Shen M, Bermudez A, Pitteri SJ, Stoyanova T. Ubiquitin C-terminal hydrolase L1 is a regulator of tumor growth and metastasis in double-negative prostate cancer. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2024; 12:306-322. [PMID: 39584005 PMCID: PMC11578776 DOI: 10.62347/jnbr1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 10/15/2024] [Indexed: 11/26/2024]
Abstract
Prostate cancer is the second leading cause of cancer-related deaths among men worldwide. With heavy androgen deprivation therapies, prostate cancer may shift to androgen receptor negative and neuroendocrine negative subtype of castration resistant prostate cancer, defined as double-negative prostate cancer. Double-negative prostate cancer is associated with poor prognosis and disease mortality. The molecular mechanisms underlying the emergence of double-negative prostate cancer remain poorly understood. Here, we demonstrate that Ubiquitin C-Terminal Hydrolase L1 (UCH-L1), is negatively correlated with androgen receptor levels in prostate cancer patients. UCH-L1 plays a functional role in tumorigenesis and metastasis in double-negative prostate cancer. Knock-down of UCH-L1 decreases double-negative prostate cancer colony formation in vitro and tumor growth in vivo. Moreover, decrease of UCH-L1 significantly delays cell migration in vitro and spontaneous metastasis and metastatic colonization in vivo. Proteomic analysis revealed that mTORC1 signaling, androgen response signaling and MYC targets are the top three decreased pathways upon UCH-L1 decrease. Further, treatment with LDN-57444, a UCH-L1 small molecule inhibitor, impairs double-negative prostate cancer cell colony formation, migration in vitro, and metastatic colonization in vivo. Our study reveals that UCH-L1 is an important regulator of double-negative prostate cancer tumor growth and progression, providing a promising therapeutic target for this subtype of metastatic prostate cancer.
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Affiliation(s)
- Shiqin Liu
- Department of Molecular and Medical Pharmacology, University of California, Los AngelesLos Angeles, CA, USA
| | | | - Michelle Shen
- Department of Molecular and Medical Pharmacology, University of California, Los AngelesLos Angeles, CA, USA
| | - Abel Bermudez
- Department of Radiology, Stanford UniversityPalo Alto, CA, USA
| | | | - Tanya Stoyanova
- Department of Molecular and Medical Pharmacology, University of California, Los AngelesLos Angeles, CA, USA
- Department of Urology, University of California, Los AngelesLos Angeles, CA, USA
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9
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Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, Lack NA, Zwart W, Quigley DA, van der Heijden MS, Feng FY. Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. J Clin Invest 2024; 134:e178604. [PMID: 39352383 PMCID: PMC11444163 DOI: 10.1172/jci178604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 08/06/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUNDAndrogen receptor signaling inhibitors (ARSIs) have improved outcomes for patients with metastatic castration-resistant prostate cancer (mCRPC), but their clinical benefit is limited by treatment resistance.METHODSTo investigate the mechanisms of ARSI resistance, we analyzed the whole-genome (n = 45) and transcriptome (n = 31) sequencing data generated from paired metastatic biopsies obtained before initiation of first-line ARSI therapy for mCRPC and after radiographic disease progression. We investigated the effects of genetic and pharmacologic modulation of SSTR1 in 22Rv1 cells, a representative mCRPC cell line.RESULTSWe confirmed the predominant role of tumor genetic alterations converging on augmenting androgen receptor (AR) signaling and the increased transcriptional heterogeneity and lineage plasticity during the emergence of ARSI resistance. We further identified amplifications involving a putative enhancer downstream of the AR and transcriptional downregulation of SSTR1, encoding somatostatin receptor 1, in ARSI-resistant tumors. We found that patients with SSTR1-low mCRPC tumors derived less benefit from subsequent ARSI therapy in a retrospective cohort. We showed that SSTR1 was antiproliferative in 22Rv1 cells and that the FDA-approved drug pasireotide suppressed 22Rv1 cell proliferation.CONCLUSIONOur findings expand the knowledge of ARSI resistance and point out actionable next steps, exemplified by potentially targeting SSTR1, to improve patient outcomes.FUNDINGNational Cancer Institute (NCI), NIH; Prostate Cancer Foundation; Conquer Cancer, American Society of Clinical Oncology Foundation; UCSF Benioff Initiative for Prostate Cancer Research; Netherlands Cancer Institute.
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MESH Headings
- Male
- Humans
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Cell Line, Tumor
- Signal Transduction/drug effects
- Transcriptome
- Neoplasm Metastasis
- Receptors, Somatostatin/genetics
- Receptors, Somatostatin/metabolism
- Gene Expression Regulation, Neoplastic/drug effects
- Androgen Receptor Antagonists/pharmacology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
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Affiliation(s)
- Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Tatyanah Farsh
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Daniël Vis
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Yu
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Tianyi Liu
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Thaidy Moreno Rodriguez
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | - Alana S. Weinstein
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rahul R. Aggarwal
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Andries M. Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Division of Hematology and Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Nathan A. Lack
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Koç University School of Medicine, Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Urology, UCSF, San Francisco, California, USA
| | | | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Department of Radiation Oncology, UCSF, San Francisco, California, USA
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10
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Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet 2024; 56:1689-1700. [PMID: 39020220 PMCID: PMC11319208 DOI: 10.1038/s41588-024-01826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2-ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.
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Grants
- R01 CA270539 NCI NIH HHS
- R01 CA276269 NCI NIH HHS
- R01 CA174777 NCI NIH HHS
- P50 CA097186 NCI NIH HHS
- 1DP2CA271832-01, P30 CA014520 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- DP2 CA271832 NCI NIH HHS
- P50 CA186786 NCI NIH HHS
- R01 CA282005 NCI NIH HHS
- R01 CA251245, P50 CA097186, P50 CA186786, P50 CA186786-07S1, P30 CA046592, and W81XWH-20-1-0405 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- P30 CA046592 NCI NIH HHS
- R01 CA251245 NCI NIH HHS
- P30 CA014520 NCI NIH HHS
- W81XWH2010799 U.S. Department of Defense (United States Department of Defense)
- W81XWH-21-1-0046 U.S. Department of Defense (United States Department of Defense)
- SU2C-AACR-DT0812 EIF | Stand Up To Cancer (SU2C)
- Prostate Cancer Foundation (PCF)
- UCSF Benioff Initiative for Prostate Cancer Research
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- Canadian Institute of Health Research (CIHR) (FRN-153234 & 168933), the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) (FRN-158225), the Ontario Institute for Cancer Research (OICR) through funding provided by the Government of Ontario (IA 031), and the Princess Margaret Cancer Foundation.
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Affiliation(s)
- Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Madison, WI, USA
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Thaidy Moreno-Rodriguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Arian Lundberg
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Chu Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James R Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alana S Weinstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas R Rydzewski
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly Lynch
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshi J Alumkal
- Department of Internal Medicine, Division of Hematology-Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Hansen H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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11
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Miyahira AK, Kamran SC, Jamaspishvili T, Marshall CH, Maxwell KN, Parolia A, Zorko NA, Pienta KJ, Soule HR. Disrupting prostate cancer research: Challenge accepted; report from the 2023 Coffey-Holden Prostate Cancer Academy Meeting. Prostate 2024; 84:993-1015. [PMID: 38682886 DOI: 10.1002/pros.24721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION The 2023 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, themed "Disrupting Prostate Cancer Research: Challenge Accepted," was convened at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA, from June 22 to 25, 2023. METHODS The 2023 marked the 10th Annual CHPCA Meeting, a discussion-oriented scientific think-tank conference convened annually by the Prostate Cancer Foundation, which centers on innovative and emerging research topics deemed pivotal for advancing critical unmet needs in prostate cancer research and clinical care. The 2023 CHPCA Meeting was attended by 81 academic investigators and included 40 talks across 8 sessions. RESULTS The central topic areas covered at the meeting included: targeting transcription factor neo-enhancesomes in cancer, AR as a pro-differentiation and oncogenic transcription factor, why few are cured with androgen deprivation therapy and how to change dogma to cure metastatic prostate cancer without castration, reducing prostate cancer morbidity and mortality with genetics, opportunities for radiation to enhance therapeutic benefit in oligometastatic prostate cancer, novel immunotherapeutic approaches, and the new era of artificial intelligence-driven precision medicine. DISCUSSION This article provides an overview of the scientific presentations delivered at the 2023 CHPCA Meeting, such that this knowledge can help in facilitating the advancement of prostate cancer research worldwide.
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Affiliation(s)
- Andrea K Miyahira
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Jamaspishvili
- Department of Pathology and Laboratory Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Catherine H Marshall
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kara N Maxwell
- Department of Medicine-Hematology/Oncology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medicine Service, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Abhijit Parolia
- Department of Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas A Zorko
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- University of Minnesota Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
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12
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Valentín López JC, Lange CA, Dehm SM. Androgen receptor and estrogen receptor variants in prostate and breast cancers. J Steroid Biochem Mol Biol 2024; 241:106522. [PMID: 38641298 PMCID: PMC11139604 DOI: 10.1016/j.jsbmb.2024.106522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/23/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The androgen receptor (AR) and estrogen receptor alpha (ERα) are steroid receptor transcription factors with critical roles in the development and progression of prostate and breast cancers. Advances in the understanding of mechanisms underlying the ligand-dependent activation of these transcription factors have contributed to the development of small molecule inhibitors that block AR and ERα actions. These inhibitors include competitive antagonists and degraders that directly bind the ligand binding domains of these receptors, luteinizing hormone releasing hormone (LHRH) analogs that suppress gonadal synthesis of testosterone or estrogen, and drugs that block specific enzymes required for biosynthesis of testosterone or estrogen. However, resistance to these therapies is frequent, and is often driven by selection for tumor cells with alterations in the AR or ESR1 genes and/or alternatively spliced AR or ESR1 mRNAs that encode variant forms AR or ERα. While most investigations involving AR have been within the context of prostate cancer, and the majority of investigations involving ERα have been within the context of breast cancer, important roles for AR have been elucidated in breast cancer, and important roles for ERα have been elucidated in prostate cancer. Here, we will discuss the roles of AR and ERα in breast and prostate cancers, outline the effects of gene- and mRNA-level alterations in AR and ESR1 on progression of these diseases, and identify strategies that are being developed to target these alterations therapeutically.
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Affiliation(s)
| | - Carol A Lange
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Medicine-Hematology, Oncology & Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA; Department of Urology, University of Minnesota, Minneapolis, MN, USA.
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