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Urabe F, Sumiyoshi T, Tashiro K, Goto T, Kimura T, Kobayashi T. Prostate cancer and liquid biopsies: Clinical applications and challenges. Int J Urol 2024; 31:617-626. [PMID: 38551314 DOI: 10.1111/iju.15441] [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: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 06/06/2024]
Abstract
Liquid biopsy has emerged as a valuable and minimally invasive tool for real-time detection of clinically actionable abnormalities across various cancer types. Its applicability is particularly compelling in the realm of prostate cancer, where novel therapeutic agents, including those targeting DNA repair systems, are under development. Despite these advancements, challenges persist in effectively screening for prostate cancer, enhancing risk stratification, and determining optimal approaches for treating advanced disease. Consequently, there is a pressing need for improved biomarkers to aid clinicians in decision-making within these contexts. Cell-free DNA and extracellular vesicle analysis have demonstrated promise in diagnosis, prognostication, assessment of treatment responses, and identification of emerging mechanisms of resistance. Nevertheless, obstacles must be addressed before liquid biopsies can be integrated into routine clinical practice. These challenges encompass preanalytical considerations such as sample collection and storage, methods of extracellular vesicle isolation and enrichment, and the need for enhanced interpretation of generated sequencing data. This review provides a comprehensive overview of current clinical opportunities in managing prostate cancer through blood-based liquid biopsy, highlighting the progress made, and acknowledging the challenges that remain. Additionally, we discuss the next steps required for the effective implementation of liquid biopsies in guiding personalized treatment strategies for prostate cancer.
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Affiliation(s)
- Fumihiko Urabe
- Department of Urology, The Jikei University School of Medicine, Minato City, Tokyo, Japan
| | - Takayuki Sumiyoshi
- Department of Urology, Kyoto University School of Medicine, Kyoto, Japan
| | - Kojiro Tashiro
- Department of Urology, The Jikei University School of Medicine, Minato City, Tokyo, Japan
| | - Takayuki Goto
- Department of Urology, Kyoto University School of Medicine, Kyoto, Japan
| | - Takahiro Kimura
- Department of Urology, The Jikei University School of Medicine, Minato City, Tokyo, Japan
| | - Takashi Kobayashi
- Department of Urology, Kyoto University School of Medicine, Kyoto, Japan
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2
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Vandekerkhove G, Giri VN, Halabi S, McNair C, Hamade K, Bitting RL, Wyatt AW. Toward Informed Selection and Interpretation of Clinical Genomic Tests in Prostate Cancer. JCO Precis Oncol 2024; 8:e2300654. [PMID: 38547422 PMCID: PMC10994438 DOI: 10.1200/po.23.00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/15/2023] [Accepted: 02/07/2024] [Indexed: 04/02/2024] Open
Abstract
Clinical genomic testing of patient germline, tumor tissue, or plasma cell-free DNA can enable a personalized approach to cancer management and treatment. In prostate cancer (PCa), broad genotyping tests are now widely used to identify germline and/or somatic alterations in BRCA2 and other DNA damage repair genes. Alterations in these genes can confer cancer sensitivity to poly (ADP-ribose) polymerase inhibitors, are linked with poor prognosis, and can have potential hereditary cancer implications for family members. However, there is huge variability in genomic tests and reporting standards, meaning that for successful implementation of testing in clinical practice, end users must carefully select the most appropriate test for a given patient and critically interpret the results. In this white paper, we outline key pre- and post-test considerations for choosing a genomic test and evaluating reported variants, specifically for patients with advanced PCa. Test choice must be based on clinical context and disease state, availability and suitability of tumor tissue, and the genes and regions that are covered by the test. We describe strategies to recognize false positives or negatives in test results, including frameworks to assess low tumor fraction, subclonal alterations, clonal hematopoiesis, and pathogenic versus nonpathogenic variants. We assume that improved understanding among health care professionals and researchers of the nuances associated with genomic testing will ultimately lead to optimal patient care and clinical decision making.
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Affiliation(s)
- Gillian Vandekerkhove
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Veda N. Giri
- Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | | | | | | | | | - Alexander W. Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
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3
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Bratic Hench I, Roma L, Conticelli F, Bubendorf L, Calgua B, Le Magnen C, Piscuoglio S, Rubin MA, Chirindel A, Nicolas GP, Vlajnic T, Zellweger T, Templeton AJ, Stenner F, Ruiz C, Rentsch C, Bubendorf L. Cell-Free DNA Genomic Profiling and Its Clinical Implementation in Advanced Prostate Cancer. Cancers (Basel) 2023; 16:45. [PMID: 38201475 PMCID: PMC10778564 DOI: 10.3390/cancers16010045] [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: 11/10/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Most men with prostate cancer (PCa), despite potentially curable localized disease at initial diagnosis, progress to metastatic disease. Despite numerous treatment options, choosing the optimal treatment for individual patients remains challenging. Biomarkers guiding treatment sequences in an advanced setting are lacking. To estimate the diagnostic potential of liquid biopsies in guiding personalized treatment of PCa, we evaluated the utility of a custom-targeted next-generation sequencing (NGS) panel based on the AmpliSeq HD Technology. Ultra-deep sequencing on plasma circulating free DNA (cfDNA) samples of 40 metastatic castration-resistant PCa (mCRPC) and 28 metastatic hormone-naive PCa (mCSPC) was performed. CfDNA somatic mutations were detected in 48/68 (71%) patients. Of those 68 patients, 42 had matched tumor and cfDNA samples. In 21/42 (50%) patients, mutations from the primary tumor tissue were detected in the plasma cfDNA. In 7/42 (17%) patients, mutations found in the primary tumor were not detected in the cfDNA. Mutations from primary tumors were detected in all tested mCRPC patients (17/17), but only in 4/11 with mCSPC. AR amplifications were detected in 12/39 (31%) mCRPC patients. These results indicate that our targeted NGS approach has high sensitivity and specificity for detecting clinically relevant mutations in PCa.
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Affiliation(s)
- Ivana Bratic Hench
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Luca Roma
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Floriana Conticelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy
| | - Lenard Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Byron Calgua
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Clémentine Le Magnen
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
- Department of Urology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
- Department of Biomedicine, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Mark A. Rubin
- Precision Oncology Laboratory, Department for Biomedical Research, Bern Center for Precision Medicine, 3008 Bern, Switzerland
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Alin Chirindel
- Division of Nuclear Medicine, Department of Theragnostics, University Hospital Basel, 4031 Basel, Switzerland
| | - Guillaume P. Nicolas
- Division of Nuclear Medicine, Department of Theragnostics, University Hospital Basel, 4031 Basel, Switzerland
| | - Tatjana Vlajnic
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | | | - Arnoud J. Templeton
- St. Claraspital, 4058 Basel, Switzerland
- St. Clara Research, Basel and Faculty of Medicine, University Basel, 4058 Basel, Switzerland
| | - Frank Stenner
- Division of Oncology, University Hospital Basel, 4031 Basel, Switzerland
| | - Christian Ruiz
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Cyrill Rentsch
- Department of Urology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
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McKinney LP, Singh R, Jordan IK, Varambally S, Dammer EB, Lillard JW. Transcriptome Analysis Identifies Tumor Immune Microenvironment Signaling Networks Supporting Metastatic Castration-Resistant Prostate Cancer. ONCO 2023; 3:81-95. [PMID: 38435029 PMCID: PMC10906979 DOI: 10.3390/onco3020007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Prostate cancer (PCa) is the second most common cause of cancer death in American men. Metastatic castration-resistant prostate cancer (mCRPC) is the most lethal form of PCa and preferentially metastasizes to the bones through incompletely understood molecular mechanisms. Herein, we processed RNA sequencing data from patients with mCRPC (n = 60) and identified 14 gene clusters (modules) highly correlated with mCRPC bone metastasis. We used a novel combination of weighted gene co-expression network analysis (WGCNA) and upstream regulator and gene ontology analyses of clinically annotated transcriptomes to identify the genes. The cyan module (M14) had the strongest positive correlation (0.81, p = 4 × 10-15) with mCRPC bone metastasis. It was associated with two significant biological pathways through KEGG enrichment analysis (parathyroid hormone synthesis, secretion, and action and protein digestion and absorption). In particular, we identified 10 hub genes (ALPL, PHEX, RUNX2, ENPP1, PHOSPHO1, PTH1R, COL11A1, COL24A1, COL22A1, and COL13A1) using cytoHubba of Cytoscape. We also found high gene expression for collagen formation, degradation, absorption, cell-signaling peptides, and bone regulation processes through Gene Ontology (GO) enrichment analysis.
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Affiliation(s)
- Lawrence P. McKinney
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Rajesh Singh
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sooryanarayana Varambally
- Division of Molecular and Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Eric B. Dammer
- Department of Biochemistry Emory, University School of Medicine, Atlanta, GA 30329, USA
| | - James W. Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA
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Raina K, Forbes CD, Stronk R, Rappi JP, Eastman KJ, Gerritz SW, Yu X, Li H, Bhardwaj A, Forgione M, Hundt A, King MP, Posner ZM, Denny A, McGovern A, Puleo DE, Garvin E, Chenard R, Zaware N, Mousseau JJ, Macaluso J, Martin M, Bassoli K, Jones K, Garcia M, Howard K, Smith LM, Chen JM, De Leon CA, Hines J, Kayser-Bricker KJ, Crews CM. Regulated Induced Proximity Targeting Chimeras (RIPTACs): a Novel Heterobifunctional Small Molecule Therapeutic Strategy for Killing Cancer Cells Selectively. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.01.522436. [PMID: 36711980 PMCID: PMC9881854 DOI: 10.1101/2023.01.01.522436] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
While specific cell signaling pathway inhibitors have yielded great success in oncology, directly triggering cancer cell death is one of the great drug discovery challenges facing biomedical research in the era of precision oncology. Attempts to eradicate cancer cells expressing unique target proteins, such as antibody-drug conjugates (ADCs), T-cell engaging therapies, and radiopharmaceuticals have been successful in the clinic, but they are limited by the number of targets given the inability to target intracellular proteins. More recently, heterobifunctional small molecules such as Proteolysis Targeting Chimera (PROTACs) have paved the way for protein proximity inducing therapeutic modalities. Here, we describe a proof-of-concept study using novel heterobifunctional small molecules called Regulated Induced Proximity Targeting Chimeras or RIPTACs, which elicit a stable ternary complex between a target protein selectively expressed in cancer tissue and a pan-expressed protein essential for cell survival. The resulting cooperative protein:protein interaction (PPI) abrogates the function of the essential protein, thus leading to cell death selectively in cells expressing the target protein. This approach not only opens new target space by leveraging differentially expressed intracellular proteins but also has the advantage of not requiring the target to be a driver of disease. Thus, RIPTACs can address non-target mechanisms of resistance given that cell killing is driven by inactivation of the essential protein. Using the HaloTag7-FKBP model system as a target protein, we describe RIPTACs that incorporate a covalent or non-covalent target ligand connected via a linker to effector ligands such as JQ1 (BRD4), BI2536 (PLK1), or multi-CDK inhibitors such as TMX3013 or dinaciclib. We show that these RIPTACs exhibit positive co-operativity, accumulate selectively in cells expressing HaloTag7-FKBP, form stable target:RIPTAC:effector trimers in cells, and induce an anti-proliferative response in target-expressing cells. We propose that RIPTACs are a novel heterobifunctional therapeutic modality to treat cancers that are known to selectively express a specific intracellular protein.
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Affiliation(s)
- Kanak Raina
- co-corresponding authors
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | - Xinheng Yu
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | - Hao Li
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kelli Jones
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | - Cesar A De Leon
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | - John Hines
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | | | - Craig M Crews
- co-corresponding authors
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
- Department of Pharmacology, Yale University New Haven CT USA
- Department of Chemistry, Yale University New Haven CT USA
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Li L, Xu J. The androgen receptor-targeted proteolysis targeting chimera and other alternative therapeutic choices in overcoming the resistance to androgen deprivation treatment in prostate cancer. Clin Transl Oncol 2023; 25:352-363. [PMID: 36203075 PMCID: PMC9873748 DOI: 10.1007/s12094-022-02957-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 01/28/2023]
Abstract
Androgen receptor (AR) plays a vital role in prostate cancer (PCa), including castration-resistant PCa, by retaining AR signalling. Androgen deprivation treatment (ADT) has been the standard treatment in the past decades. A great number of AR antagonists initially had been found effective in tumour remission; however, most PCa relapsed that caused by pre-translational resistance such as AR mutations to turn antagonist into agonist, and AR variants to bypass the androgen binding. Recently, several alternative therapeutic choices have been proposed. Among them, proteolysis targeting chimera (PROTAC) acts different from traditional drugs that usually function as inhibitors or antagonists, and it degrades oncogenic protein and does not disrupt the transcription of an oncogene. This review first discussed some essential mechanisms of ADT resistance, and then introduced the application of AR-targeted PROTAC in PCa cells, as well as other AR-targeted therapeutic choices.
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Affiliation(s)
- Liuxun Li
- grid.1006.70000 0001 0462 7212Solid Tumour Target Discovery Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Jiangli Xu
- Department of Pharmacy, No.921 Hospital of the Joint Logistics Support Force, Changsha, 410003 China
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Kwan EM, Wyatt AW, Chi KN. Towards clinical implementation of circulating tumor DNA in metastatic prostate cancer: Opportunities for integration and pitfalls to interpretation. Front Oncol 2022; 12:1054497. [PMID: 36439451 PMCID: PMC9685669 DOI: 10.3389/fonc.2022.1054497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Plasma circulating tumor DNA (ctDNA) represents short fragments of tumor-derived DNA released into the bloodstream primarily from cancer cells undergoing apoptosis. In metastatic castration-resistant prostate cancer (mCRPC), characterizing genomic alterations in ctDNA identifies mutations, copy number alterations, and structural rearrangements with predictive and prognostic biomarker utility. These associations with clinical outcomes have resulted in ctDNA increasingly incorporated into routine clinical care. In this review, we summarize current and emerging applications for ctDNA analysis in metastatic prostate cancer, including outcome prediction, treatment selection, and characterization of treatment resistance. We also discuss potential pitfalls with interpreting ctDNA findings, namely false negatives arising from low tumor content and optimal assay design, including correction for clonal hematopoiesis of indeterminate potential and germline variants. Understanding the influence of these limitations on interpretation of ctDNA results is necessary to overcome barriers to clinical implementation. Nevertheless, as assay availability and technology continue to improve, recognizing both opportunities and shortcomings of ctDNA analysis will retain relevance with informing the implementation of precision-oncology initiatives for metastatic prostate cancer.
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Affiliation(s)
- Edmond M. Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kim N. Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
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Constantinescu T, Mihis AG. Two Important Anticancer Mechanisms of Natural and Synthetic Chalcones. Int J Mol Sci 2022; 23:ijms231911595. [PMID: 36232899 PMCID: PMC9570335 DOI: 10.3390/ijms231911595] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-binding cassette subfamily G and tubulin pharmacological mechanisms decrease the effectiveness of anticancer drugs by modulating drug absorption and by creating tubulin assembly through polymerization. A series of natural and synthetic chalcones have been reported to have very good anticancer activity, with a half-maximal inhibitory concentration lower than 1 µM. By modulation, it is observed in case of the first mechanism that methoxy substituents on the aromatic cycle of acetophenone residue and substitution of phenyl nucleus by a heterocycle and by methoxy or hydroxyl groups have a positive impact. To inhibit tubulin, compounds bind to colchicine binding site. Presence of methoxy groups, amino groups or heterocyclic substituents increase activity.
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Affiliation(s)
- Teodora Constantinescu
- Department of Chemistry, Faculty of Pharmacy, Iuliu Hatieganu University, 400012 Cluj-Napoca, Romania
| | - Alin Grig Mihis
- Advanced Materials and Applied Technologies Laboratory, Institute of Research-Development-Innovation in Applied Natural Sciences, “Babes-Bolyai” University, Fantanele Str. 30, 400294 Cluj-Napoca, Romania
- Correspondence:
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