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1
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Baryshev M, Maksimova I, Sasoveca I. Allele-specific methylation of the PSA promoter in prostate cells: A new translational marker for the differential diagnosis of prostate cancer. Genes Dis 2025; 12:101487. [PMID: 39926329 PMCID: PMC11804549 DOI: 10.1016/j.gendis.2024.101487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 07/03/2024] [Accepted: 07/28/2024] [Indexed: 02/11/2025] Open
Affiliation(s)
- Mikhail Baryshev
- Institute of Microbiology and Virology, Riga Stradins University, Ratsupites Str 5, Riga LV 1067, Latvia
| | - Irina Maksimova
- Institute of Microbiology and Virology, Riga Stradins University, Ratsupites Str 5, Riga LV 1067, Latvia
| | - Ilona Sasoveca
- Institute of Microbiology and Virology, Riga Stradins University, Ratsupites Str 5, Riga LV 1067, Latvia
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2
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Baryshev M, Vjaters E. Allele-Specific CG/CCWGG Methylation of the PSA Promoter Discriminates Aggressive, Indolent, and Benign Prostate Cell Lines and Is Involved in the Regulation of PSA Expression. Int J Mol Sci 2025; 26:1243. [PMID: 39941009 PMCID: PMC11818708 DOI: 10.3390/ijms26031243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 02/16/2025] Open
Abstract
Prostate-specific antigen remains a cornerstone biomarker for prostate cancer diagnosis and management. However, the molecular mechanisms regulating its expression, particularly through DNA methylation, are not fully understood. Here, we report a comprehensive analysis of allele-specific CpG and CCWGG methylation in the proximal PSA promoter across aggressive (PC3), indolent (LNCaP), benign (BPH1), and normal (HPrEpiC) prostate cell lines and provide insights into the unique methylation patterns associated with these states. Our findings reveal that PC3 cells, representing an aggressive PCa phenotype, exhibit complete biallelic methylation of the PSA promoter, leading to PSA gene silencing. Conversely, LNCaP cells display a fully unmethylated promoter with biallelic PSA expression. Interestingly, BPH1 cells display a monoallelic CG/CCWGG methylation pattern, yet fail to express PSA, suggesting imprinting defects or RNA decay mechanisms. Notably, acquisition of biallelic PSA promoter methylation status in PC3 was accompanied by upregulation of DNMT1, whereas unmethylated PSA promoter state in LNCaP was associated with downregulation of DNMT1. These findings highlight distinct methylation patterns in the PSA promoter that differentiate between aggressive, indolent, and benign prostate states. Translating this epigenetic insight into clinical diagnostics could enhance the precision of PSA-based diagnostics, addressing limitations such as false negatives in PSA testing for aggressive PCa. Further exploration of CCWGG methylation's role in imprinting and monoallelic expression is warranted, particularly in patient-derived samples.
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Affiliation(s)
- Mikhail Baryshev
- Institute of Microbiology and Virology, Riga Stradins University, Ratsupites Str 5, LV-1067 Riga, Latvia
| | - Egils Vjaters
- Institute of Oncology and Molecular Genetics, Riga Stradins University, Pilsoņu Str 13, LV-1007 Riga, Latvia;
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3
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Ahmad SM, Ahmed BS, Khidhir KG, Rahman HS. Prospective quantitative gene expression analysis of kallikrein-related peptidase KLK10 as a diagnostic biomarker for childhood acute lymphoblastic leukemia. PeerJ 2022; 10:e13489. [PMID: 35669967 PMCID: PMC9165590 DOI: 10.7717/peerj.13489] [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: 01/21/2022] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Background The most common malignancy in children is acute lymphoblastic leukemia (ALL). This study aimed to explore KLK10 mRNA expression as a potential diagnostic biomarker for ALL in children and to examine the effect of chemotherapy on KLK10 mRNA expression following the induction and after three months of receiving chemotherapy. Methods In this prospective study, total RNA was extracted from blood samples of 23 pediatric ALL patients on diagnosis, after one month and three months of receiving chemotherapy. Healthy pediatric volunteers (n = 12) were selected as control individuals. After cDNA synthesis, KLK10 mRNA gene expression levels were quantified using quantitative real-time PCR (qRT-PCR). Results KLK10 mRNA expression levels were significantly decreased in leukemic cells compared to their levels in cells of normal blood samples (p = 0.0001). KLK10 expression levels in ALL patients after one month and three months of receiving chemotherapy decreased compared to normal blood samples (p < 0.0001 and p = 0.0175 respectively). The expression level of KLK10 mRNA in ALL patients after one month of chemotherapy was decreased compared to their level on diagnosis (p = 0.4413). KLK10 mRNA expression levels in ALL patients after three months of chemotherapy were increased compared to their level on diagnosis (p = 0.0602). The ROC curve illustrated that KLK10 mRNA expression could very efficiently discriminate ALL patients from normal counterparts (AUC=0.886, 95% CI [0.7720-1.000], SE = 0.0582, p = 0.0004). Conclusion KLK10 mRNA expression could serve as a potential diagnostic molecular biomarker for ALL in children.
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Affiliation(s)
- Shwan Majid Ahmad
- Department of Biochemistry, College of Medicine, University of Sulaimani, Sulaimaniyah, Iraq
| | - Basima Sadq Ahmed
- Department of Biochemistry & Clinical Chemistry, College of Pharmacy, University of Sulaimani, Sulaimaniyah, Iraq
| | - Karzan Ghafur Khidhir
- Department of Biology, College of Science, University of Sulaimani, Sulaimaniyah, Iraq
| | - Heshu Sulaiman Rahman
- Department of Physiology, College of Medicine, University of Sulaimani, Sulaimaniyah, Iraq
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4
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Ma X, Zou L, Chen Z, Li X, Wei L, Wu X. Demethylation of miR-195 suppresses prostate cancer cell proliferation, migration and invasion. FEBS Open Bio 2020; 10:525-534. [PMID: 31977154 PMCID: PMC7137791 DOI: 10.1002/2211-5463.12799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/20/2019] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
Prostate cancer (PCa) is the most prevalent cancer among men and the second leading cause of tumor-associated deaths worldwide, with increasing incidence rates over the last 10 years. Recently, miR-195 was reported to be hypermethylated at its promoter CpG island and down-regulated in hepatocellular carcinoma. However, the function of miR-195 and the underlying mechanisms in PCa remain unknown. Here, we report that a significant down-regulation of microRNA-195 (miR-195) in PCa tissues and cell lines was associated with promoter methylation status. Overexpression of miR-195 significantly suppressed cell proliferation, migration, invasion and epithelial-mesenchymal transition (increased E-cadherin and decreased N-cadherin) in PCa cells. We further demonstrated that transfection with a miR-195 inhibitor reversed the inhibitory effect of the DNA methyltransferase inhibitor 5-azacytidine on the proliferation, migration and invasion ability of PCa cells. In summary, our findings suggest that miR-195 may function as a crucial tumor suppressor in PCa.
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Affiliation(s)
- Xiaokun Ma
- Department of Medical OncologyThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Liyuan Zou
- Department of Prevention and Health CareThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Zhanhong Chen
- Department of Medical OncologyThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Xing Li
- Department of Medical OncologyThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Li Wei
- Department of Medical OncologyThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Xiangyuan Wu
- Department of Medical OncologyThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
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5
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Moradi A, Srinivasan S, Clements J, Batra J. Beyond the biomarker role: prostate-specific antigen (PSA) in the prostate cancer microenvironment. Cancer Metastasis Rev 2020; 38:333-346. [PMID: 31659564 DOI: 10.1007/s10555-019-09815-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The prostate-specific antigen (PSA) blood test is the accepted biomarker of tumor recurrence. PSA levels in serum correlate with disease progression, though its diagnostic accuracy is questionable. As a result, significant progress has been made in developing modified PSA tests such as PSA velocity, PSA density, 4Kscore, PSA glycoprofiling, Prostate Health Index, and the STHLM3 test. PSA, a serine protease, is secreted from the epithelial cells of the prostate. PSA has been suggested as a molecular target for prostate cancer therapy due to the fact that it is not only active in prostate tissue but also has a pivotal role on prostate cancer signaling pathways including proliferation, invasion, metastasis, angiogenesis, apoptosis, immune response, and tumor microenvironment regulation. Here, we summarize the current standing of PSA in prostate cancer progression as well as its utility in prostate cancer therapeutic approaches with an emphasis on the role of PSA in the tumor microenvironment.
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Affiliation(s)
- Afshin Moradi
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Srilakshmi Srinivasan
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia. .,Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
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6
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Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B. Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression. Clin Epigenetics 2019; 11:54. [PMID: 30917865 PMCID: PMC6438015 DOI: 10.1186/s13148-019-0651-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: 12/18/2018] [Accepted: 03/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, the identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology. Results Using a CRISPR/Cas9-derived TET2-knockout prostate cell line, and through whole-transcriptome and whole-methylome sequencing, we identified seven candidate genes—ASB2, ETNK2, MEIS2, NRG1, NTN1, NUDT10, and SRPX—exhibiting reduced expression and increased promoter methylation, a pattern characteristic of tumor suppressors. Decreased expression of these genes significantly discriminates between recurrent and non-recurrent prostate tumors from the Cancer Genome Atlas (TCGA) cohort (n = 423), and ASB2, NUDT10, and SRPX were significantly correlated with lower recurrence-free survival in patients by Kaplan-Meier analysis. ASB2, MEIS2, and SRPX also showed significantly lower expression in high-risk Gleason score 8 tumors as compared to low or intermediate risk tumors, suggesting that these genes may be particularly useful as indicators of PCa progression. Furthermore, methylation array probes in the TCGA dataset, which were proximal to the highly conserved, differentially methylated sites identified in our TET2-knockout cells, were able to significantly distinguish between matched prostate tumor and normal prostate tissues (n = 50 pairs). Except ASB2, all genes exhibited significantly increased methylation at these probes, and methylation status of at least one probe for each of these genes showed association with measures of PCa progression such as recurrence, stage, or Gleason score. Since ASB2 did not have any probes within the TET2-knockout differentially methylated region, we validated ASB2 methylation in an independent series of matched tumor-normal samples (n = 19) by methylation-specific qPCR, which revealed concordant and significant increases in promoter methylation within the TET2-knockout site. Conclusions Our study identifies seven genes governed by TET2 loss in PCa which exhibit an association between their methylation and expression status and measures of PCa progression. As differential methylation profiles and TET2 expression are associated with advanced PCa, further investigation of these specialized TET2 targets may provide important insights into patterns of carcinogenic gene dysregulation. Electronic supplementary material The online version of this article (10.1186/s13148-019-0651-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shivani Kamdar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Ruth Isserlin
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
| | - Theodorus Van der Kwast
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,Department of Pathology, University Health Network, University of Toronto, 200 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Alexandre R Zlotta
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada.,Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
| | - Neil E Fleshner
- Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. .,Department of Pathology, University Health Network, University of Toronto, 200 Elizabeth St, Toronto, ON, M5G 2C4, Canada. .,Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada.
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7
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Zhao F, Vesprini D, Liu RSC, Olkhov-Mitsel E, Klotz LH, Loblaw A, Liu SK, Bapat B. Combining urinary DNA methylation and cell-free microRNA biomarkers for improved monitoring of prostate cancer patients on active surveillance. Urol Oncol 2019; 37:297.e9-297.e17. [PMID: 30777394 DOI: 10.1016/j.urolonc.2019.01.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/18/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Prostate cancer (CaP) patients with low-grade tumors are enrolled in active surveillance (AS) programs and monitored with digital rectal exams (DREs), prostate-specific antigen (PSA) tests, and periodic invasive biopsies. Patients are "reclassified" with higher-risk disease if they show signs of disease progression. However, AS patients who will reclassify cannot be easily identified upfront and suffer morbidities associated with biopsy. Biomarkers derived from noninvasively obtained specimens such as serum or urine samples are promising alternatives to monitor patients with clinically insignificant cancer. Previously, we have characterized and validated a urinary DNA methylation panel and a serum miRNA panel for the prediction of patient reclassification in 2 independent AS cohorts. In this exploratory study, we have investigated cell-free miRNAs in the urinary supernatant combined with urinary DNA methylation markers to form an integrative panel for prediction of AS patient reclassification. METHODS Post-DRE urine was collected from 103 CaP patients on active surveillance. Urinary sediment DNA methylation levels of selected genes were previously analyzed using qPCR-based MethyLight assay. Using qRT-PCR, we analyzed the urinary supernatants for relative quantities of 10 miRNAs previously shown to be associated with AS reclassification. Logistic regression and Receiver Operating Characteristics curve analyses were performed to assess the predictive ability of miRNAs and DNA methylation biomarkers. RESULTS We identified a 3-marker panel, consisting of miR-24, miR-30c and CRIP3 methylation, that was significant for prediction of patient reclassification (Odds ratio = 2.166, 95% confidence interval = 1.22-3.847) with a negative predictive value of 90.9%. Our 3-marker panel also demonstrated additive value to PSA for prediction of patient reclassification (c-statistic = 0.717, ROC bootstrapped 1000 iteration P = 0.041). CONCLUSION A urinary integrated panel of methylation and miRNA markers is a promising approach to identify AS patients at risk for reclassification. Our 3-marker panel, with its high negative predictive value, would be beneficial to identify and preclude AS patients with truly indolent cancer and to personalize monitoring strategies for AS patients.
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Affiliation(s)
- Fang Zhao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Danny Vesprini
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Richard S C Liu
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ekaterina Olkhov-Mitsel
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Laurence H Klotz
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Andrew Loblaw
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Stanley K Liu
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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8
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Abstract
Over the last decade, advancements in massively-parallel DNA sequencing and computational biology have allowed for unprecedented insights into the fundamental mutational processes that underlie virtually every major cancer type. Two major cancer genomics consortia-The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC)-have produced rich databases of mutational, pathological, and clinical data that can be mined through web-based portals, allowing for correlative studies and testing of novel hypotheses on well-powered patient cohorts.In this chapter, we will review the impact of these technological developments on the understanding of molecular subtypes that promote prostate cancer initiation, progression, metastasis, and clinical aggression. In particular, we will focus on molecular subtypes that define clinically-relevant patient cohorts and assess how a better understanding of how these subtypes-in both somatic and germline genomes-may influence the clinical course for individual men diagnosed with prostate cancer.
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9
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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: 3.4] [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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10
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García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV. Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 2017; 54:529-550. [PMID: 29226748 DOI: 10.1080/10408363.2017.1410520] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic modifications and regulators represent potential molecular elements which control relevant physiological and pathological features, thereby contributing to the natural history of human disease. These epigenetic modulators can be employed as disease biomarkers, since they show several advantages and provide information about gene function, thus explaining differences among patient endophenotypes. In addition, epigenetic biomarkers can incorporate information regarding the effects of the environment and lifestyle on health and disease, and monitor the effect of applied therapies. Technologies used to analyze these epigenetic biomarkers are constantly improving, becoming much easier to use. Laboratory professionals can easily acquire experience and techniques are becoming more affordable. A high number of epigenetic biomarker candidates are being continuously proposed, making now the moment to adopt epigenetics in the clinical laboratory and convert epigenetic marks into reliable biomarkers. In this review, we describe some current promising epigenetic biomarkers and technologies being applied in clinical practice. Furthermore, we will discuss some laboratory strategies and kits to accelerate the adoption of epigenetic biomarkers into clinical routine. The likelihood is that over time, better markers will be identified and will likely be incorporated into future multi-target assays that might help to optimize its application in a clinical laboratory. This will improve cost-effectiveness, and consequently encourage the development of theragnosis and the application of precision medicine.
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Affiliation(s)
- José Luis García-Giménez
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain.,e EpiDisease S.L. Spin-Off of CIBERER (ISCIII) , Valencia , Spain
| | - Marta Seco-Cervera
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain
| | - Trygve O Tollefsbol
- f Department of Biology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Carlos Romá-Mateo
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
| | - Lorena Peiró-Chova
- b INCLIVA Biomedical Research Institute , Valencia , Spain.,g INCLIVA Biobank , Valencia , Spain
| | - Pablo Lapunzina
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,h Institute of Medical and Molecular Genetics (INGEMM) , IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid , Madrid , Spain
| | - Federico V Pallardó
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
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11
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Dorn J, Bayani J, Yousef GM, Yang F, Magdolen V, Kiechle M, Diamandis EP, Schmitt M. Clinical utility of kallikrein-related peptidases (KLK) in urogenital malignancies. Thromb Haemost 2017; 110:408-22. [DOI: 10.1160/th13-03-0206] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/25/2013] [Indexed: 12/19/2022]
Abstract
SummaryKallikrein-related peptidases (KLK), which represent a major tissue-associated proteolytic system, stand for a rich source of biomarkers that may allow molecular classification, early diagnosis and prognosis of human malignancies as well as prediction of response or failure to cancer-directed drugs. International research points to an important role of certain KLKs in female and male urogenital tract malignancies, in addition to cancers of the lung, brain, skin, head and neck, and the gastrointestinal tract. Regarding the female/male urogenital tract, remarkably, all of the KLKs are expressed in the normal prostate, testis, and kidney whereas the uterus, the ovary, and the urinary bladder are expressing a limited number of KLKs only. Most of the information regarding KLK expression in tumour-affected organs is available for ovarian cancer; all of the 12 KLKs tested so far were found to be elevated in the malignant state, depicting them as valuable biomarkers to distinguish between the normal and the cancerous phenotype. In contrast, for kidney cancer, a series of KLKs was found to be downregulated, while other KLKs were not expressed. Evidently, depending on the type of cancer or cancer stage, individual KLKs may show characteristics of a Janus-faced behaviour, by either expanding or inhibiting cancer progression and metastasis.
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12
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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: 0.5] [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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13
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Adamopoulos PG, Kontos CK, Scorilas A. Identification and molecular cloning of novel transcripts of the human kallikrein-related peptidase 10 (KLK10) gene using next-generation sequencing. Biochem Biophys Res Commun 2017; 487:776-781. [PMID: 28419837 DOI: 10.1016/j.bbrc.2017.04.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 04/15/2017] [Indexed: 02/04/2023]
Abstract
Tissue kallikrein and kallikrein-related peptidases (KLKs) form the largest group of serine proteases in the human genome, sharing many structural and functional characteristics. Multiple alternative transcripts have been reported for the most human KLK genes, while many of them are aberrantly expressed in various malignancies, thus possessing significant prognostic and/or diagnostic value. Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity, as it affects cell cycle control, proliferation, apoptosis, invasion, and metastasis. In this study, we describe the identification and molecular cloning of eight novel transcripts of the human KLK10 gene using 3' rapid amplification of cDNA ends (3' RACE) and next-generation sequencing (NGS), as well as their expression analysis in a wide panel of cell lines, originating from several distinct cancerous and normal tissues. Bioinformatic analysis revealed that the novel KLK10 transcripts contain new alternative splicing events between already annotated exons as well as novel exons. In addition, investigation of their expression profile in a wide panel of cell lines was performed with nested RT-PCR using variant-specific pairs of primers. Since many KLK mRNA transcripts possess clinical value, these newly discovered alternatively spliced KLK10 transcripts appear as new potential biomarkers for diagnostic and/or prognostic purposes or as targets for therapeutic strategies.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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14
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Abstract
Cervical-vaginal fluid (CVF) is a complex biological fluid that hydrates the mucosa of the lower female reproductive system. In-depth proteomic and biochemical studies on CVF have revealed that it contains large amounts of endogenous proteases and protease inhibitors, including an abundance of several members of the tissue kallikrein-related peptidase (KLK) family. Despite their ubiquitous presence in human tissues and fluids, KLK expression levels vary considerably, with maximum expression observed in reproduction-related tissues and fluids. The roles of KLKs in the lower female reproductive system are not fully understood. The activation of KLKs in CVF is dependent on pH and various modes of KLK regulation in the vagina exist. KLKs have been postulated to have roles in physiological functions related to antimicrobial processes, vaginal and cervical epithelial desquamation, sperm transport, and the processing of fetal membranes as observed in preterm premature rupture of membranes. Increased understanding of the functional roles of KLKs in the lower female reproductive system could lead to new diagnostic and therapeutic modalities for conditions such as vaginal infections and vaginal atrophy.
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15
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A cancer specific hypermethylation signature of the TERT promoter predicts biochemical relapse in prostate cancer: a retrospective cohort study. Oncotarget 2016; 7:57726-57736. [PMID: 27437772 PMCID: PMC5295385 DOI: 10.18632/oncotarget.10639] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/30/2016] [Indexed: 12/29/2022] Open
Abstract
The identification of new biomarkers to differentiate between indolent and aggressive prostate tumors is an important unmet need. We examined the role of THOR (TERT Hypermethylated Oncological Region) as a diagnostic and prognostic biomarker in prostate cancer (PCa).We analyzed THOR in common cancers using genome-wide methylation arrays. Methylation status of the whole TERT gene in benign and malignant prostate samples was determined by MeDIP-Seq. The prognostic role of THOR in PCa was assessed by pyrosequencing on discovery and validation cohorts from patients who underwent radical prostatectomy with long-term follow-up data.Most cancers (n = 3056) including PCa (n = 300) exhibited hypermethylation of THOR. THOR was the only region within the TERT gene that is differentially methylated between normal and malignant prostate tissue (p < 0.0001). Also, THOR was significantly hypermethylated in PCa when compared to paired benign tissues (n = 164, p < 0.0001). THOR hypermethylation correlated with Gleason scores and was associated with tumor invasiveness (p = 0.0147). Five years biochemical progression free survival (BPFS) for PCa patients in the discovery cohort was 87% (95% CI 73-100) and 65% (95% CI 52-78) for THOR non-hypermethylated and hypermethylated cancers respectively (p = 0.01). Similar differences in BPFS were noted in the validation cohort (p = 0.03). Importantly, THOR was able to predict outcome in the challenging (Gleason 6 and 7 (3 + 4)) PCa (p = 0.007). For this group, THOR was an independent risk factor for BPFS with a hazard-ratio of 3.685 (p = 0.0247). Finally, THOR hypermethylation more than doubled the risk of recurrence across all PSA levels (OR 2.5, p = 0.02).
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16
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Zhao F, Olkhov-Mitsel E, van der Kwast T, Sykes J, Zdravic D, Venkateswaran V, Zlotta AR, Loblaw A, Fleshner NE, Klotz L, Vesprini D, Bapat B. Urinary DNA Methylation Biomarkers for Noninvasive Prediction of Aggressive Disease in Patients with Prostate Cancer on Active Surveillance. J Urol 2016; 197:335-341. [PMID: 27545574 DOI: 10.1016/j.juro.2016.08.081] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 12/22/2022]
Abstract
PURPOSE Patients with prostate cancer on active surveillance are monitored by repeat prostate specific antigen measurements, digital rectal examinations and prostate biopsies. A subset of patients on active surveillance will later reclassify with disease progression, prompting definitive treatment. To minimize the risk of under treating such patients on active surveillance minimally invasive tests are urgently needed incorporating biomarkers to identify patients who will reclassify. MATERIALS AND METHODS We assessed post-digital rectal examination urine samples of patients on active surveillance for select DNA methylation biomarkers that were previously investigated in radical prostatectomy specimens and shown to correlate with an increasing risk of prostate cancer. Post-digital rectal examination urine samples were prospectively collected from 153 men on active surveillance who were diagnosed with Gleason score 6 disease. Urinary sediment DNA was analyzed for 8 DNA methylation biomarkers by multiplex MethyLight assay. Correlative analyses were performed on gene methylation and clinicopathological variables to test the ability to predict patient risk reclassification. RESULTS Using backward logistic regression a 4-gene methylation classifier panel (APC, CRIP3, GSTP1 and HOXD8) was identified. The classifier panel was able to predict patient reclassification (OR 2.559, 95% CI 1.257-5.212). We observed this panel to be an independent and superior predictor compared to current clinical predictors such as prostate specific antigen at diagnosis or the percent of tumor positive cores in the initial biopsy. CONCLUSION We report that a urine based classifier panel of 4 methylation biomarkers predicts disease progression in patients on active surveillance. Once validated in independent active surveillance cohorts, these promising biomarkers may help establish a less invasive method to monitor patients on active surveillance programs.
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Affiliation(s)
- Fang Zhao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ekaterina Olkhov-Mitsel
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Jenna Sykes
- St. Michael's Hospital, Toronto, Ontario, Canada
| | - Darko Zdravic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vasundara Venkateswaran
- Division of Urology, Department of Surgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexandre R Zlotta
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Urology and Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Andrew Loblaw
- Department of Radiation Oncology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Neil E Fleshner
- Department of Urology and Surgical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Laurence Klotz
- Division of Urology, Department of Surgery, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Danny Vesprini
- Department of Radiation Oncology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Pathology, University Health Network, Toronto, Ontario, Canada.
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17
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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18
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Abdel-Rahman WM, Lotsari-Salomaa JE, Kaur S, Niskakoski A, Knuutila S, Järvinen H, Mecklin JP, Peltomäki P. The Role of Chromosomal Instability and Epigenetics in Colorectal Cancers Lacking β-Catenin/TCF Regulated Transcription. Gastroenterol Res Pract 2016; 2016:6089658. [PMID: 27047543 PMCID: PMC4800109 DOI: 10.1155/2016/6089658] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/15/2022] Open
Abstract
All colorectal cancer cell lines except RKO displayed active β-catenin/TCF regulated transcription. This feature of RKO was noted in familial colon cancers; hence our aim was to dissect its carcinogenic mechanism. MFISH and CGH revealed distinct instability of chromosome structure in RKO. Gene expression microarray of RKO versus 7 colon cancer lines (with active Wnt signaling) and 3 normal specimens revealed 611 differentially expressed genes. The majority of the tested gene loci were susceptible to LOH in primary tumors with various β-catenin localizations as a surrogate marker for β-catenin activation. The immunohistochemistry of selected genes (IFI16, RGS4, MCTP1, DGKI, OBCAM/OPCML, and GLIPR1) confirmed that they were differentially expressed in clinical specimens. Since epigenetic mechanisms can contribute to expression changes, selected target genes were evaluated for promoter methylation in patient specimens from sporadic and hereditary colorectal cancers. CMTM3, DGKI, and OPCML were frequently hypermethylated in both groups, whereas KLK10, EPCAM, and DLC1 displayed subgroup specificity. The overall fraction of hypermethylated genes was higher in tumors with membranous β-catenin. We identified novel genes in colorectal carcinogenesis that might be useful in personalized tumor profiling. Tumors with inactive Wnt signaling are a heterogeneous group displaying interaction of chromosomal instability, Wnt signaling, and epigenetics.
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Affiliation(s)
- Wael M. Abdel-Rahman
- Department of Medical Laboratory Sciences, College of Health Sciences and Sharjah Institute for Medical Research (SIMR), University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | | | - Sippy Kaur
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | - Anni Niskakoski
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland
| | - Heikki Järvinen
- Second Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, 40620 Jyväskylä, Finland
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
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19
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Geybels MS, Alumkal JJ, Luedeke M, Rinckleb A, Zhao S, Shui IM, Bibikova M, Klotzle B, van den Brandt PA, Ostrander EA, Fan JB, Feng Z, Maier C, Stanford JL. Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors. Clin Epigenetics 2015; 7:128. [PMID: 26692910 PMCID: PMC4676897 DOI: 10.1186/s13148-015-0161-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/03/2015] [Indexed: 12/17/2022] Open
Abstract
Background About half of all prostate cancers harbor the TMPRSS2:ERG (T2E) gene fusion. While T2E-positive and T2E-negative tumors represent specific molecular subtypes of prostate cancer (PCa), previous studies have not yet comprehensively investigated how these tumor subtypes differ at the epigenetic level. We therefore investigated epigenome-wide DNA methylation profiles of PCa stratified by T2E status. Results The study included 496 patients with clinically localized PCa who had a radical prostatectomy as primary treatment for PCa. Fluorescence in situ hybridization (FISH) “break-apart” assays were used to determine tumor T2E-fusion status, which showed that 266 patients (53.6 %) had T2E-positive PCa. The study showed global DNA methylation differences between tumor subtypes. A large number of differentially methylated CpG sites were identified (false-discovery rate [FDR] Q-value <0.00001; n = 27,876) and DNA methylation profiles accurately distinguished between tumor T2E subgroups. A number of top-ranked differentially methylated CpGs in genes (FDR Q-values ≤1.53E−29) were identified: C3orf14, CACNA1D, GREM1, KLK10, NT5C, PDE4D, RAB40C, SEPT9, and TRIB2, several of which had a corresponding alteration in mRNA expression. These genes may have various roles in the pathogenesis of PCa, and the calcium-channel gene CACNA1D is a known ERG-target. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. Conclusions This study identified substantial differences in DNA methylation profiles of T2E-positive and T2E-negative tumors, thereby providing further evidence that different underlying oncogenic pathways characterize these molecular subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0161-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Joshi J Alumkal
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR USA
| | - Manuel Luedeke
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Antje Rinckleb
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NC Research Triangle Park, USA
| | - Irene M Shui
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | | | - Piet A van den Brandt
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD USA
| | - Jian-Bing Fan
- Illumina, Inc., San Diego, CA USA ; Present Address: AnchorDx Corp., Guangzhou, 510300 People's Republic of China
| | | | - Christiane Maier
- Institute of Human Genetics and Department of Urology, Faculty of Medicine, University of Ulm, Ulm, Germany
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA ; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA USA
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20
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Involvement of Kallikrein-Related Peptidases in Normal and Pathologic Processes. DISEASE MARKERS 2015; 2015:946572. [PMID: 26783378 PMCID: PMC4689925 DOI: 10.1155/2015/946572] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Human kallikrein-related peptidases (KLKs) are a subgroup of serine proteases that participate in proteolytic pathways and control protein levels in normal physiology as well as in several pathological conditions. Their complex network of stimulatory and inhibitory interactions may induce inflammatory and immune responses and contribute to the neoplastic phenotype through the regulation of several cellular processes, such as proliferation, survival, migration, and invasion. This family of proteases, which includes one of the most useful cancer biomarkers, kallikrein-related peptidase 3 or PSA, also has a protective effect against cancer promoting apoptosis or counteracting angiogenesis and cell proliferation. Therefore, they represent attractive therapeutic targets and may have important applications in clinical oncology. Despite being intensively studied, many gaps in our knowledge on several molecular aspects of KLK functions still exist. This review aims to summarize recent data on their involvement in different processes related to health and disease, in particular those directly or indirectly linked to the neoplastic process.
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21
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NES1/KLK10 gene represses proliferation, enhances apoptosis and down-regulates glucose metabolism of PC3 prostate cancer cells. Sci Rep 2015; 5:17426. [PMID: 26616394 PMCID: PMC4663538 DOI: 10.1038/srep17426] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/29/2015] [Indexed: 12/12/2022] Open
Abstract
The normal epithelial cell-specific-1 (NES1) gene, also named as KLK10, is recognised as a novel putative tumour suppressor in breast cancer, but few studies have focused on the function of KLK10 in human prostate cancer. Our study confirms that the expression of KLK10 in prostate cancer tissue and cell lines (PC3, DU145, and LNCaP clone FGC) is low. Given that the androgen-independent growth characteristic of the PC3 cell line is more similar to clinical castration-resistant prostate cancer, we studied the role of KLK10 in PC3. In vitro and in vivo assays showed that over-expressing KLK10 in PC3 could decelerate tumour proliferation, which was accompanied with an increase in apoptosis and suppression of glucose metabolism. The related proteins, such as Bcl-2 and HK-2, were down-regulated subsequently. Furthermore, by up-regulating Bcl-2 or HK-2 respectively in the PC3-KLK10 cell line, we observed a subsequent increase of cell proliferation and a synchronous up-regulation of HK-2 and Bcl-2. Besides, KLK10 expression was also increased by Bcl-2 and HK-2, which suggests that there is a negative feedback loop between KLK10 and Bcl-2/HK-2. Thus, our results demonstrated that KLK10 may function as a tumour suppressor by repressing proliferation, enhancing apoptosis and decreasing glucose metabolism in PC3 cells.
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22
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Horning AM, Awe JA, Wang CM, Liu J, Lai Z, Wang VY, Jadhav RR, Louie AD, Lin CL, Kroczak T, Chen Y, Jin VX, Abboud-Werner SL, Leach RJ, Hernandez J, Thompson IM, Saranchuk J, Drachenberg D, Chen CL, Mai S, Huang THM. DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. Prostate 2015; 75:1790-801. [PMID: 26332453 DOI: 10.1002/pros.23052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/02/2015] [Indexed: 01/18/2023]
Abstract
BACKGROUND Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n = 12) versus no evidence of disease (NED) (n = 15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5% overall accuracy. CONCLUSIONS Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence. .
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Affiliation(s)
- Aaron M Horning
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Julius A Awe
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Joseph Liu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Zhao Lai
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
| | - Vickie Yao Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Rohit R Jadhav
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Anna D Louie
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Tad Kroczak
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Yidong Chen
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
- Department of Epidemiology & Biostatistics, University of Texas Health Science Center, San Antonio, Texas
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
- Department of Epidemiology & Biostatistics, University of Texas Health Science Center, San Antonio, Texas
| | | | - Robin J Leach
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Javior Hernandez
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Ian M Thompson
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Jeff Saranchuk
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darrel Drachenberg
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Sabine Mai
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
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Schrader CH, Kolb M, Zaoui K, Flechtenmacher C, Grabe N, Weber KJ, Hielscher T, Plinkert PK, Hess J. Kallikrein-related peptidase 6 regulates epithelial-to-mesenchymal transition and serves as prognostic biomarker for head and neck squamous cell carcinoma patients. Mol Cancer 2015; 14:107. [PMID: 25990935 PMCID: PMC4437453 DOI: 10.1186/s12943-015-0381-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/08/2015] [Indexed: 12/14/2022] Open
Abstract
Background Dysregulated expression of Kallikrein-related peptidase 6 (KLK6) is a common feature for many human malignancies and numerous studies evaluated KLK6 as a promising biomarker for early diagnosis or unfavorable prognosis. However, the expression of KLK6 in carcinomas derived from mucosal epithelia, including head and neck squamous cell carcinoma (HNSCC), and its mode of action has not been addressed so far. Methods Stable clones of human mucosal tumor cell lines were generated with shRNA-mediated silencing or ectopic overexpression to characterize the impact of KLK6 on tumor relevant processes in vitro. Tissue microarrays with primary HNSCC samples from a retrospective patient cohort (n = 162) were stained by immunohistochemistry and the correlation between KLK6 staining and survival was addressed by univariate Kaplan-Meier and multivariate Cox proportional hazard model analysis. Results KLK6 expression was detected in head and neck tumor cell lines (FaDu, Cal27 and SCC25), but not in HeLa cervix carcinoma cells. Silencing in FaDu cells and ectopic expression in HeLa cells unraveled an inhibitory function of KLK6 on tumor cell proliferation and mobility. FaDu clones with silenced KLK6 expression displayed molecular features resembling epithelial-to-mesenchymal transition, nuclear β-catenin accumulation and higher resistance against irradiation. Low KLK6 protein expression in primary tumors from oropharyngeal and laryngeal SCC patients was significantly correlated with poor progression-free (p = 0.001) and overall survival (p < 0.0005), and served as an independent risk factor for unfavorable clinical outcome. Conclusions In summary, detection of low KLK6 expression in primary tumors represents a promising tool to stratify HNSCC patients with high risk for treatment failure. These patients might benefit from restoration of KLK6 expression or pharmacological targeting of signaling pathways implicated in EMT. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0381-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carola H Schrader
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.
| | - Markus Kolb
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.
| | - Karim Zaoui
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.
| | | | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg, Germany. .,Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Klaus-Josef Weber
- Department of Radiation Oncology, University of Heidelberg, Heidelberg, Germany.
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Peter K Plinkert
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany. .,Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Cereda V, Formica V, Menghi A, Pellicori S, Roselli M. Kallikrein-related peptidases targeted therapies in prostate cancer: perspectives and challenges. Expert Opin Investig Drugs 2015; 24:929-47. [PMID: 25858813 DOI: 10.1517/13543784.2015.1035708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Despite the emergence of several new effective treatments for metastatic castration-resistant prostate cancer patients, disease progression inevitably occurs, leading scientific community to carefully look for novel therapeutic targets of prostate cancer. Kallikrein (KLK)-related peptidases have been demonstrated to facilitate prostate tumorigenesis and disease progression through the development of an oncogenic microenvironment for prostate cells. AREAS COVERED This review first summarizes the large amount of preclinical data showing the involvement of KLKs in prostate cancer pathobiology. In the second part, the authors assess the current status and future directions for KLK-targeted therapy and briefly describe the advances and challenges implicated in the design of effective manufactured drugs. The authors then focus on the preclinical data and on Phase I/II studies of the most promising KLK-targeted agents in prostate cancer. The drugs discussed here are divided on the basis of their mechanism of action: KLK-engineered inhibitors; KLK-activated pro-drugs; KLK-targeted microRNAs and small interfering RNAs(-/)small hairpin RNAs; KLK vaccines and antibodies. EXPERT OPINION Targeting KLK expression and/or activity could be a promising direction in prostate cancer treatment. Future human clinical trials will help us to evaluate the real benefits, toxicities and the consequent optimal use of KLK-targeted drugs, as mono-therapy or in combination regimens.
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Affiliation(s)
- Vittore Cereda
- 1 University of Rome Tor Vergata, Tor Vergata University Clinical Center, Department of Systems Medicine, Medical Oncology , Viale Oxford 81, 00133 Rome , Italy +39 0620908190 ; +39 0620903504 ;
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25
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Brikun I, Nusskern D, Gillen D, Lynn A, Murtagh D, Feczko J, Nelson WG, Freije D. A panel of DNA methylation markers reveals extensive methylation in histologically benign prostate biopsy cores from cancer patients. Biomark Res 2014; 2:25. [PMID: 25548652 PMCID: PMC4278343 DOI: 10.1186/s40364-014-0025-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 11/28/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Men with a negative first prostate biopsy will undergo one or more additional biopsies if they remain at high suspicion of prostate cancer. To date, there are no diagnostic tests capable of identifying patients at risk for a positive diagnosis with the predictive power needed to eliminate unnecessary repeat biopsies. Efforts to develop clinical tests using the epigenetic signature of cores recovered from first biopsies have been limited to a few markers and lack the sensitivity and specificity needed for widespread clinical adoption. METHODS We developed methylation-specific quantitative polymerase chain reaction assays for a panel of 24 markers that are preferentially methylated in prostate cancer. We modified the bisulfite conversion conditions to allow the integration of the methylation information from multiple markers. We determined the methylation status of the 24 markers in 213 prostate biopsy cores from 104 patients, 37 prostate cancer patients and 67 controls. We performed logistic regression on combinations of markers as well as the entire panel of 24 markers to identify the best candidates for a diagnostic test. RESULTS The marker panel differentiated between cancer cores and benign cores from non-cancer patients with 100% sensitivity and 97% specificity. Furthermore, the panel detected significant methylation in benign cores from prostate cancer patients that was not present in controls. Using methylation of 5 out of 24 to define a cancer case, the analysis of a single benign biopsy core identified 62% of prostate cancer patients undergoing repeat biopsies. ROC curve analysis showed that markers commonly methylated in benign cores from cancer patients are the best candidates for a diagnostic test. The results suggest that 5 to 10 markers will be needed to achieve optimal predictive power. CONCLUSIONS This study shows that epigenetic field effects differ significantly between cancer patients and controls. Their detection in benign biopsy cores can form the basis of diagnostic tests to identify patients in need of repeat biopsies, reducing the cost of continued PCA screening by up to 40%. They could also be used to identify prostate cancer patients with low grade disease who are likely candidates for active surveillance or focal therapy.
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Affiliation(s)
- Igor Brikun
- />Euclid Diagnostics LLC, Crown Point, Indiana USA
| | | | - Daniel Gillen
- />Department of Statistics, University of California Irvine, Irvine, California USA
| | - Amy Lynn
- />Consultants in Laboratory Medicine, Toledo, Ohio USA
| | | | - John Feczko
- />Pathology Consultants, Michigan City, Indiana USA
| | - William G Nelson
- />Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland USA
| | - Diha Freije
- />Euclid Diagnostics LLC, Crown Point, Indiana USA
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26
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Lasseigne BN, Burwell TC, Patil MA, Absher DM, Brooks JD, Myers RM. DNA methylation profiling reveals novel diagnostic biomarkers in renal cell carcinoma. BMC Med 2014; 12:235. [PMID: 25472429 PMCID: PMC4265327 DOI: 10.1186/s12916-014-0235-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/12/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is the tenth most commonly diagnosed cancer in the United States. While it is usually lethal when metastatic, RCC is successfully treated with surgery when tumors are confined to the kidney and have low tumor volume. Because most early stage renal tumors do not result in symptoms, there is a strong need for biomarkers that can be used to detect the presence of the cancer as well as to monitor patients during and after therapy. METHODS We examined genome-wide DNA methylation alterations in renal cell carcinomas of diverse histologies and benign adjacent kidney tissues from 96 patients. RESULTS We observed widespread methylation differences between tumors and benign adjacent tissues, particularly in immune-, G-protein coupled receptor-, and metabolism-related genes. Additionally, we identified a single panel of DNA methylation biomarkers that reliably distinguishes tumor from benign adjacent tissue in all of the most common kidney cancer histologic subtypes, and a second panel does the same specifically for clear cell renal cell carcinoma tumors. This set of biomarkers were validated independently with excellent performance characteristics in more than 1,000 tissues in The Cancer Genome Atlas clear cell, papillary, and chromophobe renal cell carcinoma datasets. CONCLUSIONS These DNA methylation profiles provide insights into the etiology of renal cell carcinoma and, most importantly, demonstrate clinically applicable biomarkers for use in early detection of kidney cancer.
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Affiliation(s)
- Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
- Department of Biological Sciences, University of Alabama in Huntsville, Shelby Center for Science and Technology, Room 369, 301 Sparkman Drive, Huntsville, Alabama, 35899, USA.
| | - Todd C Burwell
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
| | - Mohini A Patil
- Department of Urology, Stanford University, 875 Blake Wilbur Dr. Clinic E, Stanford, California, 94305-5118, USA.
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
| | - James D Brooks
- Department of Urology, Stanford University, 875 Blake Wilbur Dr. Clinic E, Stanford, California, 94305-5118, USA.
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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Fuhrman-Luck RA, Loessner D, Clements JA. Kallikrein-Related Peptidases in Prostate Cancer: From Molecular Function to Clinical Application. EJIFCC 2014; 25:269-81. [PMID: 27683474 PMCID: PMC4975200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Prostate cancer is a leading contributor to male cancer-related deaths worldwide. Kallikrein-related peptidases (KLKs) are serine proteases that exhibit deregulated expression in prostate cancer, with KLK3, or prostate specific antigen (PSA), being the widely-employed clinical biomarker for prostate cancer. Other KLKs, such as KLK2, show promise as prostate cancer biomarkers and, additionally, their altered expression has been utilised for the design of KLK-targeted therapies. There is also a large body of in vitro and in vivo evidence supporting their role in cancer-related processes. Here, we review the literature on studies to date investigating the potential of other KLKs, in addition to PSA, as biomarkers and in therapeutic options, as well as their current known functional roles in cancer progression. Increased knowledge of these KLK-mediated functions, including degradation of the extracellular matrix, local invasion, cancer cell proliferation, interactions with fibroblasts, angiogenesis, migration, bone metastasis and tumour growth in vivo, may help define new roles as prognostic biomarkers and novel therapeutic targets for this cancer.
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Affiliation(s)
| | | | - Judith A. Clements
- Cancer Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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28
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Prognostic DNA methylation markers for prostate cancer. Int J Mol Sci 2014; 15:16544-76. [PMID: 25238417 PMCID: PMC4200823 DOI: 10.3390/ijms150916544] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.
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Scorilas A, Mavridis K. Predictions for the future of kallikrein-related peptidases in molecular diagnostics. Expert Rev Mol Diagn 2014; 14:713-22. [PMID: 24927162 DOI: 10.1586/14737159.2014.928207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Kallikrein-related peptidases (KLKs) form a cancer-related ensemble of serine proteases. This multigene family hosts the most widely used cancer biomarker that is PSA-KLK3, with millions of tests performed annually worldwide. The present report provides an overview of the biomarker potential of the extended KLK family (KLK1-KLK15) in various disease settings and envisages approaches that could lead to additional KLK-driven applications in future molecular diagnostics. Particular focus is given on the inclusion of KLKs into multifaceted cancer biomarker panels that provide enhanced diagnostic, prognostic and/or predictive accuracy in several human malignancies. Such panels have been described so far for prostate, ovarian, lung and colorectal cancers. The role of KLKs as biomarkers in non-malignant disease settings, such as Alzheimer's disease and multiple sclerosis, is also commented upon. Predictions are given on the challenges and future directions regarding clinically oriented KLK research.
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Affiliation(s)
- Andreas Scorilas
- Department of Biochemistry and Molecular Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
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Novel multiplex MethyLight protocol for detection of DNA methylation in patient tissues and bodily fluids. Sci Rep 2014; 4:4432. [PMID: 24651255 PMCID: PMC3961737 DOI: 10.1038/srep04432] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/06/2014] [Indexed: 12/20/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of cancer and is an important potential biomarker. Particularly, combined analysis of a panel of hypermethylated genes shows the most promising clinical performance. Herein, we developed, optimized and standardized a multiplex MethyLight assay to simultaneously detect hypermethylation of APC, HOXD3 and TGFB2 in DNA extracted from prostate cancer (PCa) cell lines, archival tissue specimens, and urine samples. We established that the assay is capable of discriminating between fully methylated and unmethylated alleles with 100% specificity and demonstrated the assay as highly accurate and reproducible as the singleplex approach. For proof of principle, we analyzed the methylation status of these genes in tissue and urine samples of PCa patients as well as PCa-free controls. These data show that the multiplex MethyLight assay offers a significant advantage when working with limited quantities of DNA and has potential applications in research and clinical settings.
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Mavridis K, Avgeris M, Scorilas A. Targeting kallikrein-related peptidases in prostate cancer. Expert Opin Ther Targets 2014; 18:365-83. [PMID: 24571737 DOI: 10.1517/14728222.2014.880693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Mancikova V, Buj R, Castelblanco E, Inglada-Pérez L, Diez A, de Cubas AA, Curras-Freixes M, Maravall FX, Mauricio D, Matias-Guiu X, Puig-Domingo M, Capel I, Bella MR, Lerma E, Castella E, Reverter JL, Peinado MÁ, Jorda M, Robledo M. DNA methylation profiling of well-differentiated thyroid cancer uncovers markers of recurrence free survival. Int J Cancer 2014; 135:598-610. [PMID: 24382797 DOI: 10.1002/ijc.28703] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/19/2013] [Indexed: 01/08/2023]
Abstract
Thyroid cancer is a heterogeneous disease with several subtypes characterized by cytological, histological and genetic alterations, but the involvement of epigenetics is not well understood. Here, we investigated the role of aberrant DNA methylation in the development of well-differentiated thyroid tumors. We performed genome-wide DNA methylation profiling in the largest well-differentiated thyroid tumor series reported to date, comprising 83 primary tumors as well as 8 samples of adjacent normal tissue. The epigenetic profiles were closely related to not only tumor histology but also the underlying driver mutation; we found that follicular tumors had higher levels of methylation, which seemed to accumulate in a progressive manner along the tumorigenic process from adenomas to carcinomas. Furthermore, tumors harboring a BRAF or RAS mutation had a larger number of hypo- or hypermethylation events, respectively. The aberrant methylation of several candidate genes potentially related to thyroid carcinogenesis was validated in an independent series of 52 samples. Furthermore, through the integration of methylation and transcriptional expression data, we identified genes whose expression is associated with the methylation status of their promoters. Finally, by integrating clinical follow-up information with methylation levels we propose etoposide-induced 2.4 and Wilms tumor 1 as novel prognostic markers related to recurrence-free survival. This comprehensive study provides insights into the role of DNA methylation in well-differentiated thyroid cancer development and identifies novel markers associated with recurrence-free survival.
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Affiliation(s)
- Veronika Mancikova
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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Jiao X, Lu HJ, Zhai MM, Tan ZJ, Zhi HN, Liu XM, Liu CH, Zhang DP. Overexpression of kallikrein gene 10 is a biomarker for predicting poor prognosis in gastric cancer. World J Gastroenterol 2013; 19:9425-9431. [PMID: 24409072 PMCID: PMC3882418 DOI: 10.3748/wjg.v19.i48.9425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 10/15/2013] [Accepted: 11/03/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To analyze the expression of kallikrein gene 10 (KLK10) in gastric cancer and to determine whether KLK10 has independent prognostic value in gastric cancer.
METHODS: We studied KLK10 expression in 80 histologically confirmed gastric cancer samples using real-time quantitative reverse transcription-PCR and hK10 expression using immunohistochemistry. Correlations with clinicopathological variables (lymph node metastasis, depth of invasion and histology) and with outcomes (disease-free survival and overall survival) during a median follow-up period of 31 mo were assessed. Gastric cancer tissues were then classified as KLK10 positive or negative.
RESULTS: KLK10 was found to be highly expressed in 57/80 (70%) of gastric cancer samples, while its expression was very low in normal gastric tissues. Positive relationships between KLK10 expression and lymph node metastasis (P = 0.048), depth of invasion (P = 0.034) and histology (P = 0.015) were observed. Univariate survival analysis revealed that gastric cancer patients with positive KLK10 expression had an increased risk for relapse/metastasis and death (P = 0.005 and 0.002, respectively). Cox multivariate analysis indicated that KLK10 was an independent prognostic indicator of disease-free survival and overall survival in patients with gastric cancer.
CONCLUSION: KLK10 expression is an independent biomarker of unfavorable prognosis in patients with gastric cancer.
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Emerging clinical importance of the cancer biomarkers kallikrein-related peptidases (KLK) in female and male reproductive organ malignancies. Radiol Oncol 2013; 47:319-29. [PMID: 24294176 PMCID: PMC3814276 DOI: 10.2478/raon-2013-0053] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/25/2013] [Indexed: 01/01/2023] Open
Abstract
Background Tumor tissue-associated KLKs (kallikrein-related peptidases) are clinically important biomarkers that may allow prognosis of the cancer disease and/or prediction of response/failure of cancer patients to cancer-directed drugs. Regarding the female/male reproductive tract, remarkably, all of the fifteen KLKs are expressed in the normal prostate, breast, cervix uteri, and the testis, whereas the uterus/endometrium and the ovary are expressing a limited number of KLKs only. Conclusions Most of the information regarding elevated expression of KLKs in tumor-affected organs is available for ovarian cancer; depicting them as valuable biomarkers in the cancerous phenotype. In contrast, for breast cancer, a series of KLKs was found to be downregulated. However, in breast cancer, KLK4 is elevated which is also true for ovarian and prostate cancer. In such cases, selective synthetic KLK inhibitors that aim at blocking the proteolytic activities of certain KLKs may serve as future candidate therapeutic drugs to interfere with tumor progression and metastasis.
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Haldrup C, Mundbjerg K, Vestergaard EM, Lamy P, Wild P, Schulz WA, Arsov C, Visakorpi T, Borre M, Høyer S, Orntoft TF, Sørensen KD. DNA methylation signatures for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. J Clin Oncol 2013; 31:3250-8. [PMID: 23918943 DOI: 10.1200/jco.2012.47.1847] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, causing overtreatment of indolent PC and risk of delayed treatment of aggressive PC. Here, we identify six novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential. METHODS Microarray-based screening and bisulfite sequencing of 20 nonmalignant and 29 PC tissue specimens were used to identify new candidate DNA hypermethylation markers for PC. Diagnostic and prognostic potential was evaluated in 35 nonmalignant prostate tissue samples, 293 radical prostatectomy (RP) samples (cohort 1, training), and 114 malignant RP samples (cohort 2, validation) collected in Denmark, Switzerland, Germany, and Finland. Sensitivity and specificity for PC were evaluated by receiver operating characteristic analyses. Correlations between DNA methylation levels and biochemical recurrence were assessed using log-rank tests and univariate and multivariate Cox regression analyses. RESULTS Hypermethylation of AOX1, C1orf114, GAS6, HAPLN3, KLF8, and MOB3B was highly cancer specific (area under the curve, 0.89 to 0.98). Furthermore, high C1orf114 methylation was significantly (P < .05) associated with biochemical recurrence in multivariate analysis in cohort 1 (hazard ratio [HR], 3.10; 95% CI, 1.89 to 5.09) and was successfully validated in cohort 2 (HR, 3.27; 95% CI, 1.17 to 9.12). Moreover, a significant (P < .05) three-gene prognostic methylation signature (AOX1/C1orf114/HAPLN3), classifying patients into low- and high-methylation subgroups, was trained in cohort 1 (HR, 1.91; 95% CI, 1.26 to 2.90) and validated in cohort 2 (HR, 2.33; 95% CI, 1.31 to 4.13). CONCLUSION We identified six novel candidate DNA methylation markers for PC. C1orf114 hypermethylation and a three-gene methylation signature were independent predictors of time to biochemical recurrence after RP in two PC patient cohorts.
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Affiliation(s)
- Christa Haldrup
- Christa Haldrup, Kamilla Mundbjerg, Else Marie Vestergaard, Philippe Lamy, Michael Borre, Søren Høyer, Torben F. Ørntoft, and Karina D. Sørensen, Aarhus University Hospital, Aarhus, Denmark; Peter Wild, University Hospital Zurich, Zurich, Switzerland; Wolfgang A. Schulz and Christian Arsov, Heinrich Heine University, Düsseldorf, Germany; and Tapio Visakorpi, University of Tampere and Tampere University Hospital, Tampere, Finland
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