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Kulac I, Roudier MP, Haffner MC. Molecular Pathology of Prostate Cancer. Clin Lab Med 2024; 44:161-180. [PMID: 38821639 DOI: 10.1016/j.cll.2023.08.003] [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] [Indexed: 06/02/2024]
Abstract
Molecular profiling studies have shed new light on the complex biology of prostate cancer. Genomic studies have highlighted that structural rearrangements are among the most common recurrent alterations. In addition, both germline and somatic mutations in DNA repair genes are enriched in patients with advanced disease. Primary prostate cancer has long been known to be multifocal, but recent studies demonstrate that a large fraction of prostate cancer shows evidence of multiclonality, suggesting that genetically distinct, independently arising tumor clones coexist. Metastatic prostate cancer shows a high level of morphologic and molecular diversity, which is associated with resistance to systemic therapies. The resulting high level of intratumoral heterogeneity has important implications for diagnosis and poses major challenges for the implementation of molecular studies. Here we provide a concise review of the molecular pathology of prostate cancer, highlight clinically relevant alterations, and discuss opportunities for molecular testing.
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Affiliation(s)
- Ibrahim Kulac
- Department of Pathology, Koç University School of Medicine, Davutpasa Caddesi No:4, Istanbul 34010, Turkey
| | - Martine P Roudier
- Department of Urology, University of Washington, Northeast Pacific Street, Seattle, WA 98195, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Akram F, Tanveer R, Andleeb S, Shah FI, Ahmad T, Shehzadi S, Akhtar AM, Syed G. Deciphering the Epigenetic Symphony of Cancer: Insights and Epigenetic Therapies Implications. Technol Cancer Res Treat 2024; 23:15330338241250317. [PMID: 38780251 PMCID: PMC11119348 DOI: 10.1177/15330338241250317] [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: 12/31/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Epigenetic machinery is a cornerstone in normal cell development, orchestrating tissue-specific gene expression in mammalian cells. Aberrations in this intricate landscape drive substantial changes in gene function, emerging as a linchpin in cancer etiology and progression. While cancer was conventionally perceived as solely a genetic disorder, its contemporary definition encompasses genetic alterations intertwined with disruptive epigenetic abnormalities. This review explores the profound impact of DNA methylation, histone modifications, and noncoding RNAs on fundamental cellular processes. When these pivotal epigenetic mechanisms undergo disruption, they intricately guide the acquisition of the 6 hallmark characteristics of cancer within seemingly normal cells. Leveraging the latest advancements in decoding these epigenetic intricacies holds immense promise, heralding a new era in developing targeted and more efficacious treatment modalities against cancers driven by aberrant epigenetic modifications.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Rida Tanveer
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Sahar Andleeb
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fatima Iftikhar Shah
- Department of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | - Tayyab Ahmad
- Department of Medicine, Fatima Memorial Hospital, Lahore, Pakistan
| | - Somia Shehzadi
- Department of Medical Lab Technology, The University of Lahore, Lahore, Pakistan
| | | | - Ghania Syed
- Centre for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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3
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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4
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DeLouize AM, Eick G, Karam SD, Snodgrass JJ. Current and future applications of biomarkers in samples collected through minimally invasive methods for cancer medicine and population-based research. Am J Hum Biol 2022; 34:e23665. [PMID: 34374148 PMCID: PMC9894104 DOI: 10.1002/ajhb.23665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/04/2023] Open
Abstract
Despite advances in cancer medicine and research, invasive and potentially risky procedures such as biopsies, venous blood tests, imaging, colonoscopy, and pap smear tests are still primarily used for screening, staging, and assessing response to therapy. The development and interdisciplinary use of biomarkers from urine, feces, saliva, scent, and capillary blood collected with minimally invasive methods represents a potential opportunity for integration with biomarker analysis for cancers, both in clinical practice (e.g., in screening, treatment, and disease monitoring, and improved quality of life for patients) and population-based research (e.g., in epidemiology/public health, studies of social and environmental determinants, and evolutionary medicine). In this article, we review the scientific rationale, benefits, challenges, and potential opportunities for measuring cancer-related biomarkers in samples collected through minimally invasive methods.
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Affiliation(s)
| | - Geeta Eick
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J. Josh Snodgrass
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
- Center for Global Health, University of Oregon, Eugene, Oregon, USA
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Urinary marker panels for aggressive prostate cancer detection. Sci Rep 2022; 12:14837. [PMID: 36050450 PMCID: PMC9437030 DOI: 10.1038/s41598-022-19134-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Majority of patients with indolent prostate cancer (PCa) can be managed with active surveillance. Therefore, finding biomarkers for classifying patients between indolent and aggressive PCa is essential. In this study, we investigated urinary marker panels composed of urinary glycopeptides and/or urinary prostate-specific antigen (PSA) for their clinical utility in distinguishing non-aggressive (Grade Group 1) from aggressive (Grade Group ≥ 2) PCa. Urinary glycopeptides acquired via data-independent acquisition mass spectrometry (DIA-MS) were quantitatively analyzed, where prostatic acid phosphatase (ACPP), clusterin (CLU), alpha-1-acid glycoprotein 1 (ORM1), and CD antigen 97 (CD97) were selected to be evaluated in various combinations with and without urinary PSA. Targeted parallel reaction monitoring (PRM) assays of the glycopeptides from urinary ACPP and CLU were investigated along with urinary PSA for the ability of aggressive PCa detection. The multi-urinary marker panels, combined via logistic regression, were statistically evaluated using bootstrap resampling and validated by an independent cohort. Majority of the multi-urinary marker panels (e.g., a panel consisted of ACPP, CLU, and Urinary PSA) achieved area under the curve (AUC) ranged from 0.70 to 0.85. Thus, multi-marker panels investigated in this study showed clinically meaningful results on aggressive PCa detection to separate Grade Group 1 from Grade Group 2 and above warranting further evaluation in clinical setting in future.
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A Model to Detect Significant Prostate Cancer Integrating Urinary Peptide and Extracellular Vesicle RNA Data. Cancers (Basel) 2022; 14:cancers14081995. [PMID: 35454901 PMCID: PMC9027643 DOI: 10.3390/cancers14081995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
There is a clinical need to improve assessment of biopsy-naïve patients for the presence of clinically significant prostate cancer (PCa). In this study, we investigated whether the robust integration of expression data from urinary extracellular vesicle RNA (EV-RNA) with urine proteomic metabolites can accurately predict PCa biopsy outcome. Urine samples collected within the Movember GAP1 Urine Biomarker study (n = 192) were analysed by both mass spectrometry-based urine-proteomics and NanoString gene-expression analysis (167 gene-probes). Cross-validated LASSO penalised regression and Random Forests identified a combination of clinical and urinary biomarkers for predictive modelling of significant disease (Gleason Score (Gs) ≥ 3 + 4). Four predictive models were developed: ‘MassSpec’ (CE-MS proteomics), ‘EV-RNA’, and ‘SoC’ (standard of care) clinical data models, alongside a fully integrated omics-model, deemed ‘ExoSpec’. ExoSpec (incorporating four gene transcripts, six peptides, and two clinical variables) is the best model for predicting Gs ≥ 3 + 4 at initial biopsy (AUC = 0.83, 95% CI: 0.77−0.88) and is superior to a standard of care (SoC) model utilising clinical data alone (AUC = 0.71, p < 0.001, 1000 resamples). As the ExoSpec Risk Score increases, the likelihood of higher-grade PCa on biopsy is significantly greater (OR = 2.8, 95% CI: 2.1−3.7). The decision curve analyses reveals that ExoSpec provides a net benefit over SoC and could reduce unnecessary biopsies by 30%.
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7
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Lin Y, Liu G, Liu C, Xie H, Wang X, Huang Y, Jin L, Chen H. Urothelial carcinoembryonic antigen 1 score for early detection of prostate cancer and risk prediction. Cancer Med 2022; 11:2875-2885. [PMID: 35289508 PMCID: PMC9359874 DOI: 10.1002/cam4.4629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
UCA1 score appears useful in detecting nonhigh-risk (including very low-, low-, or intermediate-risk) prostate cancer. Combination of the PSA level and the UCA1 score may significantly reduce the burden of prostate biopsy.
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Affiliation(s)
- Youdong Lin
- Department of Clinical Laboratory Medicine, Fujian Provincial Hospital, Fujian Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Guihua Liu
- Department of Children Health Care, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Chun Liu
- Department of urinary surgery, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Hui Xie
- Department of urinary surgery, Fuzhou NO. 1 Hospital Affiliated with Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaoxian Wang
- Department of Clinical Laboratory Medicine, Fuzhou NO. 1 Hospital Affiliated with Fujian Medical University, Fuzhou, Fujian, China
| | - Yudian Huang
- Department of Pathology, Fuzhou NO. 1 Hospital Affiliated with Fujian Medical University, Fuzhou, Fujian, China
| | - Long Jin
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Huidan Chen
- Department of Clinical Laboratory Medicine, Fujian Provincial Hospital, Fujian Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
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Systemic Effects Reflected in Specific Biomarker Patterns Are Instrumental for the Paradigm Change in Prostate Cancer Management: A Strategic Paper. Cancers (Basel) 2022; 14:cancers14030675. [PMID: 35158943 PMCID: PMC8833369 DOI: 10.3390/cancers14030675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) is reported as the most common malignancy and second leading cause of death in America. In Europe, PCa is considered the leading type of tumour in 28 European countries. The costs of treating PCa are currently increasing more rapidly than those of any other cancer. Corresponding economic burden is enormous, due to an overtreatment of slowly developing disease on one hand and underestimation/therapy resistance of particularly aggressive PCa subtypes on the other hand. The incidence of metastatic PCa is rapidly increasing that is particularly characteristic for young adults. PCa is a systemic multi-factorial disease resulting from an imbalanced interplay between risks and protective factors. Sub-optimal behavioural patterns, abnormal stress reactions, imbalanced antioxidant defence, systemic ischemia and inflammation, mitochondriopathies, aberrant metabolic pathways, gene methylation and damage to DNA, amongst others, are synergistically involved in pathomechanisms of PCa development and progression. To this end, PCa-relevant systemic effects are reflected in liquid biopsies such as blood patterns which are instrumental for predictive diagnostics, targeted prevention and personalisation of medical services (PPPM/3P medicine) as a new paradigm in the overall PCa management. This strategic review article highlights systemic effects in prostate cancer development and progression, demonstrates evident challenges in PCa management and provides expert recommendations in the framework of 3P medicine.
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9
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Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis. BMC Bioinformatics 2021; 22:492. [PMID: 34641790 PMCID: PMC8507340 DOI: 10.1186/s12859-021-04416-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/29/2021] [Indexed: 01/14/2023] Open
Abstract
Background Detecting prostate cancer at a non-aggressive stage is the main goal of prostate cancer screening. DNA methylation has been widely used as biomarkers for cancer diagnosis and prognosis, however, with low clinical translation rate. By taking advantage of multi-cancer data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we aimed to identify prostate cancer specific biomarkers which can separate between non-aggressive and aggressive prostate cancer based on DNA methylation patterns. Results We performed a comparison analysis of DNA methylation status between normal prostate tissues and prostate adenocarcinoma (PRAD) samples at different Gleason stages. The candidate biomarkers were selected by excluding the biomarkers existing in multiple cancers (pan-cancer) and requiring significant difference between PRAD and other urinary samples. By least absolute shrinkage and selection operator (LASSO) selection, 8 biomarkers (cg04633600, cg05219445, cg05796128, cg10834205, cg16736826, cg23523811, cg23881697, cg24755931) were identified and in-silico validated by model constructions. First, all 8 biomarkers could separate PRAD at different stages (Gleason 6 vs. Gleason 3 + 4: AUC = 0.63; Gleason 6 vs. Gleason 4 + 3 and 8–10: AUC = 0.87). Second, 5 biomarkers (cg04633600, cg05796128, cg23523811, cg23881697, cg24755931) effectively detected PRAD from normal prostate tissues (AUC ranged from 0.88 to 0.92). Last, 6 biomarkers (cg04633600, cg05219445, cg05796128, cg23523811, cg23881697, cg24755931) completely distinguished PRAD with other urinary samples (AUC = 1). Conclusions Our study identified and in-silico validated a panel of prostate cancer specific DNA methylation biomarkers with diagnosis value. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04416-w.
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Clinical Relevance of Circulating Tumor Cells in Prostate Cancer Management. Biomedicines 2021; 9:biomedicines9091179. [PMID: 34572366 PMCID: PMC8471111 DOI: 10.3390/biomedicines9091179] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/29/2021] [Accepted: 09/04/2021] [Indexed: 02/08/2023] Open
Abstract
Given the low specificity of the routinely used biomarker prostate-specific antigen, circulating tumor cell (CTC) enumeration seems to be particularly useful in the monitoring of prostate cancer. In this review, we focused on a few aspects of CTC enumeration in prostate malignancies: prognostic value in metastatic and non-metastatic tumors, role in the monitoring of treatment outcomes, use as a surrogate marker for survival, and other applications, mostly for research purposes. CTC enumeration, without a doubt, offers an attractive perspective in the management of prostate cancer. However, the vast majority of available data about the role of CTC in this malignancy originate from randomized studies of anticancer agents and do not necessarily translate into real-world clinical practice. Further, most studies on the application of CTC in prostate cancer patients were limited to advanced stages of this malignancy. Meanwhile, the role of CTC in the early stages of prostate cancer, in which some patients may present with occult disseminated disease, is still relatively poorly understood, and should thus be studied extensively. Other obstacles in the widespread application of CTC enumeration in routine clinical practice include considerable discrepancies in the number of cells determined with various commercially available systems.
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Meehan J, Gray M, Martínez-Pérez C, Kay C, McLaren D, Turnbull AK. Tissue- and Liquid-Based Biomarkers in Prostate Cancer Precision Medicine. J Pers Med 2021; 11:jpm11070664. [PMID: 34357131 PMCID: PMC8306523 DOI: 10.3390/jpm11070664] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/24/2022] Open
Abstract
Worldwide, prostate cancer (PC) is the second-most-frequently diagnosed male cancer and the fifth-most-common cause of all cancer-related deaths. Suspicion of PC in a patient is largely based upon clinical signs and the use of prostate-specific antigen (PSA) levels. Although PSA levels have been criticised for a lack of specificity, leading to PC over-diagnosis, it is still the most commonly used biomarker in PC management. Unfortunately, PC is extremely heterogeneous, and it can be difficult to stratify patients whose tumours are unlikely to progress from those that are aggressive and require treatment intensification. Although PC-specific biomarker research has previously focused on disease diagnosis, there is an unmet clinical need for novel prognostic, predictive and treatment response biomarkers that can be used to provide a precision medicine approach to PC management. In particular, the identification of biomarkers at the time of screening/diagnosis that can provide an indication of disease aggressiveness is perhaps the greatest current unmet clinical need in PC management. Largely through advances in genomic and proteomic techniques, exciting pre-clinical and clinical research is continuing to identify potential tissue, blood and urine-based PC-specific biomarkers that may in the future supplement or replace current standard practices. In this review, we describe how PC-specific biomarker research is progressing, including the evolution of PSA-based tests and those novel assays that have gained clinical approval. We also describe alternative diagnostic biomarkers to PSA, in addition to biomarkers that can predict PC aggressiveness and biomarkers that can predict response to certain therapies. We believe that novel biomarker research has the potential to make significant improvements to the clinical management of this disease in the near future.
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Affiliation(s)
- James Meehan
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Correspondence:
| | - Mark Gray
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK;
| | - Carlos Martínez-Pérez
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Charlene Kay
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Duncan McLaren
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK;
| | - Arran K. Turnbull
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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Salivary DNA Methylation as an Epigenetic Biomarker for Head and Neck Cancer. Part I: A Diagnostic Accuracy Meta-Analysis. J Pers Med 2021; 11:jpm11060568. [PMID: 34204396 PMCID: PMC8233749 DOI: 10.3390/jpm11060568] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/31/2022] Open
Abstract
DNA hypermethylation is an important epigenetic mechanism for gene expression inactivation in head and neck cancer (HNC). Saliva has emerged as a novel liquid biopsy representing a potential source of biomarkers. We performed a comprehensive meta-analysis to evaluate the overall diagnostic accuracy of salivary DNA methylation for detecting HNC. PubMed EMBASE, Web of Science, LILACS, and the Cochrane Library were searched. Study quality was assessed by the Quality Assessment for Studies of Diagnostic Accuracy-2, and sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (dOR), and their corresponding 95% confidence intervals (CIs) were calculated using a bivariate random-effect meta-analysis model. Meta-regression and subgroup analyses were performed to assess heterogeneity. Eighty-four study units from 18 articles with 8368 subjects were included. The pooled sensitivity and specificity of salivary DNA methylation were 0.39 and 0.87, respectively, while PLR and NLR were 3.68 and 0.63, respectively. The overall area under the curve (AUC) was 0.81 and the dOR was 8.34. The combination of methylated genes showed higher diagnostic accuracy (AUC, 0.92 and dOR, 36.97) than individual gene analysis (AUC, 0.77 and dOR, 6.02). These findings provide evidence regarding the potential clinical application of salivary DNA methylation for HNC diagnosis.
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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14
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Saliva Gene Promoter Hypermethylation as a Biomarker in Oral Cancer. J Clin Med 2021; 10:jcm10091931. [PMID: 33947071 PMCID: PMC8124791 DOI: 10.3390/jcm10091931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022] Open
Abstract
Oral carcinogenesis is a multistep process characterized by a summation of multiple genetic and epigenetic alterations in key regulatory genes. The silencing of genes by aberrant promoter hypermethylation is thought to be an important epigenetic event in cancer development and progression which has great potential as a biomarker for early diagnosis, tumor molecular subtyping, prognosis, monitoring, and therapy. Aberrant DNA methylation has been detected in different liquid biopsies, which may represent a potential alternative to solid biopsies. The detection of methylated genes in saliva may have clinical application for noninvasive oral cancer screening and early diagnosis. Here, we review the current evidence on gene promoter hypermethylation in saliva.
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15
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Connell SP, Mills R, Pandha H, Morgan R, Cooper CS, Clark J, Brewer DS. Integration of Urinary EN2 Protein & Cell-Free RNA Data in the Development of a Multivariable Risk Model for the Detection of Prostate Cancer Prior to Biopsy. Cancers (Basel) 2021; 13:cancers13092102. [PMID: 33925381 PMCID: PMC8123800 DOI: 10.3390/cancers13092102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Prostate cancer is a disease responsible for a large proportion of all male cancer deaths but there is a high chance that a patient will die with the disease rather than from. Therefore, there is a desperate need for improvements in diagnosing and predicting outcomes for prostate cancer patients to minimise overdiagnosis and overtreatment whilst appropriately treating men with aggressive disease, especially if this can be done without taking an invasive biopsy. In this work we develop a test that predicts whether a patient has prostate cancer and how aggressive the disease is from a urine sample. This model combines the measurement of a protein-marker called EN2 and the levels of 10 genes measured in urine and proves that integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy. Abstract The objective is to develop a multivariable risk model for the non-invasive detection of prostate cancer prior to biopsy by integrating information from clinically available parameters, Engrailed-2 (EN2) whole-urine protein levels and data from urinary cell-free RNA. Post-digital-rectal examination urine samples collected as part of the Movember Global Action Plan 1 study which has been analysed for both cell-free-RNA and EN2 protein levels were chosen to be integrated with clinical parameters (n = 207). A previously described robust feature selection framework incorporating bootstrap resampling and permutation was applied to the data to generate an optimal feature set for use in Random Forest models for prediction. The fully integrated model was named ExoGrail, and the out-of-bag predictions were used to evaluate the diagnostic potential of the risk model. ExoGrail risk (range 0–1) was able to determine the outcome of an initial trans-rectal ultrasound guided (TRUS) biopsy more accurately than clinical standards of care, predicting the presence of any cancer with an area under the receiver operator curve (AUC) = 0.89 (95% confidence interval(CI): 0.85–0.94), and discriminating more aggressive Gleason ≥ 3 + 4 disease returning an AUC = 0.84 (95% CI: 0.78–0.89). The likelihood of more aggressive disease being detected significantly increased as ExoGrail risk score increased (Odds Ratio (OR) = 2.21 per 0.1 ExoGrail increase, 95% CI: 1.91–2.59). Decision curve analysis of the net benefit of ExoGrail showed the potential to reduce the numbers of unnecessary biopsies by 35% when compared to current standards of care. Integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy.
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Affiliation(s)
- Shea P. Connell
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Robert Mills
- Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, Norfolk NR4 7UY, UK;
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford GU2 7XH, UK;
| | - Richard Morgan
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford BD7 1DP, UK;
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
- The Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
- Correspondence: ; Tel.: +44-(0)-1603-593761
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16
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Duffy MJ. Biomarkers for prostate cancer: prostate-specific antigen and beyond. Clin Chem Lab Med 2021; 58:326-339. [PMID: 31714881 DOI: 10.1515/cclm-2019-0693] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/19/2019] [Indexed: 12/21/2022]
Abstract
In recent years, several new biomarkers supplementing the role of prostate-specific antigen (PSA) have become available for men with prostate cancer. Although widely used in an ad hoc manner, the role of PSA in screening asymptomatic men for prostate cancer is controversial. Several expert panels, however, have recently recommended limited PSA screening following informed consent in average-risk men, aged 55-69 years. As a screening test for prostate cancer however, PSA has limited specificity and leads to overdiagnosis which in turn results in overtreatment. To increase specificity and reduce the number of unnecessary biopsies, biomarkers such as percent free PSA, prostate health index (PHI) or the 4K score may be used, while Progensa PCA3 may be measured to reduce the number of repeat biopsies in men with a previously negative biopsy. In addition to its role in screening, PSA is also widely used in the management of patients with diagnosed prostate cancer such as in surveillance following diagnosis, monitoring response to therapy and in combination with both clinical and histological criteria in risk stratification for recurrence. For determining aggressiveness and predicting outcome, especially in low- or intermediate-risk men, tissue-based multigene tests such as Decipher, Oncotype DX (Prostate), Prolaris and ProMark, may be used. Emerging therapy predictive biomarkers include AR-V7 for predicting lack of response to specific anti-androgens (enzalutamide, abiraterone), BRAC1/2 mutations for predicting benefit from PARP inhibitor and PORTOS for predicting benefit from radiotherapy. With the increased availability of multiple biomarkers, personalised treatment for men with prostate cancer is finally on the horizon.
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Affiliation(s)
- Michael J Duffy
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland.,UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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17
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Velmanickam L, Jayasooriya V, Nawarathna D. Integrated dielectrophoretic and impedimetric biosensor provides a template for universal biomarker sensing in clinical samples. Electrophoresis 2021; 42:1060-1069. [PMID: 33506957 DOI: 10.1002/elps.202000347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
The detection and quantification of nucleic acid and proteomic biomarkers in bodily fluids is a critical part of many medical screening and diagnoses. However, majority of the current detection platforms are not ideal for routine, rapid, and low-cost testing in point-of-care settings. To address this issue, we developed a concept for a disposable universal point-of-care biosensor that can detect and quantify nucleic acid and proteomic biomarkers in diluted serum samples. The central tenet of sensing is the use of dielectrophoresis, electrothermal effects, and thermophoresis to selectively and rapidly isolate the biomarkers of interest in electrodes and then quantify using electrical impedance. When the sensor was applied to quantify microRNA and antigen biomarker molecules directly in diluted serum samples, it produced a LOD values in the fM range and sensitivity values from 1012 to 1015 Ω/M with a 30 min assay time and assay cost of less than $50 per assay.
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Affiliation(s)
- Logeeshan Velmanickam
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA
| | - Vidura Jayasooriya
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA
| | - Dharmakeerthi Nawarathna
- Department of Electrical and Computer Engineering, North Dakota State University, Fargo, ND, USA.,Biomedical Engineering Program, North Dakota State University, Fargo, ND, USA
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18
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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19
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Wang YA, Sfakianos J, Tewari AK, Cordon-Cardo C, Kyprianou N. Molecular tracing of prostate cancer lethality. Oncogene 2020; 39:7225-7238. [PMID: 33046797 DOI: 10.1038/s41388-020-01496-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 01/14/2023]
Abstract
Prostate cancer is diagnosed mostly in men over the age of 50 years, and has favorable 5-year survival rates due to early cancer detection and availability of curative surgical management. However, progression to metastasis and emergence of therapeutic resistance are responsible for the majority of prostate cancer mortalities. Recent advancement in sequencing technologies and computational capabilities have improved the ability to organize and analyze large data, thus enabling the identification of novel biomarkers for survival, metastatic progression and patient prognosis. Large-scale sequencing studies have also uncovered genetic and epigenetic signatures associated with prostate cancer molecular subtypes, supporting the development of personalized targeted-therapies. However, the current state of mainstream prostate cancer management does not take full advantage of the personalized diagnostic and treatment modalities available. This review focuses on interrogating biomarkers of prostate cancer progression, including gene signatures that correspond to the acquisition of tumor lethality and those of predictive and prognostic value in progression to advanced disease, and suggest how we can use our knowledge of biomarkers and molecular subtypes to improve patient treatment and survival outcomes.
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Affiliation(s)
- Yuanshuo Alice Wang
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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20
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Carson JJK, Di Lena MA, Berman DM, Siemens DR, Mueller CR. Development and initial clinical correlation of a DNA methylation-based blood test for prostate cancer. Prostate 2020; 80:1038-1042. [PMID: 32506642 DOI: 10.1002/pros.24025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND One of the principle limitations for more precise management of advanced prostate cancer is the lack of accurate biomarkers allowing estimation of tumor burden, ongoing assessment of progression, and response to treatment. Although prostate-specific antigen (PSA) performs modestly, nonsecreting cancers including those with early castrate-resistance warrant investigation of other predictive biomarkers. The objectives of these studies were to develop and perform initial validation of a circulating tumor DNA (ctDNA) methylation assay. METHODS Methylation DETection of Circulating Tumor DNA (mDETECT) is a highly multiplexed targeted sequencing DNA methylation-based ctDNA blood test that captures the vast majority of prostate cancer phenotypes due to a careful development process that ensures that each probe region is methylated in at least 50% of all methylation-based subtypes and is not methylated in normal tissues. Next-generation sequencing of targeted polymerase chain reaction (PCR) products whose amplification is biased towards methylated DNA ensures the specificity of the assay by identifying multiple tumor-specific methylated CpG residues in each read. RESULTS The final test is comprised of 46 PCR probes to 40 regions. It is relatively resistant to contaminating normal DNA and as a result functions in both serum and plasma samples. The assay was initially validated in a variety of prostate cancer cell lines to ensure specificity. Using a small number of longitudinal samples from prostate cancer patients initiating androgen deprivation therapy, the ability of mDETECT to track tumor burden was assessed compared with PSA. The mDETECT test signal generally paralleled that of PSA increasing and decreasing commensurate with tumor evolution in these patients. In two cases it appeared to anticipate clinical progression by a number of months compared to PSA and in a PSA nonproducing case, it was able to track tumor progression. CONCLUSIONS mDETECT offers a promising tool for the assessment of prostate cancer burden based on the sensitive detection of prostate-specific ctDNA and requires further validation.
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Affiliation(s)
- Jacob J K Carson
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael A Di Lena
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - D Robert Siemens
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - Christopher R Mueller
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Department of Biological and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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21
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Connell SP, O'Reilly E, Tuzova A, Webb M, Hurst R, Mills R, Zhao F, Bapat B, Cooper CS, Perry AS, Clark J, Brewer DS. Development of a multivariable risk model integrating urinary cell DNA methylation and cell-free RNA data for the detection of significant prostate cancer. Prostate 2020; 80:547-558. [PMID: 32153047 PMCID: PMC7383590 DOI: 10.1002/pros.23968] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/17/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Prostate cancer exhibits severe clinical heterogeneity and there is a critical need for clinically implementable tools able to precisely and noninvasively identify patients that can either be safely removed from treatment pathways or those requiring further follow up. Our objectives were to develop a multivariable risk prediction model through the integration of clinical, urine-derived cell-free messenger RNA (cf-RNA) and urine cell DNA methylation data capable of noninvasively detecting significant prostate cancer in biopsy naïve patients. METHODS Post-digital rectal examination urine samples previously analyzed separately for both cellular methylation and cf-RNA expression within the Movember GAP1 urine biomarker cohort were selected for a fully integrated analysis (n = 207). A robust feature selection framework, based on bootstrap resampling and permutation, was utilized to find the optimal combination of clinical and urinary markers in a random forest model, deemed ExoMeth. Out-of-bag predictions from ExoMeth were used for diagnostic evaluation in men with a clinical suspicion of prostate cancer (PSA ≥ 4 ng/mL, adverse digital rectal examination, age, or lower urinary tract symptoms). RESULTS As ExoMeth risk score (range, 0-1) increased, the likelihood of high-grade disease being detected on biopsy was significantly greater (odds ratio = 2.04 per 0.1 ExoMeth increase, 95% confidence interval [CI]: 1.78-2.35). On an initial TRUS biopsy, ExoMeth accurately predicted the presence of Gleason score ≥3 + 4, area under the receiver-operator characteristic curve (AUC) = 0.89 (95% CI: 0.84-0.93) and was additionally capable of detecting any cancer on biopsy, AUC = 0.91 (95% CI: 0.87-0.95). Application of ExoMeth provided a net benefit over current standards of care and has the potential to reduce unnecessary biopsies by 66% when a risk threshold of 0.25 is accepted. CONCLUSION Integration of urinary biomarkers across multiple assay methods has greater diagnostic ability than either method in isolation, providing superior predictive ability of biopsy outcomes. ExoMeth represents a more holistic view of urinary biomarkers and has the potential to result in substantial changes to how patients suspected of harboring prostate cancer are diagnosed.
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Affiliation(s)
- Shea P. Connell
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Eve O'Reilly
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Alexandra Tuzova
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Martyn Webb
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Rachel Hurst
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Robert Mills
- Department of UrologyNorfolk and Norwich University Hospitals NHS Foundation TrustNorfolkUK
| | - Fang Zhao
- Division of Urology, University Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - Bharati Bapat
- Division of Urology, University Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - Colin S. Cooper
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Antoinette S. Perry
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Jeremy Clark
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Daniel S. Brewer
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
- Science DivisionThe Earlham InstituteNorwich Research ParkNorwichNorfolkUK
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22
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Connor AE, Jordan AC, Perry AS. Holding a MIRror up to the robustness of the prostate cancer urinary transcriptome. Transl Androl Urol 2020; 8:S488-S490. [PMID: 32042627 DOI: 10.21037/tau.2019.09.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Adele E Connor
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Cancer Biology and Therapeutics Laboratory, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
| | - Asia C Jordan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Cancer Biology and Therapeutics Laboratory, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
| | - Antoinette S Perry
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Cancer Biology and Therapeutics Laboratory, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
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23
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Lobo J, Jerónimo C, Henrique R. Targeting the Immune system and Epigenetic Landscape of Urological Tumors. Int J Mol Sci 2020; 21:ijms21030829. [PMID: 32012885 PMCID: PMC7037817 DOI: 10.3390/ijms21030829] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/18/2020] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
In the last years, we have witnessed remarkable advances in targeted therapies for cancer patients. There is a growing effort to either replace or reduce the dose of unspecific, systemic (chemo)therapies, given the associated short- and long-term side effects, by introducing more specific targeted therapies as single or combination agents. Due to the well-known implications of the immune system and epigenetic landscape in modulating cancer development, both have been explored as potential targets in several malignancies, including those affecting the genitourinary tract. As the immune system function is also epigenetically regulated, there is rationale for combining both strategies. However, this is still rather underexplored, namely in urological tumors. We aim to briefly review the use of immune therapies in prostate, kidney, bladder, and testicular cancer, and further describe studies providing supporting evidence on their combination with epigenetic-based therapies.
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Affiliation(s)
- João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
- Correspondence: (J.L.); (R.H.)
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
- Correspondence: (J.L.); (R.H.)
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Brikun I, Nusskern D, Freije D. An expanded biomarker panel for the detection of prostate cancer from urine DNA. Exp Hematol Oncol 2019; 8:13. [PMID: 31297302 PMCID: PMC6598372 DOI: 10.1186/s40164-019-0137-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer diagnosis using the PSA test remains controversial because of overdiagnosis and overtreatment of potentially indolent cancers. There remains a need to increase the diagnostic lead time and to target treatment to patients with significant disease. One possible approach to overcome the limitations of PSA is to screen men for the molecular signature of early PCA, monitor the rate of disease progression and target treatment to patients who are likely to benefit from it. Such an approach requires a large panel of markers that define a molecular clock for PCA. We recently developed a panel of 19 markers for the non-invasive detection of PCA from urine DNA. It raised the possibility that additional methylation markers could be successfully analyzed from urine DNA, a prerequisite for increasing the diagnostic lead time and enabling disease monitoring. Methods We developed semi-quantitative polymerase chain reaction assays for 13 additional markers and determined their methylation status in 150 urine DNAs from 94 patients with elevated PSA. Eighty five samples were obtained following DRE and 65 samples were from first void. We combined the data of the 13 new markers with the previously reported 19 markers and calculated the sensitivity, specificity, negative and positive predictive values at every threshold from one to 32 positive markers. Results Using 10of32 positive markers as the threshold to recommend a biopsy yields a sensitivity of 81% (95% CI 0.68–0.93) and 93% (95% CI 0.84–1.02) and a specificity of 76% (95% CI 0.63–0.88) and 77% (95% CI 0.63–0.91) from DRE and FV DNA, respectively. The PPV was 71% and 77% and the NPV was 85% and 93% from DRE and FV, respectively. Conclusions This study shows that large marker panels can be analyzed from urine DNA without loss of sensitivity or specificity. Using 32 markers improved the stratification of patients undergoing screening for PCA particularly for patients below the 10of32 threshold. The results show the utility of larger biomarker panels for PCA diagnosis and suggest that the development of the panels needed to monitor disease progression could be successfully accomplished. Electronic supplementary material The online version of this article (10.1186/s40164-019-0137-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Igor Brikun
- Euclid Diagnostics LLC, 9800 Connecticut Dr., Crown Point, IN 46307 USA
| | - Deborah Nusskern
- Euclid Diagnostics LLC, 9800 Connecticut Dr., Crown Point, IN 46307 USA.,Present Address: Luminex Corporation, 4088 Commercial Ave, Northbrook, IL 60062 USA
| | - Diha Freije
- Euclid Diagnostics LLC, 9800 Connecticut Dr., Crown Point, IN 46307 USA
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