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Gerke MB, Jansen CS, Bilen MA. Circulating Tumor DNA in Genitourinary Cancers: Detection, Prognostics, and Therapeutic Implications. Cancers (Basel) 2024; 16:2280. [PMID: 38927984 PMCID: PMC11201475 DOI: 10.3390/cancers16122280] [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: 05/25/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
CtDNA is emerging as a non-invasive clinical detection method for several cancers, including genitourinary (GU) cancers such as prostate cancer, bladder cancer, and renal cell carcinoma (RCC). CtDNA assays have shown promise in early detection of GU cancers, providing prognostic information, assessing real-time treatment response, and detecting residual disease and relapse. The ease of obtaining a "liquid biopsy" from blood or urine in GU cancers enhances its potential to be used as a biomarker. Interrogating these "liquid biopsies" for ctDNA can then be used to detect common cancer mutations, novel genomic alterations, or epigenetic modifications. CtDNA has undergone investigation in numerous clinical trials, which could address clinical needs in GU cancers, for instance, earlier detection in RCC, therapeutic response prediction in castration-resistant prostate cancer, and monitoring for recurrence in bladder cancers. The utilization of liquid biopsy for ctDNA analysis provides a promising method of advancing precision medicine within the field of GU cancers.
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Affiliation(s)
- Margo B. Gerke
- Emory University School of Medicine, Atlanta, GA 30322, USA; (M.B.G.); (C.S.J.)
| | - Caroline S. Jansen
- Emory University School of Medicine, Atlanta, GA 30322, USA; (M.B.G.); (C.S.J.)
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Enikeeva K, Rafikova G, Sharifyanova Y, Mulyukova D, Vanzin A, Pavlov V. Epigenetics as a Key Factor in Prostate Cancer. Adv Biol (Weinh) 2024; 8:e2300520. [PMID: 38379272 DOI: 10.1002/adbi.202300520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/01/2024] [Indexed: 02/22/2024]
Abstract
Nowadays, prostate cancer is one of the most common forms of malignant neoplasms in men all over the world. Against the background of increasing incidence, there is a high mortality rate from prostate cancer, which is associated with an inadequate treatment strategy. Such a high prevalence of prostate cancer requires the development of methods that can ensure early detection of the disease, improve the effectiveness of treatment, and predict the therapeutic effect. Under these circumstances, it becomes crucial to focus on the development of effective diagnostic and therapeutic approaches. Due to the development of molecular genetic methods, a large number of studies have been accumulated on the role of epigenetic regulation of gene activity in cancer development, since it is epigenetic changes that can be detected at the earliest stages of cancer development. The presence of epigenetic aberrations in tumor tissue and correlations with drug resistance suggest new therapeutic approaches. Detection of epigenetic alterations such as CpG island methylation, histone modification, and microRNAs as biomarkers will improve the diagnosis of the disease, and the use of these strategies as targets for therapy will allow for greater personalization of prostate cancer treatment.
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Affiliation(s)
- Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Yuliya Sharifyanova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Diana Mulyukova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Alexandr Vanzin
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
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Dickey BL, Putney RM, Schell MJ, Berglund AE, Amelio AL, Caudell JJ, Chung CH, Giuliano AR. Identification of a Biomarker Panel from Genome-Wide Methylation to Detect Early HPV-Associated Oropharyngeal Cancer. Cancer Prev Res (Phila) 2024; 17:169-176. [PMID: 38286404 PMCID: PMC10987272 DOI: 10.1158/1940-6207.capr-23-0317] [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: 08/08/2023] [Revised: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
As oropharyngeal cancer (OPC) associated with human papillomavirus (HPV) increases in men, the need for a screening test to diagnose OPC early is crucial. This study agnostically identified differentially methylated CpG sites to identify additional biomarkers to improve screening for early OPC.DNA was extracted from oral gargles of 89 early cases and 108 frequency matched healthy controls, and processed for genome-wide methylation using the Illumina Infinium MethylationEPIC BeadChip. Selected sites were combined with our prior methylation data in the EPB41L3 gene (CpG sites 438, 427, and 425) and oral HPV16 and HPV18 status were considered as binary variables (positive/negative). Lasso regression identified CpG sites strongly associated with early OPC. ROC curves with AUC were generated. The panel was validated utilizing bootstrap resampling.Machine learning analyses identified 14 markers that are significantly associated with early OPC, including one EPB41L3 CpG site (438) and oral HPV16 status. A final model was trained on all available samples using the discovered panel and was able to predict early OPC compared with controls with an AUC of 0.970 on the training set. In the bootstrap validation sets, the average AUC was 0.935, indicating adequate internal validity.Our data suggest that this panel can detect OPC early, however external validation of this panel is needed. Further refinement of a panel of biomarkers to diagnose OPC earlier is urgently needed to prevent complex treatment of OPC and associated comorbidities, while reducing risk of recurrence. PREVENTION RELEVANCE This study identified biomarkers using genome-wide methylation to create a panel capable of discerning early oropharyngeal cancer (OPC) from those without OPC. Such a biomarker panel would be an effective tool to detect OPC early and prevent complications of treatment associated with later diagnosis.
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Affiliation(s)
- Brittney L. Dickey
- Center for Immunization and infection Research in Cancer and the Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida USA
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Michael J. Schell
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Antonio L. Amelio
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, Florida, USA
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Jimmy J. Caudell
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Christine H. Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Anna R. Giuliano
- Center for Immunization and infection Research in Cancer and the Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida USA
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Sequeira JP, Salta S, Freitas R, López-López R, Díaz-Lagares Á, Henrique R, Jerónimo C. Biomarkers for Pre-Treatment Risk Stratification of Prostate Cancer Patients: A Systematic Review. Cancers (Basel) 2024; 16:1363. [PMID: 38611041 PMCID: PMC11011064 DOI: 10.3390/cancers16071363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most frequently occurring malignancies. Although most cases are not life-threatening, approximately 20% endure an unfavorable outcome. PSA-based screening reduced mortality but at the cost of an increased overdiagnosis/overtreatment of low-risk (lrPCa) and favorable intermediate-risk (firPCa) PCa. PCa risk-groups are usually identified based on serum Prostate-Specific Antigen (PSA), the Gleason score, and clinical T stage, which have consistent although variable specificity or subjectivity. Thus, more effective and specific tools for risk assessment are needed, ideally making use of minimally invasive methods such as liquid biopsies. In this systematic review we assessed the clinical potential and analytical performance of liquid biopsy-based biomarkers for pre-treatment risk stratification of PCa patients. METHODS Studies that assessed PCa pre-treatment risk were retrieved from PubMed, Scopus, and MedLine. PCa risk biomarkers were analyzed, and the studies' quality was assessed using the QUADAS-2 tool. RESULTS The final analysis comprised 24 full-text articles, in which case-control studies predominated, mostly reporting urine-based biomarkers (54.2%) and biomarker quantification by qPCR (41.7%). Categorization into risk groups was heterogeneous, predominantly making use of the Gleason score. CONCLUSION This systematic review unveils the substantial clinical promise of using circulating biomarkers in assessing the risk for prostate cancer patients. However, the standardization of groups, categories, and biomarker validation are mandatory before this technique can be implemented. Circulating biomarkers might represent a viable alternative to currently available tools, obviating the need for tissue biopsies, and allowing for faster and more cost-effective testing, with superior analytical performance, specificity, and reproducibility.
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Affiliation(s)
- José Pedro Sequeira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Doctoral Program in Biomedical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Doctoral Program in Pathology and Molecular Genetics, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Freitas
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Urology & Urology Clinic, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rafael López-López
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
| | - Ángel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (R.L.-L.); (Á.D.-L.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029 Madrid, Spain
- Department of Clinical Analysis, University Hospital Complex of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP @RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (S.S.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Pitaksalee R, Parmar R, Hodgett R, Emery P, Ponchel F. DNA Hypomethylation in the TNF-Alpha Gene Predicts Rheumatoid Arthritis Classification in Patients with Early Inflammatory Symptoms. Cells 2023; 12:2376. [PMID: 37830590 PMCID: PMC10571942 DOI: 10.3390/cells12192376] [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: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023] Open
Abstract
Biomarkers for the classification of rheumatoid arthritis (RA), and particularly for anti-citrullinated peptide antibody (ACPA)-negative patients, remain an important hurdle for the early initiation of treatment. Taking advantage of DNA-methylation patterns specific to early RA, quantitative methylation-specific qPCR (qMSP) offers a robust technology for the development of biomarkers. We developed assays and established their value as RA classification biomarkers. METHODS DNA-methylation data were screened to select candidate CpGs to design qMSP assays. Eight assays were developed and tested on two early inflammatory arthritis cohorts. Logistic regression and bootstrapping were used to demonstrate the added value of the qMSP assays. RESULT Differentially methylated CpG data were screened for candidate CpG, thereby meeting the qMSP assay requirements. The top CpG candidate was in the TNF gene, for which we successfully developed a qMSP assay. Significantly lower DNA-methylation levels were observed in RA (p < 4 × 10-9), with a high predictive value (OR < 0.54/AUC < 0.198) in both cohorts (n = 127/n = 157). Regression using both datasets showed improved accuracy = 87.7% and AUC = 0.944 over the model using only clinical variables (accuracy = 85.2%, AUC = 0.917). Similar data were obtained in ACPA-negative patients (n = 167, accuracy = 82.6%, AUC = 0.930) compared to the clinical variable model (accuracy = 79.5%, AUC = 0.892). Bootstrapping using 2000 datasets confirmed that the AUCs for the clinical+TNF-qMSP model had significant added value in both analyses. CONCLUSION The qMSP technology is robust and can successfully be developed with a high specificity of the TNF qMSP assay for RA in patients with early inflammatory arthritis. It should assist classification in ACPA-negative patients, providing a means of reducing time to diagnosis and treatment.
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Affiliation(s)
- Rujiraporn Pitaksalee
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Rekha Parmar
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Richard Hodgett
- Leeds University Business School, University of Leeds, Leeds LS2 9JT, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds LS1 9LF, UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds LS2 9JT, UK
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Ye J, Wu M, He L, Chen P, Liu H, Yang H. Glutathione-S-Transferase p1 Gene Promoter Methylation in Cell-Free DNA as a Diagnostic and Prognostic Tool for Prostate Cancer: A Systematic Review and Meta-Analysis. Int J Endocrinol 2023; 2023:7279243. [PMID: 36747996 PMCID: PMC9899149 DOI: 10.1155/2023/7279243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Promoter methylation of glutathione-S-transferase p1 (GSTP1) is related to the occurrence of prostate cancer (PCa), but reports are inconsistent about the accuracy of GSTP1 promoter methylation in PCa diagnosis and prognosis. Therefore, we systematically evaluated the diagnostic and prognostic value of GSTP1 promoter methylation in PCa. METHODS The PubMed, EMBASE, Web of Science, and PMC databases were searched for all relevant studies from the date of inception to November 31, 2021. We compared differences in the incidence of GSTP1 promoter methylation in cfDNA between prostate cancer patients and controls. The odds ratio (OR) and hazard ratio (HR) were used as effect sizes, and the result of each effect size is expressed as a 95% confidence interval (95% CI). RESULTS Our meta-analysis showed that the combined sensitivity and specificity of GSTP1 promoter methylation in cfDNA for the diagnosis of prostate cancer were 0.37 (95% CI = 0.23, 0.53) and 0.97 (95% CI = 0.88, 0.99), respectively. The area under the curve (AUC) with 95% CI was 0.78 (95% CI = 0.75, 0.82). For prognostic variables, hypermethylation of GSTP1 was associated with shorter survival in PCa (HR = 2.57, 95% CI = 1.30, 5.10), with statistical significance in between-study heterogeneity (I 2 = 72%, P=0.006). The results of the subgroup analysis indicated that the heterogeneity of studies may be due to differences in the observed indicators. CONCLUSIONS The results of the meta-analysis substantiate the high specificity of promoter methylation of GSTP1 in cfDNA for the diagnosis of prostate cancer, and it may be used to more precisely evaluate the prognosis of patients with prostate cancer. It may be helpful for the early detection of prostate cancer, but it still must be combined with traditional prostate-specific antigen (PSA) or other methylated genes to accomplish this goal.
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Affiliation(s)
- Jinghe Ye
- Department of Graduate School, China Medical University, Shenyang, China
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
| | - Mao Wu
- Department of Graduate School, China Medical University, Shenyang, China
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Long He
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
| | - Peng Chen
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Hongtao Liu
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Hongwei Yang
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
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Islam A, Shaukat Z, Hussain R, Gregory SL. One-Carbon and Polyamine Metabolism as Cancer Therapy Targets. Biomolecules 2022; 12:biom12121902. [PMID: 36551330 PMCID: PMC9775183 DOI: 10.3390/biom12121902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer metabolic reprogramming is essential for maintaining cancer cell survival and rapid replication. A common target of this metabolic reprogramming is one-carbon metabolism which is notable for its function in DNA synthesis, protein and DNA methylation, and antioxidant production. Polyamines are a key output of one-carbon metabolism with widespread effects on gene expression and signaling. As a result of these functions, one-carbon and polyamine metabolism have recently drawn a lot of interest for their part in cancer malignancy. Therapeutic inhibitors that target one-carbon and polyamine metabolism have thus been trialed as anticancer medications. The significance and future possibilities of one-carbon and polyamine metabolism as a target in cancer therapy are discussed in this review.
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Affiliation(s)
- Anowarul Islam
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Zeeshan Shaukat
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Rashid Hussain
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Stephen L. Gregory
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Correspondence: ; Tel.: +61-0466987583
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He W, Xiao Y, Yan S, Zhu Y, Ren S. Cell-free DNA in the management of prostate cancer: Current status and future prospective. Asian J Urol 2022. [PMID: 37538150 PMCID: PMC10394290 DOI: 10.1016/j.ajur.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state of cfDNA as a biomarker for PCa and to examine its merits and obstacles for future clinical utilization. Methods Relevant peer-reviewed manuscripts on cfDNA as a PCa marker were evaluated by PubMed search (2010-2022) to evaluate the roles of cfDNA in PCa diagnosis, prognosis, and prediction, respectively. Results cfDNA is primarily released from cells undergoing necrosis and apoptosis, allowing for non-invasive insight into the genomic, transcriptomic, and epigenomic alterations within various PCa disease states. Next-generation sequencing, among other detection methods, enables the assessment of cfDNA abundance, mutation status, fragment characteristics, and epigenetic modifications. Multidimensional analysis based on cfDNA can facilitate early detection of PCa, risk stratification, and treatment monitoring. However, standardization of cfDNA detection methods is still required to expedite its clinical application. Conclusion cfDNA provides a non-invasive, rapid, and repeatable means of acquiring multidimensional information from PCa patients, which can aid in guiding clinical decisions and enhancing patient management. Overcoming the application barriers of cfDNA necessitates increased data sharing and international collaboration.
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Stan M, Botnarciuc V, Suceveanu AI, Mazilu L, Costea DO, Suceveanu AP, Serban D, Tudor C, Mitroi A, Brinzan C, Voinea F. Role of glutathione-S-transferase gene P1 in the diagnosis of prostate cancer in patients with 'grey level' prostate-specific antigen values. Exp Ther Med 2022; 24:591. [PMID: 35949339 PMCID: PMC9353464 DOI: 10.3892/etm.2022.11528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/11/2022] [Indexed: 11/06/2022] Open
Abstract
Prostate cancer (PC) represents the second most frequent cancer diagnosis in men and, at the same time, is one of the top six causes of death worldwide. The aim of the present study was to evaluate the diagnostic value of glutathione-S-transferase gene P1 (GST-P1) in patients that fall within the 'grey area' of the prostate-specific antigen (PSA) values. A retrospective observational study on 80 patients with prostate abnormal volumes and PSA values in the range 4-10 ng/ml was performed. The prostate gland was extracted following transrectal ultrasonography, and GST-P1 gene expression was analysed. A histopathological examination was considered the gold standard for PC diagnosis. Among the 53 patients diagnosed with PC, 69.8% (n=37) were GST-P1-positive, whereas, among the 27 patients diagnosed with benign prostatic hyperplasia, 18.5% (n=5) were GST-P1-positive. The sensitivity for diagnosing PC in patients with PSA values between 4 and 10 ng/ml was 69.81%, and the specificity was 81.48%. The positive predictive value was 88.1% [95% confidence interval (CI), 74.37-96.02%] and the negative predictive value was 57.89% (95% CI, 40.82-73.69%). Collectively, these results show the potential of using GST-P1 gene expression in patients who are suspected of having PC, but where the PSA values are inconclusive.
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Affiliation(s)
- Marius Stan
- Urology Clinic, Emergency Clinical Hospital Constanta, 900591 Constanta, Romania
- Doctoral School of Medicine, ‘Ovidius’ University Constanta, 900470 Constanta, Romania
| | - Vladimir Botnarciuc
- Doctoral School of Medicine, ‘Ovidius’ University Constanta, 900470 Constanta, Romania
| | | | - Laura Mazilu
- Faculty of Medicine, ‘Ovidius’ University Constanta, 900470 Constanta, Romania
| | | | | | - Dragos Serban
- Faculty of Medicine, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 050474, Romania
- Fourth Department of Surgery, Emergency University Hospital Bucharest, 050098 Bucharest, Romania
| | - Corneliu Tudor
- Fourth Department of Surgery, Emergency University Hospital Bucharest, 050098 Bucharest, Romania
| | - Anca Mitroi
- Department of Anatomopathology, Emergency Clinical Hospital Constanta, 900591 Constanta, Romania
| | - Costel Brinzan
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), ‘Ovidius’ University Constanta, 900470 Constanta, Romania
| | - Felix Voinea
- Urology Clinic, Emergency Clinical Hospital Constanta, 900591 Constanta, Romania
- Faculty of Medicine, ‘Ovidius’ University Constanta, 900470 Constanta, Romania
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Conduit C, Mak B, Qu W, Lulio JD, Burder R, Bressel M, Cusick T, Dhillon HM, Lourenço RDA, Underhill C, Torres J, Crumbaker M, Honeyball F, Linton A, Allen R, Davis ID, Clark SJ, Horvath LG, Mahon KL. GUIDE: a randomised non-comparative phase II trial of biomarker-driven intermittent docetaxel versus standard-of-care docetaxel in metastatic castration-resistant prostate cancer (clinical trial protocol). Ther Adv Med Oncol 2022; 14:17588359221092486. [PMID: 35465297 PMCID: PMC9019311 DOI: 10.1177/17588359221092486] [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: 02/07/2022] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Objective: To determine the efficacy and safety of intermittent docetaxel chemotherapy guided by circulating methylated glutathione S-transferase Pi-1 (mGSTP1) in men with metastatic castration-resistant prostate cancer (CRPC). Patients and Methods: GUIDE (NCT04918810) is a randomised, two-arm, non-comparative phase-2 trial recruiting 120 patients at six Australian centres. Patients with Prostate Cancer Working Group-3 defined metastatic CRPC who are commencing docetaxel 75 mg/m2 q3w will be pre-screened for detectable mGSTP1 at baseline ± following two cycles of treatment. Those with detectable plasma mGSTP1 at baseline that becomes undetectable after two cycles of chemotherapy will be eligible for GUIDE. Prior to Cycle 4 of docetaxel, these patients are randomised 2:1 to one of two treatment arms: Arm A (cease docetaxel and reinstitute if mGSTP1 becomes detectable) or Arm B (continue docetaxel 75 mg/m2 q3w in accordance with clinician’s usual practice). The primary endpoint is radiographic progression-free survival. Secondary endpoints include time on treatment holidays, safety, patient-reported outcomes, overall survival, health resource use, and cost associated with treatment. Enrolment commenced November 2021. Results and Conclusion: The results of this trial will generate data on the clinical utility of mGSTP1 as a novel biomarker to guide treatment de-escalation in metastatic CRPC.
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Affiliation(s)
- Ciara Conduit
- Australian and New Zealand Urogenital and Prostate (ANZUP) Cancer Trials Group, Camperdown, NSW, Australia Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Blossom Mak
- Chris O’Brien Lifehouse, Camperdown, NSW, Australia Garvan Institute of Medical Research, Darlinghurst, NSW, Australia The University of Sydney, Sydney, NSW, Australia
| | - Wenjia Qu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Juliana Di Lulio
- Centre for Biostatistics and Clinical Trials (BaCT), Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ronan Burder
- Centre for Biostatistics and Clinical Trials (BaCT), Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthias Bressel
- Centre for Biostatistics and Clinical Trials (BaCT), Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Thomas Cusick
- Australian and New Zealand Urogenital and Prostate (ANZUP) Cancer Trials Group, Camperdown, NSW, Australia
| | - Haryana M. Dhillon
- Australian and New Zealand Urogenital and Prostate (ANZUP) Cancer Trials Group, Camperdown, NSW, Australia Centre for Medical Psychology and Evidence-Based Decision-Making, School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW, Australia Psycho-Oncology Cooperative Research Group, School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Richard De Abreu Lourenço
- Centre for Health Economics Research and Evaluation, University of Technology Sydney, Sydney, NSW, Australia
| | - Craig Underhill
- Border Medical Oncology Research Unit, Albury Wodonga Regional Cancer Centre, Albury, NSW, Australia University of NSW Rural Clinical School, Albury, NSW, Australia
| | - Javier Torres
- Goulburn Valley Health, Shepparton, VIC, Australia Rural Medical School, The University of Melbourne, Shepparton, VIC, Australia
| | - Megan Crumbaker
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW, Australia The Kinghorn Cancer Centre, St. Vincent’s Hospital Sydney, Darlinghurst, NSW, Australia
| | - Florian Honeyball
- Dubbo Base Hospital, Dubbo, NSW, Australia School of Rural Health, The University of Sydney, Dubbo, NSW, Australia
| | - Anthony Linton
- The University of Sydney, Sydney, NSW, Australia Concord Cancer Centre, Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Ray Allen
- Australian and New Zealand Urogenital and Prostate (ANZUP) Cancer Trials Group, Camperdown, NSW, Australia
| | - Ian D. Davis
- Australian and New Zealand Urogenital and Prostate (ANZUP) Cancer Trials Group, Camperdown, NSW, Australia Eastern Health Clinical School, Monash University, Box Hill, VIC, Australia Eastern Health, Box Hill, VIC, Australia
| | - Susan J. Clark
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia UNSW Sydney, Sydney, NSW, Australia
| | - Lisa G. Horvath
- Chris O’Brien Lifehouse, Camperdown, NSW, Australia Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Kate L. Mahon
- Chris O’Brien Lifehouse, 119-143 Missenden Rd, Camperdown, NSW 2050, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- The University of Sydney, Sydney, NSW, AustraliaRoyal Prince Alfred Hospital, Camperdown, NSW, Australia
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11
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Liu D, Che B, Chen P, He J, Mu Y, Chen K, Zhang W, Xu S, Tang K. GSTT1, an increased risk factor for prostate cancer in patients with metabolic syndrome. J Clin Lab Anal 2022; 36:e24352. [PMID: 35293017 PMCID: PMC8993662 DOI: 10.1002/jcla.24352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background Glutathione S‐transferase (GSTs) gene polymorphism and metabolic syndrome (Mets) are generally considered to be risk factors for prostate cancer (PCa). However, this conclusion is still controversial. There is a close relationship between GSTs gene polymorphism and Mets. We suspect that the effect of GSTs gene polymorphism and Mets on PCa may be the result of their joint action. As a result, the purpose of this study was to investigate the potential effect of GSTs gene polymorphism on PCa in patients with Mets. Methods We collected blood samples from 128 patients with PCa and 200 controls. The GSTs gene polymorphism was detected by polymerase chain reaction‐restriction fragment length polymorphism (PCR–RFLP). Age, characteristics of Mets, frequencies of GSTs gene polymorphism, total prostate volume (TPV), Gleason score, and prostate‐specific antigen (PSA) were recorded and analyzed. Results There were significant differences in BMI, TG, LDL‐C, FBG, SBP, DBP, and HDL‐C among the control group, N‐PCa group, and Mets‐PCa group (p < 0.05). GSTT1 null genotype (OR = 2.844, 95% CI: 1.791–4.517), GSTM1 null genotype (OR = 2.192, 95% CI: 1.395–3.446), and GSTP1 (A/G + G/G) genotype (OR = 2.315, 95% CI: 1.465–3.657) were associated with PCa susceptibility and malignancy. Only the GSTT1 null genotype in Mets patients was positively correlated with PCa. Conclusions Our study suggests that GSTs gene polymorphism may be a risk factor for PCa and can predict the susceptibility and malignancy of PCa. Secondly, in Mets patients, GSTT1 null genotype significantly increased the risk of PCa. GSTM1 null genotype and the effect of GSTP1 (AG + GG) on PCa were not significantly related to Mets.
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Affiliation(s)
- Dongdong Liu
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Bangwei Che
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Pan Chen
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jun He
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yi Mu
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kehang Chen
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wenjun Zhang
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shenghan Xu
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kaifa Tang
- Department of Urology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,Institute of Medical Science of Guizhou Medical University, Guiyang, China
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12
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Locus-Specific Methylation of GSTP1, RNF219, and KIAA1539 Genes with Single Molecule Resolution in Cell-Free DNA from Healthy Donors and Prostate Tumor Patients: Application in Diagnostics. Cancers (Basel) 2021; 13:cancers13246234. [PMID: 34944854 PMCID: PMC8699300 DOI: 10.3390/cancers13246234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is the second most commonly diagnosed cancer in men, which is constantly accompanied by benign prostate hyperplasia (BPH). To reach a 100% 5-year survival rate in PCa, which is characteristic for PCa if it is diagnosed in early stages, efficient PCa diagnostics against the background of BPH are demanded. The article describes a liquid biopsy approach to differential PCa diagnostics based on the data on locus-specific methylation of the three genes (GSTP1, RNF219, and KIAA1539) obtained with NGS of cell-free DNA from blood plasma of PCa, BPH, and healthy individuals. We offered a diagnostic approach including the analysis of simultaneous methylation status of two CpGs in one cell-free DNA molecule, allowing the discrimination of all patients with absolute sensitivity and specificity. Abstract The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539 (also known as FAM214B)) in the blood plasma cell-free DNA (cfDNA) of 20 patients with prostate cancer (PCa), 18 healthy donors (HDs), and 17 patients with benign prostatic hyperplasia (BPH) was studied via the MiSeq platform. The methylation status of two CpGs within the same loci were used as the diagnostic feature for discriminating the patient groups. Many variables had good diagnostic characteristics, e.g., each of the variables GSTP1.C3.C9, GSTP1.C9, and GSTP1.C9.T17 demonstrated an 80% sensitivity at a 100% specificity for PCa patients vs. the others comparison. The analysis of RNF219 gene loci methylation allowed discriminating BPH patients with absolute sensitivity and specificity. The data on the methylation of the genes GSTP1 and RNF219 allowed discriminating PCa patients, as well as HDs, with absolute sensitivity and specificity. Thus, the data on the locus-specific methylation of cfDNA (with single-molecule resolution) combined with a diagnostic approach considering the simultaneous methylation of several CpGs in one locus enabled the discrimination of HD, BPH, and PCa patients.
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13
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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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Chen C, Chen C, Sadeghi M. Evaluation of cell-free DNA accuracy as diagnostic biomarker for prostate cancer: A systematic review and meta-analysis. Biotechnol Appl Biochem 2021; 69:749-766. [PMID: 33749048 DOI: 10.1002/bab.2149] [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: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 12/09/2022]
Abstract
PURPOSE This updated meta-analysis aimed to assess the diagnostic performance of circulating cell-free DNA (cf-DNA) for prostate cancer (PCa). METHODS A systematic search was conducted in PubMed, Scopus, Web of Science, and Embase databases to retrieve related studies. Several diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), and diagnostic odds ratio (DOR) were also used to perform the meta-synthesis. Additionally, the area under hierarchical summary receiver operating characteristic curves (AU-HSROC) was used as a global measure of test accuracy. RESULTS Twenty-nine unique articles were enrolled in the meta-analysis. Pooled SE and SP for overall accuracy of cf-DNA in PCa were obtained as 0.54 (95% CI: 0.47-0.61) and 0.92 (95% CI: 0.88-0.95), respectively. Positive LR (PLR) was 6.8 (95% CI: 4.9-9.5, I2 : 92.98%) and negative LR (NLR) was 0.5 (95% CI: 0.43-0.58). Pooled DOR was 13.56 (95% CI: 9.49-19.37) and the AU-HSROC was 0.83 (95% CI: 0.79-0.86). CONCLUSION The present study suggested that cf-DNA assays have comparable SE as well as remarkably higher SP (qualitative assays) than common biomarkers in the detection of PCa like prostate-specific antigen (PSA). In addition, cf-DNA assays have better performance in PCa confirmation and almost similar performance to PSA in excluding PCa patients.
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Affiliation(s)
- Caixia Chen
- Department of Laboratory Medicine, Henan Provincial People's Hospital, Zhengzhou, China
| | - Chunfeng Chen
- Department of the Third Affiliated Hospital, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Morteza Sadeghi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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15
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Aberrant Hypermethylation-Mediated Suppression of PYCARD Is Extremely Frequent in Prostate Cancer with Gleason Score ≥ 7. DISEASE MARKERS 2021; 2021:8858905. [PMID: 33628338 PMCID: PMC7881737 DOI: 10.1155/2021/8858905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 12/24/2022]
Abstract
Epigenetic gene silencing by aberrant DNA methylation leads to loss of key cellular pathways in tumorigenesis. In order to analyze the effects of DNA methylation on prostate cancer, we established LNCaP-derived human prostate cancer cells that can pharmacologically induce global reactivation of hypermethylated genes by the methyl-CpG targeted transcriptional activation (MeTA) method. The MeTA suppressed the growth of LNCaP-derived cells and induced apoptosis. Microarray analysis indicated that PYCARD (PYD and CARD domain containing) encoding an apoptosis-inducing factor was upregulated by 65-fold or more after treatment with MeTA. We analyzed DNA methylation statuses using 50 microdissected primary prostate cancer tissues and found an extremely high frequency of tumor-specific promoter hypermethylation of PYCARD (90%, 45/50). Moreover, DNA methylation status was significantly associated with Gleason score (P = 0.0063); the frequency of tumor-specific hypermethylation was 96% (44/46) in tumors with Gleason score ≥ 7, whereas that in tumors with Gleason score 6 was 25% (1/4). Immunohistochemical analyses using these 50 cases indicated that only 8% (4/50) of cancerous tissues expressed PYCARD, whereas 80% (40/50) of corresponding normal prostate epithelial and/or basal cells expressed PYCARD. In addition, there was no relationship between PYCARD immunostaining and the Gleason score in cancerous tissue and surrounding normal tissue. Inducible expression of PYCARD inhibited cell proliferation by induction of apoptosis. These results suggest that aberrant methylation of PYCARD is a distinctive feature of prostate cancers with Gleason score ≥ 7 and may play an important role in escaping from apoptosis in prostatic tumorigenesis.
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16
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Syedmoradi L, Norton ML, Omidfar K. Point-of-care cancer diagnostic devices: From academic research to clinical translation. Talanta 2020; 225:122002. [PMID: 33592810 DOI: 10.1016/j.talanta.2020.122002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Early and timely diagnosis of cancer plays a decisive role in appropriate treatment and improves clinical outcomes, improving public health. Significant advances in biosensor technologies are leading to the development of point-of-care (POC) diagnostics, making the testing process faster, easier, cost-effective, and suitable for on-site measurements. Moreover, the incorporation of various nanomaterials into the sensing platforms has yielded POC testing (POCT) platforms with enhanced sensitivity, cost-effectiveness and simplified detection schemes. POC cancer diagnostic devices provide promising platforms for cancer biomarker detection as compared to conventional in vitro diagnostics, which are time-consuming and require sophisticated instrumentation, centralized laboratories, and experienced operators. Current innovative approaches in POC technologies, including biosensors, smartphone interfaces, and lab-on-a-chip (LOC) devices are expected to quickly transform the healthcare landscape. However, only a few cancer POC devices (e.g. lateral flow platforms) have been translated from research laboratories to clinical care, likely due to challenges include sampling procedures, low levels of sensitivity and specificity in clinical samples, system integration and signal readout requirements. In this review, we emphasize recent advances in POC diagnostic devices for cancer biomarker detection and discuss the critical challenges which must be surmounted to facilitate their translation into clinical settings.
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Affiliation(s)
- Leila Syedmoradi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV, 25755, USA
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
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17
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Sugiura M, Sato H, Kanesaka M, Imamura Y, Sakamoto S, Ichikawa T, Kaneda A. Epigenetic modifications in prostate cancer. Int J Urol 2020; 28:140-149. [PMID: 33111429 DOI: 10.1111/iju.14406] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Prostate cancer is a major cause of cancer-related deaths among men worldwide. In addition to genomic alterations, epigenetic alterations accumulated in prostate cancer have been elucidated. While aberrant deoxyribonucleic acid hypermethylation in promoter CpG islands inactivates crucial genes associated with deoxyribonucleic acid repair, cell cycle, apoptosis or cell adhesion, aberrant deoxyribonucleic acid hypomethylation can lead to oncogene activation. Acetylation of histone is also deregulated in prostate cancer, which could cause aberrant super-enhancer formation and activation of genes associated with cancer development. Deregulations of histone methylation, such as an increase of trimethylation at position 27 of histone H3 by enhancer of zeste homolog2 overexpression, or other modifications, such as phosphorylation and ubiquitination, are also involved in prostate cancer development, and inhibitors targeting these epigenomic aberrations might be novel therapeutic strategies. In this review, we provide an overview of epigenetic alterations in the development and progression of prostate cancer, focusing on deoxyribonucleic acid methylation and histone modifications.
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Affiliation(s)
- Masahiro Sugiura
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiroaki Sato
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Manato Kanesaka
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yusuke Imamura
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shinichi Sakamoto
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Tomohiko Ichikawa
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Atsushi Kaneda
- Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
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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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Chen S, Su J, Zhao Z, Shao Y, Dou Y, Li F, Deng W, Shi J, Li Q, Zuo X, Song S, Fan C. DNA Framework-Supported Electrochemical Analysis of DNA Methylation for Prostate Cancers. NANO LETTERS 2020; 20:7028-7035. [PMID: 32857520 DOI: 10.1021/acs.nanolett.0c01898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Epigenetic alterations hold great promise as biomarkers for early stage cancer diagnosis. Nevertheless, direct identification of rare methylated DNA in the genome remains challenging. Here, we report an ultrasensitive framework nucleic acid-based electrochemical sensor for quantitative and highly selective analysis of DNA methylation. Notably, we can detect 160 fg of methylated DNA in million-fold unmethylated DNA samples using this electrochemical methylation-specific polymerase chain reaction (E-MSP) method. The high sensitivity of E-MSP enables one-step detection of low-abundance methylation at two different genes in patient serum samples. By using a combination test with two methylation alterations, we achieve high accuracy and sensitivity for reliable differentiation of prostate cancer and benign prostate hypertrophy (BPH). This new method sheds new light on translational use in early cancer diagnosis and in monitoring patients' responses to therapeutic agents.
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Affiliation(s)
- Shixing Chen
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Institute of Microsystem and information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Jing Su
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhihan Zhao
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yuan Shao
- Department of Urology, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai 201801, China
| | - Yanzhi Dou
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fuwu Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Wangping Deng
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiping Song
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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20
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Li M, Zhang C, Zhou L, Li S, Cao YJ, Wang L, Xiang R, Shi Y, Piao Y. Identification and validation of novel DNA methylation markers for early diagnosis of lung adenocarcinoma. Mol Oncol 2020; 14:2744-2758. [PMID: 32688456 PMCID: PMC7607165 DOI: 10.1002/1878-0261.12767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Lung cancer has the highest mortality of all cancers worldwide. Epigenetic alterations have emerged as potential biomarkers for early diagnosis of various cancer tissue types. To identify methylation markers for early diagnosis of lung adenocarcinoma, we aimed to integrate genome‐wide DNA methylation and gene expression data from The Cancer Genome Atlas. To this end, we first examined the global DNA methylation pattern of lung adenocarcinoma and investigated the relationship between DNA methylation subtypes and clinical features. We then extracted differentially methylated and expressed genes, and adopted feature selection techniques to determine the final methylation markers. The performance of the markers in predicting lung adenocarcinoma was evaluated on three independent datasets from Gene Expression Omnibus. Protein levels of marker genes were validated by immunohistochemistry, and their biological function was further verified in vivo. We identified three novel methylation markers in lung adenocarcinoma including cg08032924, cg14823851, and cg19161124, mapping to CMTM2, TBX4, and DPP6, respectively. Validating these results on three independent datasets indicated that the three markers can achieve extremely high sensitivity and specificity in distinguishing lung adenocarcinoma from normal samples. Immunohistochemistry quantification results confirmed that markers are weakly expressed in human lung adenocarcinoma, and CMTM2 decreased tumor growth of mouse Lewis lung carcinoma in vivo. Overall, our study identified three novel methylation markers in lung adenocarcinoma which may contribute toward an improved diagnosis potentially leading to a better outcome for patients with lung adenocarcinoma.
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Affiliation(s)
- Miao Li
- School of Medicine, Nankai University, Tianjin, China
| | - Chen Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Lijun Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Siyu Li
- School of Medicine, Nankai University, Tianjin, China
| | - Yuan Jie Cao
- Department of Radiation and Oncology, National Clinical Research Center for Cancer and Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Longlong Wang
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Shi
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
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21
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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22
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Constâncio V, Nunes SP, Moreira-Barbosa C, Freitas R, Oliveira J, Pousa I, Oliveira J, Soares M, Dias CG, Dias T, Antunes L, Henrique R, Jerónimo C. Early detection of the major male cancer types in blood-based liquid biopsies using a DNA methylation panel. Clin Epigenetics 2019; 11:175. [PMID: 31791387 PMCID: PMC6889617 DOI: 10.1186/s13148-019-0779-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Lung (LC), prostate (PCa) and colorectal (CRC) cancers are the most incident in males worldwide. Despite recent advances, optimal population-based cancer screening methods remain an unmet need. Due to its early onset, cancer specificity and accessibility in body fluids, aberrant DNA promoter methylation might be a valuable minimally invasive tool for early cancer detection. Herein, we aimed to develop a minimally invasive methylation-based test for simultaneous early detection of LC, PCa and CRC in males, using liquid biopsies. RESULTS Circulating cell-free DNA was extracted from 102 LC, 121 PCa and 100 CRC patients and 136 asymptomatic donors' plasma samples. Sodium-bisulfite modification and whole-genome amplification was performed. Promoter methylation levels of APCme, FOXA1me, GSTP1me, HOXD3me, RARβ2me, RASSF1Ame, SEPT9me and SOX17me were assessed by multiplex quantitative methylation-specific PCR. SEPT9me and SOX17me were the only biomarkers shared by all three cancer types, although they detected CRC with limited sensitivity. A "PanCancer" panel (FOXA1me, RARβ2me and RASSF1Ame) detected LC and PCa with 64% sensitivity and 70% specificity, complemented with "CancerType" panel (GSTP1me and SOX17me) which discriminated between LC and PCa with 93% specificity, but with modest sensitivity. Moreover, a HOXD3me and RASSF1Ame panel discriminated small cell lung carcinoma from non-small cell lung carcinoma with 75% sensitivity, 88% specificity, 6.5 LR+ and 0.28 LR-. An APCme and RASSF1Ame panel independently predicted disease-specific mortality in LC patients. CONCLUSIONS We concluded that a DNA methylation-based test in liquid biopsies might enable minimally invasive screening of LC and PCa, improving patient compliance and reducing healthcare costs. Moreover, it might assist in LC subtyping and prognostication.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Sandra P Nunes
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Catarina Moreira-Barbosa
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Freitas
- Urology Clinic, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Urology Clinic, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Inês Pousa
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Júlio Oliveira
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Marta Soares
- Lung Cancer Clinic and Department of Medical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Carlos Gonçalves Dias
- Digestive Tract Pathology Clinic and Surgical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Teresa Dias
- Digestive Tract Pathology Clinic and Surgical Oncology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Rua 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 de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), LAB 3, F Bdg, 1st floor Rua 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 de Jorge Viterbo Ferreira no. 228, 4050-313, Porto, Portugal.
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23
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Asai A, Konno M, Koseki J, Taniguchi M, Vecchione A, Ishii H. One-carbon metabolism for cancer diagnostic and therapeutic approaches. Cancer Lett 2019; 470:141-148. [PMID: 31759958 DOI: 10.1016/j.canlet.2019.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022]
Abstract
Altered metabolism is critical for the rapid and unregulated proliferation of cancer cells; hence the requirement for an abundant source of nucleotides. One characteristic of this metabolic reprogramming is in one-carbon (1C) metabolism, which is particularly noteworthy for its role in DNA synthesis. Various forms of methylation are also noteworthy as they relate to cancer cell survival and proliferation. In recent years, 1C metabolism has received substantial attention for its role in cancer malignancy via these functions. Therefore, therapeutic inhibitors targeting 1C metabolism have been utilized as anticancer drugs. This review outlines the importance of 1C metabolism and its clinical application in cancer. Understanding 1C metabolism could aid the development of novel cancer diagnostic and therapeutic methods.
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Affiliation(s)
- Ayumu Asai
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan; Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan; Artificial Intelligence Research Center, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Jun Koseki
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Masateru Taniguchi
- Artificial Intelligence Research Center, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome "Sapienza", Santo Andrea Hospital, Via di Grottarossa, Rome, 1035-00189, Italy
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan.
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24
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Ibrahim J, Op de Beeck K, Fransen E, Peeters M, Van Camp G. The Gasdermin E Gene Has Potential as a Pan-Cancer Biomarker, While Discriminating between Different Tumor Types. Cancers (Basel) 2019; 11:cancers11111810. [PMID: 31752152 PMCID: PMC6896019 DOI: 10.3390/cancers11111810] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023] Open
Abstract
Due to the elevated rates of incidence and mortality of cancer, early and accurate detection is crucial for achieving optimal treatment. Molecular biomarkers remain important screening and detection tools, especially in light of novel blood-based assays. DNA methylation in cancer has been linked to tumorigenesis, but its value as a biomarker has not been fully explored. In this study, we have investigated the methylation patterns of the Gasdermin E gene across 14 different tumor types using The Cancer Genome Atlas (TCGA) methylation data (N = 6502). We were able to identify six CpG sites that could effectively distinguish tumors from normal samples in a pan-cancer setting (AUC = 0.86). This combination of pan-cancer biomarkers was validated in six independent datasets (AUC = 0.84–0.97). Moreover, we tested 74,613 different combinations of six CpG probes, where we identified tumor-specific signatures that could differentiate one tumor type versus all the others (AUC = 0.79–0.98). In all, methylation patterns exhibited great variation between cancer and normal tissues, but were also tumor specific. Our analyses highlight that a Gasdermin E methylation biomarker assay, not only has the potential for being a methylation-specific pan-cancer detection marker, but it also possesses the capacity to discriminate between different types of tumors.
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Affiliation(s)
- Joe Ibrahim
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Ken Op de Beeck
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
| | - Erik Fransen
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- StatUa Centre for Statistics, University of Antwerp, 2000 Antwerp, Belgium
| | - Marc Peeters
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Guy Van Camp
- Centre of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Edegem, Belgium; (J.I.); (K.O.d.B.); (E.F.)
- Centre for Oncological Research, University of Antwerp and Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium;
- Correspondence: ; Tel.: +32-3275-9762
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25
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Patel PG, Wessel T, Kawashima A, Okello JBA, Jamaspishvili T, Guérard KP, Lee L, Lee AYW, How NE, Dion D, Scarlata E, Jackson CL, Boursalie S, Sack T, Dunn R, Moussa M, Mackie/ K, Ellis A, Marra E, Chin J, Siddiqui K, Hetou K, Pickard LA, Arthur-Hayward V, Bauman G, Chevalier S, Brimo F, Boutros PC, Lapointe PhD J, Bartlett JMS, Gooding RJ, Berman DM. A three-gene DNA methylation biomarker accurately classifies early stage prostate cancer. Prostate 2019; 79:1705-1714. [PMID: 31433512 DOI: 10.1002/pros.23895] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/29/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND We identify and validate accurate diagnostic biomarkers for prostate cancer through a systematic evaluation of DNA methylation alterations. MATERIALS AND METHODS We assembled three early prostate cancer cohorts (total patients = 699) from which we collected and processed over 1300 prostatectomy tissue samples for DNA extraction. Using real-time methylation-specific PCR, we measured normalized methylation levels at 15 frequently methylated loci. After partitioning sample sets into independent training and validation cohorts, classifiers were developed using logistic regression, analyzed, and validated. RESULTS In the training dataset, DNA methylation levels at 7 of 15 genomic loci (glutathione S-transferase Pi 1 [GSTP1], CCDC181, hyaluronan, and proteoglycan link protein 3 [HAPLN3], GSTM2, growth arrest-specific 6 [GAS6], RASSF1, and APC) showed large differences between cancer and benign samples. The best binary classifier was the GAS6/GSTP1/HAPLN3 logistic regression model, with an area under these curves of 0.97, which showed a sensitivity of 94%, and a specificity of 93% after external validation. CONCLUSION We created and validated a multigene model for the classification of benign and malignant prostate tissue. With false positive and negative rates below 7%, this three-gene biomarker represents a promising basis for more accurate prostate cancer diagnosis.
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Affiliation(s)
- Palak G Patel
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Thomas Wessel
- Life Sciences Group, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Atsunari Kawashima
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Department of Urology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - John B A Okello
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tamara Jamaspishvili
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Karl-Philippe Guérard
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - Laura Lee
- Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Anna Ying-Wah Lee
- Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Nathan E How
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Dan Dion
- Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Eleonora Scarlata
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - Chelsea L Jackson
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Suzanne Boursalie
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Tanya Sack
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Rachel Dunn
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Madeleine Moussa
- Division of Surgical Pathology, Departmant of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Karen Mackie/
- Division of Surgical Pathology, Departmant of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Audrey Ellis
- Division of Surgical Pathology, Departmant of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth Marra
- Division of Surgical Pathology, Departmant of Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Joseph Chin
- Department of Surgery (Urology), London Health Sciences Centre, London, ON, Canada
| | - Khurram Siddiqui
- Department of Surgery (Urology), London Health Sciences Centre, London, ON, Canada
| | - Khalil Hetou
- Department of Surgery (Urology), London Health Sciences Centre, London, ON, Canada
| | | | | | - Glenn Bauman
- Division of Radiation Oncology, London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Physics and Astronomy, University of Western Ontario, London, Ontario, Canada
| | - Simone Chevalier
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University Health Center and McGill University, Montreal, Québec, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Departments of Urology and Human Genetics, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Jacques Lapointe PhD
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Robert J Gooding
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Department of Physics, Engineering Physics & Astronomy, Queen's University, Kingston, Ontario, Canada
| | - David M Berman
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
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Mahon KL, Qu W, Lin HM, Spielman C, Cain D, Jacobs C, Stockler MR, Higano CS, de Bono JS, Chi KN, Clark SJ, Horvath LG. Serum Free Methylated Glutathione S-transferase 1 DNA Levels, Survival, and Response to Docetaxel in Metastatic, Castration-resistant Prostate Cancer: Post Hoc Analyses of Data from a Phase 3 Trial. Eur Urol 2019; 76:306-312. [DOI: 10.1016/j.eururo.2018.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 11/01/2018] [Indexed: 11/25/2022]
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Abstract
Over the last years, epigenetic changes, including DNA methylation and histone modifications detected in early tumorigenesis and cancer progression, have been proposed as biomarkers for cancer detection, tumor prognosis, and prediction to treatment response. Importantly for the clinical use of DNA methylation biomarkers, specific methylation signatures can be detected in many body fluids including serum/plasma samples. Several of these potential epigenetic biomarkers detected in women's cancers, colorectal cancers, prostate, pancreatic, gastric, and lung cancers are discussed. Studies conducted in breast cancer, for example, found that aberrant methylation detection of several genes in serum DNA and genome-wide epigenetic change could be used for early breast cancer diagnosis and prediction of breast cancer risk. In colorectal cancers, numerous studies have been conducted to identify specific methylation markers important for CRC detection and in fact clinical assays evaluating the methylation status of SEPT19 gene and vimentin, became commercially available. Furthermore, some epigenetic changes detected in gastric washes have been suggested as potential circulating noninvasive biomarkers for the early detection of gastric cancers. For the early detection of prostate cancer, few epigenetic markers have shown a better sensitivity and specificity than serum PSA, indicating that the inclusion of these markers together with current screening tools, could improve early diagnosis and may reduce unnecessary repeat biopsies. Similarly, in pancreatic cancers, abnormal DNA methylation of several genes including NPTX2, have been suggested as a diagnostic biomarker. Epigenetic dysregulation was also observed in several tumor suppressor genes and miRNAs in lung cancer patients, suggesting the important role of these changes in cancer initiation and progression. In conclusion, epigenetic changes detected in biological fluids could play an essential role in the early detection of several cancer types and this may have a great impact for the cancer precision medicine field.
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Constâncio V, Barros-Silva D, Jerónimo C, Henrique R. Known epigenetic biomarkers for prostate cancer detection and management: exploring the potential of blood-based liquid biopsies. Expert Rev Mol Diagn 2019; 19:367-375. [PMID: 30961397 DOI: 10.1080/14737159.2019.1604224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Although prostate cancer (PCa) stands as an important cause of cancer-related deaths, a sizeable proportion of diagnosed cases are clinically insignificant. Hence, novel and more specific biomarkers to identify clinically significant PCa are needed. Liquid biopsies offer the potential to accurately identify cancer markers, including PCa. Epigenetic biomarkers such as cell-free DNA and circulating RNAs have emerged as minimally invasive cancer markers. Areas covered: Herein, we provide an overview of epigenetic biomarkers current state based on a comprehensive review of the relevant literature in blood-based liquid biopsies and challenges/limitations of this new and growing field of cancer biomarkers. Expert opinion: The epigenetic-based biomarkers characteristics make them attractive to the clinics and their minimally invasive assessment are a promising opportunity for PCa detection/management. The main limitations are the lack of robust validation studies and integrated approaches. Future studies would benefit from a change in focus to a 'selected PCa detection'.
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Affiliation(s)
- Vera Constâncio
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Daniela Barros-Silva
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Carmen Jerónimo
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal
| | - Rui Henrique
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal.,c Department of Pathology , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
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Gurioli G, Martignano F, Salvi S, Costantini M, Gunelli R, Casadio V. GSTP1 methylation in cancer: a liquid biopsy biomarker? Clin Chem Lab Med 2019; 56:702-717. [PMID: 29305565 DOI: 10.1515/cclm-2017-0703] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/31/2017] [Indexed: 12/14/2022]
Abstract
The coding region of GSTP1 gene is preceded by a large CpG-rich region that is frequently affected by methylation. In many cancer types, GSTP1 is affected by hypermethylation and, as a consequence, it has a low expression. The aim of this review is to give an overview on GSTP1 methylation studies with a special focus on liquid biopsy, thus to summarize methods, results, sample types, different diseases, to have a complete information regarding this promising epigenetic biomarker. We used all the most valuable scientific search engines (PubMed, Medline, Scopus and Web of Science) searching the following keywords: GSTP1, methylation, cancer, urine, serum, plasma and blood. GSTP1 is a largely investigated tissue biomarker in several malignancies such as prostate, breast, lung and hepatocellular carcinoma with good performances especially for diagnostic purposes. As a liquid biopsy biomarker, it has been mainly investigated in prostate cancer (PCa) where it showed a high specificity but a low sensitivity; thus, it is recommended in combination with other biomarkers. Despite the large number of published papers and the promising results, GSTP1 has not yet entered the clinical practice even for PCa diagnosis. For this reason, further large and prospective studies are needed to validate this assay.
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Affiliation(s)
- Giorgia Gurioli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Filippo Martignano
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Matteo Costantini
- Pathology Unit, Department of Medical Oncology, Morgagni Pierantoni Hospital, Forlì, Italy
| | - Roberta Gunelli
- Department of Urology, Morgagni Pierantoni Hospital, Forli, Italy
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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Yegnasubramanian S, De Marzo AM, Nelson WG. Prostate Cancer Epigenetics: From Basic Mechanisms to Clinical Implications. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a030445. [PMID: 29959132 DOI: 10.1101/cshperspect.a030445] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A level of epigenetic programming, encoded by complex sets of chemical marks on DNA and histones, and by context-specific DNA, RNA, protein interactions, that all regulate the structure, organization, and function of the genome, is critical to establish both normal and neoplastic cell identities and functions. This structure-function relationship of the genome encoded by the epigenetic programming can be thought of as an epigenetic cityscape that is built on the underlying genetic landscape. Alterations in the epigenetic cityscape of prostate cancer cells compared with normal prostate tissues have a complex interplay with genetic alterations to drive prostate cancer initiation and progression. Indeed, mutations in genes encoding epigenetic enzymes are often observed in human cancers including prostate cancer. Interestingly, alterations in the prostate cancer epigenetic cityscape can be highly recurrent, a facet that can be exploited for development of biomarkers and potentially as therapeutic targets.
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Affiliation(s)
- Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
| | - William G Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
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31
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Scott E, Munkley J. Glycans as Biomarkers in Prostate Cancer. Int J Mol Sci 2019; 20:E1389. [PMID: 30893936 PMCID: PMC6470778 DOI: 10.3390/ijms20061389] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/07/2019] [Accepted: 03/17/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer is the most commonly diagnosed malignancy in men, claiming over350,000 lives worldwide annually. Current diagnosis relies on prostate-specific antigen (PSA)testing, but this misses some aggressive tumours, and leads to the overtreatment of non-harmfuldisease. Hence, there is an urgent unmet clinical need to identify new diagnostic and prognosticbiomarkers. As prostate cancer is a heterogeneous and multifocal disease, it is likely that multiplebiomarkers will be needed to guide clinical decisions. Fluid-based biomarkers would be ideal, andattention is now turning to minimally invasive liquid biopsies, which enable the analysis oftumour components in patient blood or urine. Effective diagnostics using liquid biopsies willrequire a multifaceted approach, and a recent high-profile review discussed combining multipleanalytes, including changes to the tumour transcriptome, epigenome, proteome, and metabolome.However, the concentration on genomics-based paramaters for analysing liquid biopsies ispotentially missing a goldmine. Glycans have shown huge promise as disease biomarkers, anddata suggests that integrating biomarkers across multi-omic platforms (including changes to theglycome) can improve the stratification of patients with prostate cancer. A wide range ofalterations to glycans have been observed in prostate cancer, including changes to PSAglycosylation, increased sialylation and core fucosylation, increased O-GlcNacylation, theemergence of cryptic and branched N-glyans, and changes to galectins and proteoglycans. In thisreview, we discuss the huge potential to exploit glycans as diagnostic and prognostic biomarkersfor prostate cancer, and argue that the inclusion of glycans in a multi-analyte liquid biopsy test forprostate cancer will help maximise clinical utility.
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Affiliation(s)
- Emma Scott
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Jennifer Munkley
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK.
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32
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Abstract
Cell-free DNA can be evaluated for the epigenetic component. Epigenetic alterations consist of changes in gene functions that do not involve changes in DNA sequence. The mainly studied epigenetic alteration is DNA methylation occurring at CpG islands in the promoter regions for which several literature data showed clinical relevance. This chapter is an overview of the epigenetic alterations detected in cell-free DNA.
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34
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Zhao F, Olkhov-Mitsel E, Kamdar S, Jeyapala R, Garcia J, Hurst R, Hanna MY, Mills R, Tuzova AV, O'Reilly E, Kelly S, Cooper C, Brewer D, Perry AS, Clark J, Fleshner N, Bapat B. A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer. Clin Epigenetics 2018; 10:147. [PMID: 30470249 PMCID: PMC6260648 DOI: 10.1186/s13148-018-0575-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/28/2018] [Indexed: 12/12/2022] Open
Abstract
Background Prevention of unnecessary biopsies and overtreatment of indolent disease remains a challenge in the management of prostate cancer. Novel non-invasive tests that can identify clinically significant (intermediate-risk and high-risk) diseases are needed to improve risk stratification and monitoring of prostate cancer patients. Here, we investigated a panel of six DNA methylation biomarkers in urine samples collected post-digital rectal exam from patients undergoing prostate biopsy, for their utility to guide decision making for diagnostic biopsy and early detection of aggressive prostate cancer. Results We recruited 408 patients in risk categories ranging from benign to low-, intermediate-, and high-risk prostate cancer from three international cohorts. Patients were separated into 2/3 training and 1/3 validation cohorts. Methylation biomarkers were analyzed in post-digital rectal exam urinary sediment DNA by quantitative MethyLight assay and investigated for their association with any or aggressive prostate cancers. We developed a Prostate Cancer Urinary Epigenetic (ProCUrE) assay based on an optimal two-gene (HOXD3 and GSTP1) LASSO model, derived from methylation values in the training cohort, and assessed ProCUrE’s diagnostic and prognostic ability for prostate cancer in both the training and validation cohorts. ProCUrE demonstrated improved prostate cancer diagnosis and identification of patients with clinically significant disease in both the training and validation cohorts. Using three different risk stratification criteria (Gleason score, D’Amico criteria, and CAPRA score), we found that the positive predictive value for ProCUrE was higher (59.4–78%) than prostate specific antigen (PSA) (38.2–72.1%) for all risk category comparisons. ProCUrE also demonstrated additive value to PSA in identifying GS ≥ 7 PCa compared to PSA alone (DeLong’s test p = 0.039), as well as additive value to the PCPT risk calculator for identifying any PCa and GS ≥ 7 PCa (DeLong’s test p = 0.011 and 0.022, respectively). Conclusions ProCUrE is a promising non-invasive urinary methylation assay for the early detection and prognostication of prostate cancer. ProCUrE has the potential to supplement PSA testing to identify patients with clinically significant prostate cancer. Electronic supplementary material The online version of this article (10.1186/s13148-018-0575-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fang Zhao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | - Ekaterina Olkhov-Mitsel
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | - Shivani Kamdar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | - Renu Jeyapala
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Julia Garcia
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Rachel Hurst
- Schools of Medicine and Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | | | - Robert Mills
- Schools of Medicine and Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Alexandra V Tuzova
- Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Eve O'Reilly
- Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sarah Kelly
- Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Colin Cooper
- Schools of Medicine and Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | | | - Daniel Brewer
- Schools of Medicine and Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.,The Earlham Institute, Norwich, Norfolk, UK
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jeremy Clark
- Schools of Medicine and Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Neil Fleshner
- Division of Urology, University Health Network, University of Toronto, Toronto, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada. .,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada. .,Division of Urology, University Health Network, University of Toronto, Toronto, Canada.
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35
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Riaz IB, Wang L, Kohli M. Liquid biopsy approach in the management of prostate cancer. Transl Res 2018; 201:60-70. [PMID: 29936077 PMCID: PMC6631037 DOI: 10.1016/j.trsl.2018.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 01/29/2023]
Abstract
Liquid biopsies examine tumor cells or tumor genomic content in circulating fluids. In advanced prostate cancer which metastasizes frequently to the bone, it is difficult to evaluate underlying and evolving genomic heterogeneity of skeletal metastases for effecting clinical care for which reason liquid biopsies offer an alternate approach. In this review, we will summarize the current state of a wide variety of liquid biopsy-based biomarker assays currently being investigated and developed for managing prostate cancer. We will also highlight technical and clinical challenges and opportunities for translating liquid biopsies into clinical applications.
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Affiliation(s)
- Irbaz Bin Riaz
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin.
| | - Manish Kohli
- Department of Oncology, Mayo Clinic, Rochester, Minnesota.
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36
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Syedmoradi L, Esmaeili F, Norton ML. Towards DNA methylation detection using biosensors. Analyst 2018; 141:5922-5943. [PMID: 27704092 DOI: 10.1039/c6an01649a] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates. To overcome these obstacles, great efforts have been made toward the development of reliable sensor devices to solve these limitations, providing sensitive, fast and cost-effective measurements. The use of biosensors for DNA methylation biomarkers has increased in recent years, because they are portable, simple, rapid, and inexpensive which offers a straightforward way to detect methylated biomarkers. In this review, we give an overview of the conventional techniques for the detection of DNA methylation and then will focus on recent advances in biosensor based methylation detection that eliminate bisulfite conversion and PCR amplification.
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Affiliation(s)
- Leila Syedmoradi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Esmaeili
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, USA.
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Meronard K, Josowicz M, Saheb A. Voltammetric Application of Polypyrrole-Modified Microelectrode Array for the Characterization of DNA Methylation in Glutathione S-Transferase Pi 1. ANAL LETT 2018; 51:2612-2625. [PMID: 30245524 DOI: 10.1080/00032719.2018.1437623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Direct and efficient label-free voltammetric detection of Glutathione S-Transferase Pi 1 (GSTP1) hypermethylation is reported using a custom developed 16-channel Microelectrode Array chip. The microelectrode array chip is used in a dipstick configuration allowing detection of DNA hybridization in a solution volume of only 0.35 mL. Platinum microelectrode disks (n = 16) 30 µm in diameter have been modified with a polypyrrole bilayer before any contact with the oligonucleotides. The attachment of the 15-mer Probe DNA to the bilayer is random but controlled by the presence of aliphatic tether groups allowing it to form a bidentate complex with the probe DNA. The voltammetric detection procedure of methylated GSTP1-specific target DNA is combined with bisulfite treatment of target DNA. Changes at the interface of the modified microelectrodes in an array configuration are used to record simultaneously cyclic voltammetry on all of the devices. The detection of the hybridization is evaluated statistically for a yes or no event by comparing the changes in recorded cyclic voltammograms before and after exposure to the Target DNA. All cyclic voltammograms of the methylated target show a greater percentage change than those with the non-methylated target exposure and show a greater change in cyclic voltammogram area after methylated target exposure. We observe an average percentage difference of 25.6% ± 4.9 with a variation of 19.1%. These results demonstrate that the fast sensing strategy possesses sensitivity and good specificity. Furthermore, this technology can potentially support rapid, accurate diagnosis and risk assessment of patients with prostate cancer.
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Affiliation(s)
- Kenton Meronard
- Department of Chemistry and Forensic Science, Albany State University, Albany, Georgia 31705.
| | - Mira Josowicz
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Amir Saheb
- Department of Chemistry and Forensic Science, Albany State University, Albany, Georgia 31705.
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Sánchez BE, Aguayo A, Martínez B, Rodríguez F, Marmolejo M, Svyryd Y, Luna L, Muñoz LA, Jiménez MA, Sotomayor M, Vargas V F, Mutchinick OM. Using Genetic and Epigenetic Markers to Improve Differential Diagnosis of Prostate Cancer and Benign Prostatic Hyperplasia by Noninvasive Methods in Mexican Patients. Clin Genitourin Cancer 2018; 16:e867-e877. [DOI: 10.1016/j.clgc.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/31/2018] [Accepted: 02/18/2018] [Indexed: 10/17/2022]
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Potential Epigenetic Biomarkers for Prostate Cancer Screening. Int Neurourol J 2018; 22:142-144. [PMID: 29991236 PMCID: PMC6059910 DOI: 10.5213/inj.1836096.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/24/2018] [Indexed: 11/08/2022] Open
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40
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Brikun I, Nusskern D, Decatus A, Harvey E, Li L, Freije D. A panel of DNA methylation markers for the detection of prostate cancer from FV and DRE urine DNA. Clin Epigenetics 2018; 10:91. [PMID: 29988684 PMCID: PMC6029393 DOI: 10.1186/s13148-018-0524-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/21/2018] [Indexed: 12/11/2022] Open
Abstract
Background Early screening for prostate cancer (PCA) remains controversial because of overdiagnosis and overtreatment of clinically insignificant cancers. Even though a number of diagnostic tests have been developed to improve on PSA testing, there remains a need for a more informative non-invasive test for PCA. The objective of this study is to identify a panel of DNA methylation markers suitable for a non-invasive diagnostic test from urine DNA collected following a digital rectal exam (DRE) and/or from first morning void (FV). A secondary objective is to determine if the cumulative methylation is indicative of biopsy findings. Methods DRE and FV urine samples were prospectively collected from 94 patients and analyzed using 24 methylation-specific quantitative PCR assays derived from 19 CpG islands. The methylation of individual markers and various combinations of markers was compared to biopsy results. A methylation threshold for cancer classification was determined using a target specificity of 70%. The average methylation and the number of positive markers were also compared to the result of the biopsy, and the area under the receiver operating characteristic curves (AUCs) were calculated. Results Methylation of all 19 markers was detected in FV and DRE DNAs. Combining the methylation of two or more markers improved on individual marker results. Using 6of19 methylated markers as the threshold for cancer classification yielded a specificity of 71% (95% CI, 0.57-0.86) from both DRE and FV and a sensitivity of 89% (95% CI, 0.79-0.97) from DRE and 94% (95% CI, 0.84-1.0) from FV. The negative predictive value at the 6of19 threshold was ≥ 90 for both DNA types. Conclusions PCA-specific methylation was detected in both FV and DRE DNA. There was no significant difference in diagnostic accuracy at the 6of19 threshold between DRE and FV urine DNA. The results support the development of a non-invasive diagnostic test to reduce unnecessary biopsies in men with elevated PSA. The test can also provide patients with personalized recommendations based on their own methylation profile.
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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
| | - Andrew Decatus
- BioStat Solutions Inc., 5280 Corporate Dr., Suite C200, Frederick, MD 21703 USA
| | - Eric Harvey
- 3Health Decisions Inc., 2510 Meridian Parkway, Durham, NC 27713 USA
| | - Lin Li
- BioStat Solutions Inc., 5280 Corporate Dr., Suite C200, Frederick, MD 21703 USA
| | - Diha Freije
- Euclid Diagnostics LLC, 9800 Connecticut Dr., Crown Point, IN 46307 USA
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Abstract
Epigenetic alterations such as DNA methylation defects and aberrant covalent histone modifications occur within all cancers and are selected for throughout the natural history of tumor formation, with changes being detectable in early onset, progression, and ultimately recurrence and metastasis. The ascertainment and use of these marks to identify at-risk patient populations, refine diagnostic criteria, and provide prognostic and predictive factors to guide treatment decisions are of growing clinical relevance. Furthermore, the targetable nature of epigenetic modifications provides a unique opportunity to alter treatment paradigms and provide new therapeutic options for patients whose malignancies possess these aberrant epigenetic modifications, paving the way for new and personalized medicine. DNA methylation has proven to be of significant clinical utility for its stability and relative ease of testing. The intent of this review is to elaborate upon well-supported examples of epigenetic precision medicine and how the field is moving forward, primarily in the context of aberrant DNA methylation.
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Affiliation(s)
- Rachael J Werner
- From the *Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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Haldrup C, Pedersen AL, Øgaard N, Strand SH, Høyer S, Borre M, Ørntoft TF, Sørensen KD. Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies. Mol Oncol 2018; 12:545-560. [PMID: 29465788 PMCID: PMC5891052 DOI: 10.1002/1878-0261.12183] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 10/17/2017] [Accepted: 02/14/2018] [Indexed: 01/04/2023] Open
Abstract
Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, leading to overdiagnosis and overtreatment. Aberrant promoter hypermethylation of specific genes has been suggested as novel candidate biomarkers for PC that may improve diagnosis and prognosis. We here analyzed ST6GALNAC3 and ZNF660 promoter methylation in prostate tissues, and ST6GALNAC3,ZNF660,CCDC181, and HAPLN3 promoter methylation in liquid biopsies. First, using four independent patient sample sets, including a total of 110 nonmalignant (NM) and 705 PC tissue samples, analyzed by methylation‐specific qPCR or methylation array, we found that hypermethylation of ST6GALNAC3 and ZNF660 was highly cancer‐specific with areas under the curve (AUC) of receiver operating characteristic (ROC) curve analysis of 0.917–0.995 and 0.846–0.903, respectively. Furthermore, ZNF660 hypermethylation was significantly associated with biochemical recurrence in two radical prostatectomy (RP) cohorts of 158 and 392 patients and remained significant also in the subsets of patients with Gleason score ≤7 (univariate Cox regression and log‐rank tests, P < 0.05), suggesting that ZNF660 methylation analysis can potentially help to stratify low‐/intermediate‐grade PCs into indolent vs. more aggressive subtypes. Notably, ZNF660 hypermethylation was also significantly associated with poor overall and PC‐specific survival in the RP cohort (n = 158) with long clinical follow‐up available. Moreover, as proof of principle, we successfully detected highly PC‐specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3,ZNF660,HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation‐specific PCR analysis. Finally, we generated a three‐gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity. In conclusion, we here for the first time demonstrate diagnostic biomarker potential of ST6GALNAC3 and ZNF660 methylation, as well as prognostic biomarker potential of ZNF660. Furthermore, we show that hypermethylation of four genes can be detected in ctDNA in liquid biopsies (serum) from patients with PC.
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Affiliation(s)
- Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Anne L Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Siri H Strand
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Søren Høyer
- Department of Histopathology, Aarhus University Hospital, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Denmark
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
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43
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Vrba L, Futscher BW. A suite of DNA methylation markers that can detect most common human cancers. Epigenetics 2018; 13:61-72. [PMID: 29212414 DOI: 10.1080/15592294.2017.1412907] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cancer-specific DNA methylation from the tumor derived fraction of cell free DNA found in blood samples could be used for minimally invasive detection and monitoring of cancer. The knowledge of marker regions with cancer-specific DNA methylation is necessary to the success of such a process. We analyzed the largest cancer DNA methylation dataset available-TCGA Illumina HumanMethylation450 data with over 8,500 tumors-in order to find cancer-specific DNA methylation markers for most common human cancers. First, we identified differentially methylated regions for individual cancer types and those were further filtered against data from normal tissues to obtain marker regions with cancer-specific methylation, resulting in a total of 1,250 hypermethylated and 584 hypomethylated marker CpGs. From hypermethylated markers, optimal sets of six markers for each TCGA cancer type were chosen that could identify most tumors with high specificity and sensitivity [area under the curve (AUC): 0.969-1.000] and a universal 12 marker set that can detect tumors of all 33 TCGA cancer types (AUC >0.84). In addition to hundreds of new DNA methylation markers, our approach also identified markers that are in current clinical use, SEPT9 and GSTP1, indicating the validity of our approach and a significant potential utility for the newly discovered markers. The hypermethylated markers are linked to polycomb associated loci and a significant fraction of the discovered markers is within noncoding RNA genes; one of the best markers is MIR129-2. Future clinical testing of herein discovered markers will confirm new markers that will improve minimally invasive diagnosis and monitoring for multiple cancers.
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Affiliation(s)
- Lukas Vrba
- a The University of Arizona Cancer Center , Tucson , AZ 85724 , USA
| | - Bernard W Futscher
- a The University of Arizona Cancer Center , Tucson , AZ 85724 , USA.,b Department of Pharmacology & Toxicology, College of Pharmacy , The University of Arizona , Tucson , AZ 85724 , USA
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Kim H, Wang X, Jin P. Developing DNA methylation-based diagnostic biomarkers. J Genet Genomics 2018; 45:87-97. [PMID: 29496486 DOI: 10.1016/j.jgg.2018.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
Abstract
An emerging paradigm shift for disease diagnosis is to rely on molecular characterization beyond traditional clinical and symptom-based examinations. Although genetic alterations and transcription signature were first introduced as potential biomarkers, clinical implementations of these markers are limited due to low reproducibility and accuracy. Instead, epigenetic changes are considered as an alternative approach to disease diagnosis. Complex epigenetic regulation is required for normal biological functions and it has been shown that distinctive epigenetic disruptions could contribute to disease pathogenesis. Disease-specific epigenetic changes, especially DNA methylation, have been observed, suggesting its potential as disease biomarkers for diagnosis. In addition to specificity, the feasibility of detecting disease-associated methylation marks in the biological specimens collected noninvasively, such as blood samples, has driven the clinical studies to validate disease-specific DNA methylation changes as a diagnostic biomarker. Here, we highlight the advantages of DNA methylation signature for diagnosis in different diseases and discuss the statistical and technical challenges to be overcome before clinical implementation.
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Affiliation(s)
- Hyerim Kim
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xudong Wang
- Department of Gastroenterological Surgery, The Second Hospital, Jilin University, Changchun 130041, China.
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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45
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Grelus A, Nica DV, Miklos I, Belengeanu V, Ioiart I, Popescu C. Clinical Significance of Measuring Global Hydroxymethylation of White Blood Cell DNA in Prostate Cancer: Comparison to PSA in a Pilot Exploratory Study. Int J Mol Sci 2017; 18:ijms18112465. [PMID: 29156615 PMCID: PMC5713431 DOI: 10.3390/ijms18112465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
This is the first study investigating the clinical relevance of 5-hydroxymethylcytosine (5hmC) in genomic DNA from white blood cells (WBC) in the context of prostate cancer (PCa) and other prostate pathologies. Using an enzyme-linked immunosorbent assay, we identified significantly different distributions of patients with low and elevated 5hmC content in WBC DNA across controls and patients with prostate cancer (PCa), atypical small acinar proliferation (ASAP), and benign prostatic hyperplasia (BPH). The measured values were within the normal range for most PCa patients, while the latter category was predominant for ASAP. We observed a wider heterogeneity in 5hmC content in all of the prostate pathologies analyzed when compared to the healthy age-matched controls. When compared to blood levels of prostate-specific antigen (PSA), this 5hmC-based biomarker had a lower performance in PCa detection than the use of a PSA cut-off of 2.5 nanograms per milliliter (ng/mL). Above this threshold, however, it delineated almost three quarters of PCa patients from controls and patients with other prostate pathologies. Overall, genome-wide 5hmC content of WBC DNA appears to be applicable for detecting non-cancerous prostate diseases, rather than PCa. Our results also suggest a potential clinical usefulness of complementing PSA as a PCa marker by the addition of a set of hydroxymethylation markers in the blood, but further studies are necessary to confirm these findings.
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Affiliation(s)
- Alin Grelus
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
- Arad County Emergency Clinical Hospital, Str. Andreny Karoly nr. 2-4, 310037 Arad, Romania.
| | - Dragos V Nica
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
| | - Imola Miklos
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
- Arad County Emergency Clinical Hospital, Str. Andreny Karoly nr. 2-4, 310037 Arad, Romania.
| | - Valerica Belengeanu
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
| | - Ioan Ioiart
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
- Arad County Emergency Clinical Hospital, Str. Andreny Karoly nr. 2-4, 310037 Arad, Romania.
| | - Cristina Popescu
- Institute of Life Sciences, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
- Faculty of Pharmacy, "Vasile Goldis" Western University of Arad, Str. Liviu Rebreanu 86, 310045 Arad, Romania.
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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Wu D, Ni J, Beretov J, Cozzi P, Willcox M, Wasinger V, Walsh B, Graham P, Li Y. Urinary biomarkers in prostate cancer detection and monitoring progression. Crit Rev Oncol Hematol 2017; 118:15-26. [DOI: 10.1016/j.critrevonc.2017.08.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/08/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022] Open
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48
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Pan Y, Liu G, Zhou F, Su B, Li Y. DNA methylation profiles in cancer diagnosis and therapeutics. Clin Exp Med 2017; 18:1-14. [PMID: 28752221 DOI: 10.1007/s10238-017-0467-0] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
Cancer initiation and proliferation is regulated by both epigenetic and genetic events with epigenetic modifications being increasingly identified as important targets for cancer research. DNA methylation catalyzed by DNA methyltransferases (DNMTs) is one of the essential epigenetic mechanisms that control cell proliferation, apoptosis, differentiation, cell cycle, and transformation in eukaryotes. Recent progress in epigenetics revealed a deeper understanding of the mechanisms of tumorigenesis and provided biomarkers for early detection, diagnosis, and prognosis in cancer patients. Although DNA methylation biomarker possesses potential contributing to precision medicine, there are still limitations to be overcome before it reaches clinical setting. Hence, the current status of DNA methylation biomarkers was reviewed and the future use in clinic was also predicted.
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Affiliation(s)
- Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, No.169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Guohong Liu
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX, 77030, USA
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Bojin Su
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX, 77030, USA.
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, No.169 Donghu Road, Wuchang District, Wuhan, 430071, China.
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49
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Lin SY, Linehan JA, Wilson TG, Hoon DS. Emerging Utility of Urinary Cell-free Nucleic Acid Biomarkers for Prostate, Bladder, and Renal Cancers. Eur Urol Focus 2017; 3:265-272. [DOI: 10.1016/j.euf.2017.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/05/2023]
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50
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Abstract
Normal cells have a level of epigenetic programming that is superimposed on the genetic code to establish and maintain their cell identity and phenotypes. This epigenetic programming can be thought as the architecture, a sort of cityscape, that is built upon the underlying genetic landscape. The epigenetic programming is encoded by a complex set of chemical marks on DNA, on histone proteins in nucleosomes, and by numerous context-specific DNA, RNA, protein interactions that all regulate the structure, organization, and function of the genome in a given cell. It is becoming increasingly evident that abnormalities in both the genetic landscape and epigenetic cityscape can cooperate to drive carcinogenesis and disease progression. Large-scale cancer genome sequencing studies have revealed that mutations in genes encoding the enzymatic machinery for shaping the epigenetic cityscape are among the most common mutations observed in human cancers, including prostate cancer. Interestingly, although the constellation of genetic mutations in a given cancer can be quite heterogeneous from person to person, there are numerous epigenetic alterations that appear to be highly recurrent, and nearly universal in a given cancer type, including in prostate cancer. The highly recurrent nature of these alterations can be exploited for development of biomarkers for cancer detection and risk stratification and as targets for therapeutic intervention. Here, we explore the basic principles of epigenetic processes in normal cells and prostate cancer cells and discuss the potential clinical implications with regards to prostate cancer biomarker development and therapy.
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Affiliation(s)
- Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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