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Matulevičius A, Žukauskaitė K, Gineikaitė R, Dasevičius D, Trakymas M, Naruševičiūtė I, Ušinskienė J, Ulys A, Jankevičius F, Jarmalaitė S. Combination of DNA methylation biomarkers with multiparametric magnetic resonance and ultrasound imaging fusion biopsy to detect the local spread of prostate cancer. Prostate 2023; 83:1572-1583. [PMID: 37614027 DOI: 10.1002/pros.24615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/04/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND This study aimed to investigate the extent of field cancerization adjacent to index lesions in prostate cancer (PCa) by measuring DNA methylation of selected tumor suppressor genes in the perifocal tissue of PCa not visible on multiparametric magnetic resonanse imaging (mpMRI) for the safe zone of focal therapy identification. METHODS A total of 272 patients were enrolled in this study, 44 patients' tissue biosamples were included in the field cancerization research, and 272 urine samples were included in the urine-based test development. Targeted biopsies were performed using the mpMRI/ultrasoundimage fusion system. RESULTS Quantitative analysis revealed significantly higher DNA methylation levels of RARB, RASSF1, GSTP1 & APC genes in the index lesion compared with perifocal tissue samples 10 mm away from it (p < 0.0001). Notably, the RARB, GSTP1 & APC and RARB, RASSF1, GSTP1 & APC biomarker combinations exhibited the highest sensitivity and specificity comparing the extent of DNA methylation in index lesions and noncancerous prostate tissues 20 mm away (both area under the curve [AUC] = 0.98; p < 0.0001). The analysis of the potential urinary biomarkers showed that the combination of all four DNA methylation biomarkers with prostate-specific antigen (PSA) or PSA density (PSAD) in the blood significantly improves the detection of clinically significant PCa (csPCa). The combination of the four-biomarker test with PSAD allowed the identification of csPCa with ≥90% sensitivity and specificity. CONCLUSION Thus, this study suggests that for focal therapy by region target hemi-ablation, the safe distance from the index lesion is no less than 10 mm. Noninvasive urine DNA methylation tests in combination with PSAD could be used for further follow-up of the patients, but larger prospective studies with external validation are needed.
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Affiliation(s)
- Augustinas Matulevičius
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Kristina Žukauskaitė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
| | | | - Darius Dasevičius
- National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | | | | | | | | | - Feliksas Jankevičius
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaitė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
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Lv SD, Wang HY, Yu XP, Zhai QL, Wu YB, Wei Q, Huang WH. Integrative molecular characterization of Chinese prostate cancer specimens. Asian J Androl 2021; 22:162-168. [PMID: 31134918 PMCID: PMC7155802 DOI: 10.4103/aja.aja_36_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) exhibits epidemiological and molecular heterogeneity. Despite extensive studies of its phenotypic and genetic properties in Western populations, its molecular basis is not clear in Chinese patients. To determine critical molecular characteristics and explore correlations between genomic markers and clinical parameters in Chinese populations, we applied an integrative genetic/transcriptomic assay that combines targeted next-generation sequencing and quantitative real-time PCR (qRT-PCR) on samples from 46 Chinese patients with PCa. Lysine (K)-specific methyltransferase 2D (KMT2D), zinc finger homeobox 3 (ZFHX3), A-kinase anchoring protein 9 (AKAP9), and GLI family zinc finger 1 (GLI1) were frequently mutated in our cohort. Moreover, a clinicopathological analysis showed that RB transcriptional corepressor 1 (RB1) deletion was common in patients with a high risk of disease progression. Remarkably, four genomic events, MYC proto-oncogene (MYC) amplification, RB1 deletion, APC regulator of WNT signaling pathway (APC) mutation or deletion, and cyclin-dependent kinase 12 (CDK12) mutation, were correlated with poor disease-free survival. In addition, a close link between KMT2D expression and the androgen receptor (AR) signaling pathway was observed both in our cohort and in The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) data. In summary, our results demonstrate the feasibility and benefits of integrative molecular characterization of PCa samples in disease pathology research and personalized medicine.
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Affiliation(s)
- Shi-Dong Lv
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China.,Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hong-Yi Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xin-Pei Yu
- Department of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Qi-Liang Zhai
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yao-Bin Wu
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China
| | - Qiang Wei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wen-Hua Huang
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China
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3
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Cardelli M, Doorn RV, Larcher L, Donato MD, Piacenza F, Pierpaoli E, Giacconi R, Malavolta M, Rachakonda S, Gruis NA, Molven A, Andresen PA, Pjanova D, van den Oord JJ, Provinciali M, Nagore E, Kumar R. Association of HERV-K and LINE-1 hypomethylation with reduced disease-free survival in melanoma patients. Epigenomics 2020; 12:1689-1706. [PMID: 33125285 DOI: 10.2217/epi-2020-0127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate CpG methylation of long interspersed nuclear elements 1 (LINE-1) and human endogenous retrovirus K (HERV-K) retroelements as potential prognostic biomarkers in cutaneous melanoma. Materials & methods: Methylation of HERV-K and LINE-1 retroelements was assessed in resected melanoma tissues from 82 patients ranging in age from 14 to 88 years. In addition, nevi from eight patients were included for comparison with nonmalignant melanocytic lesions. Results: Methylation levels were lower in melanomas than in nevi. HERV-K and LINE-1 methylation were decreased in melanoma patients with clinical parameters associated with adverse prognosis, while they were independent of age and gender. Hypomethylation of HERV-K (but not LINE-1) was an independent predictor of reduced disease-free survival. Conclusion: HERV-K hypomethylation can be a potential independent biomarker of melanoma recurrence.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Lares Larcher
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Michela Di Donato
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Elisa Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Sivaramakrishna Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Per Arne Andresen
- Department of Pathology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Dace Pjanova
- Latvian Biomedical Research & Study Centre, LV-1067 Riga, Latvia
| | | | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, 46009 València, Spain
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
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4
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Wang L, Ni S, Du Z, Li X. A six‐CpG‐based methylation markers for the diagnosis of ovarian cancer in blood. J Cell Biochem 2019; 121:1409-1419. [PMID: 31502352 DOI: 10.1002/jcb.29376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Lei Wang
- Department of Obstetrics and Gynecology Shengjing Hospital of China Medical University Shenyang China
| | - Sha Ni
- Department of Obstetrics and Gynecology Shengjing Hospital of China Medical University Shenyang China
| | - Zhenhua Du
- Department of Obstetrics and Gynecology Shengjing Hospital of China Medical University Shenyang China
| | - Xiuqin Li
- Department of Obstetrics and Gynecology Shengjing Hospital of China Medical University Shenyang China
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5
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Fang F, Wang X, Song T. Five-CpG-based prognostic signature for predicting survival in hepatocellular carcinoma patients. Cancer Biol Med 2018; 15:425-433. [PMID: 30766752 PMCID: PMC6372912 DOI: 10.20892/j.issn.2095-3941.2018.0027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective: Hepatocellular carcinoma (HCC) is a common malignancy associated with high morbidity and mortality rates worldwide. Early diagnosis plays an important role in the improvement of HCC prognosis. Methods: In this study, we conducted a comprehensive analysis of HCC DNA methylation and gene expression datasets in The Cancer Genome Atlas (TCGA), to identify a prognostic signature for HCC diagnosis and survival prediction. First, we identified differential methylation CpG (dmCpG) sites in HCC samples and compared them with those in adjacent normal liver tissues; this was followed by univariate analysis and Sure Independence Screening (SIS) in the training set. The robustness of the identified prognostic signature was evaluated using the testing set. To explore the biological processes involved in HCC progression, we also performed functional enrichment analysis for overlapping genes between genes containing dmCpG sites (DMGs) and differential expression genes (DEGs) in HCC patients, using data from the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Results: As a result, we identified five CpG sites that were significantly associated with HCC survival through univariate analysis and SIS. Univariate analysis of clinical characteristics identified age and risk factors (including alcohol consumption and smoking) as independent factors that indicated HCC survival. Multivariate analysis indicated that the integrated prognostic signature (weighted combination of the five CpG sites) that took age and risk factors into consideration resulted in more accurate survival prediction. Conclusions: This study provides a novel signature for predicting HCC survival, and should be helpful for early HCC diagnosis and personalized treatment.
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Affiliation(s)
- Feng Fang
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaoqing Wang
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Tianqiang Song
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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6
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Multiple endpoints to evaluate pristine and remediated titanium dioxide nanoparticles genotoxicity in lung epithelial A549 cells. Toxicol Lett 2017; 276:48-61. [DOI: 10.1016/j.toxlet.2017.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 12/14/2022]
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7
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Geng JH, Lin VC, Yu CC, Huang CY, Yin HL, Chang TY, Lu TL, Huang SP, Bao BY. Inherited Variants in Wnt Pathway Genes Influence Outcomes of Prostate Cancer Patients Receiving Androgen Deprivation Therapy. Int J Mol Sci 2016; 17:E1970. [PMID: 27898031 PMCID: PMC5187770 DOI: 10.3390/ijms17121970] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 12/29/2022] Open
Abstract
Aberrant Wnt signaling has been associated with many types of cancer. However, the association of inherited Wnt pathway variants with clinical outcomes in prostate cancer patients receiving androgen deprivation therapy (ADT) has not been determined. Here, we comprehensively studied the contribution of common single nucleotide polymorphisms (SNPs) in Wnt pathway genes to the clinical outcomes of 465 advanced prostate cancer patients treated with ADT. Two SNPs, adenomatous polyposis coli (APC) rs2707765 and rs497844, were significantly (p ≤ 0.009 and q ≤ 0.043) associated with both prostate cancer progression and all-cause mortality, even after multivariate analyses and multiple testing correction. Patients with a greater number of favorable alleles had a longer time to disease progression and better overall survival during ADT (p for trend ≤ 0.003). Additional, cDNA array and in silico analyses of prostate cancer tissue suggested that rs2707765 affects APC expression, which in turn is correlated with tumor aggressiveness and patient prognosis. This study identifies the influence of inherited variants in the Wnt pathway on the efficacy of ADT and highlights a preclinical rationale for using APC as a prognostic marker in advanced prostate cancer.
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Affiliation(s)
- Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
- Department of Urology, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung 812, Taiwan.
| | - Victor C Lin
- Department of Urology, E-Da Hospital, Kaohsiung 824, Taiwan.
- School of Medicine for International Students, I-Shou University, Kaohsiung 840, Taiwan.
| | - Chia-Cheng Yu
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan.
- Department of Urology, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.
- Department of Pharmacy, Tajen University, Pingtung 907, Taiwan.
| | - Chao-Yuan Huang
- Department of Urology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
- Department of Urology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu 300, Taiwan.
| | - Hsin-Ling Yin
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
- Department of Pathology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Ta-Yuan Chang
- Department of Occupational Safety and Health, China Medical University, Taichung 404, Taiwan.
| | - Te-Ling Lu
- Department of Pharmacy, China Medical University, Taichung 404, Taiwan.
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
- Department of Urology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Bo-Ying Bao
- Department of Pharmacy, China Medical University, Taichung 404, Taiwan.
- Sex Hormone Research Center, China Medical University Hospital, Taichung 404, Taiwan.
- Department of Nursing, Asia University, Taichung 413, Taiwan.
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8
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De Luca C, Guadagni F, Sinibaldi-Vallebona P, Sentinelli S, Gallucci M, Hoffmann A, Schumann GG, Spadafora C, Sciamanna I. Enhanced expression of LINE-1-encoded ORF2 protein in early stages of colon and prostate transformation. Oncotarget 2016; 7:4048-61. [PMID: 26716650 PMCID: PMC4826189 DOI: 10.18632/oncotarget.6767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/30/2015] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) retrotransposons are a source of endogenous reverse transcriptase (RT) activity, which is expressed as part of the L1-encoded ORF2 protein (L1-ORF2p). L1 elements are highly expressed in many cancer types, while being silenced in most differentiated somatic tissues. We previously found that RT inhibition reduces cell proliferation and promotes differentiation in neoplastic cells, indicating that high endogenous RT activity promotes cancer growth. Here we investigate the expression of L1-ORF2p in several human types of cancer. We have developed a highly specific monoclonal antibody (mAb chA1-L1) to study ORF2p expression and localization in human cancer cells and tissues. We uncover new evidence for high levels of L1-ORF2p in transformed cell lines and staged epithelial cancer tissues (colon, prostate, lung and breast) while no or only basal ORF2p expression was detected in non-transformed cells. An in-depth analysis of colon and prostate tissues shows ORF2p expression in preneoplastic stages, namely transitional mucosa and prostate intraepithelial neoplasia (PIN), respectively. Our results show that L1-ORF2p is overexpressed in tumor and in preneoplastic colon and prostate tissues; this latter finding suggests that ORF2p could be considered as a potential early diagnostic biomarker.
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Affiliation(s)
| | - Fiorella Guadagni
- Laboratory BioDAT SR Research, IRCCS San Raffaele Pisana, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy.,Institute of Translational Pharmacology, CNR, Rome, Italy
| | - Steno Sentinelli
- I.F.O. Regina Elena, UOC Pathological Anatomy/Urology, Rome, Italy
| | - Michele Gallucci
- I.F.O. Regina Elena, UOC Pathological Anatomy/Urology, Rome, Italy
| | - Andreas Hoffmann
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Gerald G Schumann
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
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9
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Hafez MM, Al-Shabanah OA, Al-Rejaie SS, Al-Harbi NO, Hassan ZK, Alsheikh A, Al Theyab AI, Aldelemy ML, Sayed-Ahmed MM. Increased hypermethylation of glutathione S-transferase P1, DNA-binding protein inhibitor, death associated protein kinase and paired box protein-5 genes in triple-negative breast cancer Saudi females. Asian Pac J Cancer Prev 2015; 16:541-9. [PMID: 25684485 DOI: 10.7314/apjcp.2015.16.2.541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer (BC) with higher metastatic rate and both local and systemic recurrence compared to non-TNBC. The generation of reactive oxygen species (ROS) secondary to oxidative stress is associated with DNA damage, chromosomal degradation and alterations of both hypermethylation and hypomethylation of DNA. This study concerns differential methylation of promoter regions in specific groups of genes in TNBC and non-TNBC Saudi females in an effort to understand whether epigenetic events might be involved in breast carcinogenesis, and whether they might be used as markers for Saudi BCs. Methylation of glutathione S-transferase P1 (GSTP1), T-cadherin (CDH13), Paired box protein 5 (PAX5), death associated protein kinase (DAPK), twist-related protein (TWIST), DNA-binding protein inhibitor (ID4), High In Normal-1 (HIN-1), cyclin-dependent kinase inhibitor 2A (p16), cyclin D2 and retinoic acid receptor-β (RARβ1) genes was analyzed by methylation specific polymerase chain reaction (MSP) in 200 archival formalin- fixed paraffin embedded BC tissues divided into 3 groups; benign breast tissues (20), TNBC (80) and non-TNBC (100). The relationships between methylation status, and clinical and pathological characteristics of patients and tumors were assessed. Higher frequencies of GSTP1, ID4, TWIST, DAPK, PAX5 and HIN-1 hypermethylation were found in TNBC than in non-TNBC. Hypermethylation of GSTP1, CDH13, ID4, DAPK, HIN-1 and PAX5 increased with tumor grade increasing. Other statistically significant correlations were identified with studied genes. Data from this study suggest that increased hypermethylation of GSTP1, ID4, TWIST, DAPK, PAX5 and HIN-1 genes in TNBC than in non-TNBC can act as useful biomarker for BCs in the Saudi population. The higher frequency of specific hypermethylated genes paralleling tumor grade, size and lymph node involvement suggests contributions to breast cancer initiation and progression.
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Affiliation(s)
- Mohamed M Hafez
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia E-mail :
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Abstract
Constitutional epimutation, which is an aberration in gene expression due to an altered epigenotype that is widely distributed in normal tissues (albeit frequently mosaic), provides an alternative mechanism to genetic mutation for cancer predisposition. Observational studies in cancer-affected families have revealed intergenerational inheritance of constitutional epimutation, providing unique insights into the heritability of epigenetic traits in humans. In this Opinion article, the potential contribution of constitutional epimutation to the 'missing' causality and heritability of cancer is explored.
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Affiliation(s)
- Megan P Hitchins
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Grant Building S169, 1291 Welch Road, Stanford, California 94305, USA
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11
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Ngollo M, Dagdemir A, Karsli-Ceppioglu S, Judes G, Pajon A, Penault-Llorca F, Boiteux JP, Bignon YJ, Guy L, Bernard-Gallon DJ. Epigenetic modifications in prostate cancer. Epigenomics 2015; 6:415-26. [PMID: 25333850 DOI: 10.2217/epi.14.34] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the most common cancer in men and the second leading cause of cancer deaths in men in France. Apart from the genetic alterations in prostate cancer, epigenetics modifications are involved in the development and progression of this disease. Epigenetic events are the main cause in gene regulation and the three most epigenetic mechanisms studied include DNA methylation, histone modifications and microRNA expression. In this review, we summarized epigenetic mechanisms in prostate cancer. Epigenetic drugs that inhibit DNA methylation, histone methylation and histone acetylation might be able to reactivate silenced gene expression in prostate cancer. However, further understanding of interactions of these enzymes and their effects on transcription regulation in prostate cancer is needed and has become a priority in biomedical research. In this study, we summed up epigenetic changes with emphasis on pharmacologic epigenetic target agents.
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Affiliation(s)
- Marjolaine Ngollo
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand, France
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12
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Prognostic significance of promoter CpG island hypermethylation and repetitive DNA hypomethylation in stage I lung adenocarcinoma. Virchows Arch 2015; 466:675-83. [DOI: 10.1007/s00428-015-1749-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/15/2015] [Accepted: 02/24/2015] [Indexed: 12/15/2022]
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13
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Global DNA hypomethylation in prostate cancer development and progression: a systematic review. Prostate Cancer Prostatic Dis 2014; 18:1-12. [PMID: 25384337 DOI: 10.1038/pcan.2014.45] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/10/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND The role of global DNA methylation in prostate cancer (PCa) remains largely unknown. Our aim was to summarize evidence on the role of global DNA hypomethylation in PCa development and progression. METHODS We searched PubMed through December 2013 for all studies containing information on global methylation levels in PCa tissue and at least one non-tumor comparison tissue and/or studies reporting association between global methylation levels in PCa tissue and survival, disease recurrence or at least one clinicopathological prognostic factor. We summarized results using non-parametric comparisons and P-value summary methods. RESULTS We included 15 studies in the review: 6 studies with both diagnostic and prognostic information, 5 studies with only diagnostic information and 4 studies with only prognostic information. Quantitative meta-analysis was not possible because of the large heterogeneity in molecular techniques, types of tissues analyzed, aims and study designs. Summary statistical tests showed association of DNA hypomethylation with PCa diagnosis (P<0.006) and prognosis (P<0.001). Restriction to studies assessing 5-methylcytosine or long interspersed nucleotide element-1 revealed results in the same direction. Analyses restricted to specific clinicopathological features showed association with the presence of metastasis and tumor stage in all tests with P<0.03, and no association with Gleason score (all tests P>0.1 except for the weighted Z-test, P=0.05). CONCLUSION DNA hypomethylation was associated with PCa development and progression. However, due to the heterogeneity and small sample sizes of the included studies, along with the possibility of publication bias, this association requires additional assessment.
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14
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Heterogeneity of DNA methylation in multifocal prostate cancer. Virchows Arch 2014; 466:53-9. [DOI: 10.1007/s00428-014-1678-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/17/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
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15
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Brauze D, Fijalkiewicz K, Szaumkessel M, Kiwerska K, Bednarek K, Rydzanicz M, Richter J, Grenman R, Jarmuz-Szymczak M. Diversified expression of aryl hydrocarbon receptor dependent genes in human laryngeal squamous cell carcinoma cell lines treated with β-naphthoflavone. Toxicol Lett 2014; 231:99-107. [DOI: 10.1016/j.toxlet.2014.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 08/08/2014] [Accepted: 09/05/2014] [Indexed: 02/05/2023]
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Prostate cancer epigenetic biomarkers: next-generation technologies. Oncogene 2014; 34:1609-18. [PMID: 24837368 DOI: 10.1038/onc.2014.111] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 12/15/2022]
Abstract
Cancer is caused by a combination of genetic alterations and gross changes to the epigenetic landscape that together result in aberrant cancer gene regulation. Therefore, we need to fully sequence both the cancer genome and the matching cancer epigenomes before we can fully integrate the suite of molecular mechanisms involved in initiation and progression of cancer. A further understanding of epigenetic aberrations has a great potential in the next era of molecular genomic pathology in cancer detection and treatment in all types of cancer, including prostate cancer. In this review, we discuss the most common epigenetic aberrations identified in prostate cancer with the biomarker potential. We also describe the innovative and current epigenomic technologies used for the identification of epigenetic-associated changes in prostate cancer and future translational applications in molecular pathology for cancer detection and prognosis.
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Damaschke NA, Yang B, Bhusari S, Svaren JP, Jarrard D. Epigenetic susceptibility factors for prostate cancer with aging. Prostate 2013; 73:1721-30. [PMID: 23999928 PMCID: PMC4237278 DOI: 10.1002/pros.22716] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/06/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Increasing age is a significant risk factor for prostate cancer. The prostate is exposed to environmental and endogenous stress that may underlie this remarkable incidence. DNA methylation, genomic imprinting, and histone modifications are examples of epigenetic factors known to undergo change in the aging and cancerous prostate. In this review we examine the data linking epigenetic alterations in the prostate with aging to cancer development. METHODS An online search of current and past peer reviewed literature on epigenetic changes with cancer and aging was performed. Relevant articles were analyzed. RESULTS Epigenetic changes are responsible for modifying expression of oncogenes and tumor suppressors. Several of these changes may represent a field defect that predisposes to cancer development. Focal hypermethylation occurs at CpG islands in the promoters of certain genes including GSTP1, RARβ2, and RASSF1A with both age and cancer, while global hypomethylation is seen in prostate cancer and known to occur in the colon and other organs. A loss of genomic imprinting is responsible for biallelic expression of the well-known Insulin-like Growth Factor 2 (IGF2) gene. Loss of imprinting (LOI) at IGF2 has been documented in cancer and is also known to occur in benign aging prostate tissue marking the presence of cancer. Histone modifications have the ability to dictate chromatin structure and direct gene expression. CONCLUSIONS Epigenetic changes with aging represent molecular mechanisms to explain the increased susceptibly of the prostate to develop cancer in older men. These changes may provide an opportunity for diagnostic and chemopreventive strategies given the epigenome can be modified.
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Affiliation(s)
- N. A. Damaschke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - B. Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - S. Bhusari
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - J. P. Svaren
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, 53972
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
| | - D.F. Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
- University of Wisconsin Carbone Comprehensive Cancer Center, Madison, Wisconsin
- Environmental and Molecular Toxicology, University of Wisconsin, Madison, Wisconsin
- Correspondence to: D.F. Jarrard, MD, 7037 Wisconsin Institutes of Medical Research, 1111 Highland Avenue, Madison, WI 53792.
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Chen Y, Li J, Yu X, Li S, Zhang X, Mo Z, Hu Y. APC gene hypermethylation and prostate cancer: a systematic review and meta-analysis. Eur J Hum Genet 2013; 21:929-35. [PMID: 23299921 PMCID: PMC3746257 DOI: 10.1038/ejhg.2012.281] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/09/2012] [Accepted: 11/21/2012] [Indexed: 01/22/2023] Open
Abstract
Prostate cancer (PCa) is a worldwide disease that affects a large number of males. Although prostate-specific antigen (PSA) screening is used, the specificity is limited. This study analyzes the sensitivity and specificity of adenomatous polyposis coli (APC) methylation for PCa detection in body fluids and tissues. Combining search results from PubMed and Embase, 19 studies were included, 5 involving body fluids and 14 involving prostate tissue, with 2344 subjects. In body fluid subgroups, the pooled sensitivity and specificity was 0.53 (95% confidence interval (CI): 0.28-0.78) and 0.92 (95% CI: 0.86-0.95), respectively. From tissue studies, the results presented as 0.84 (95% CI: 0.70-0.92) and 0.91 (95% CI: 0.77-0.97). To confirm the results, we conducted a further analysis by removing studies which introduced high heterogeneity due to the type of cases and controls. The same degree of sensitivity and specificity was presented in two subgroups (urine: sensitivity 0.46, 95% CI: 0.39-0.53; specificity 0.87, 95% CI: 0.64-0.96; tissue: sensitivity 0.87, 95% CI: 0.72-0.94; specificity 0.89, 95% CI: 0.68-0.97). In addition, analysis of the interaction between APC methylation and PCa showed strong association in the whole data set (odds ratio (OR)=24.91, 95% CI: 12.86-48.24, I(2)=72.5%). Pooling the same two main subgroups (tissue/fluid) gave a pooled OR of 33.54 (95% CI: 14.88-75.59; I(2)=70.7%) and 8.20 (95% CI: 2.84-23.74, I(2)=64.2%), respectively. From this study, the results suggest that APC promoter methylation may be the potential testing for PCa diagnosis and provide a new viewpoint in the treatment of PCa.
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Affiliation(s)
- Yang Chen
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Jie Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Xiaoxiang Yu
- Institute of Urology and Nephrology, the People's Liberation Army 303 Hospital of Guangxi, Nanning, China
| | - Shuai Li
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Xuerong Zhang
- Medical Research Center, Guangxi Medical University, Nanning, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yanling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
- Medical Research Center, Guangxi Medical University, Nanning, China
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Prognostic Value of Promoter Hypermethylation of Retinoic Acid Receptor Beta (RARB) and CDKN2 (p16/MTS1) in Prostate Cancer. Chin J Cancer Res 2013; 23:306-11. [PMID: 23358881 DOI: 10.1007/s11670-011-0306-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Accepted: 07/20/2011] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE The molecular mechanism of prostate cancer is poorly understood. The aim of the study was to investigate the prevalence and prognostic value of promoter hypermethylation of retinoic acid receptor beta (RARB) and p16 among benign prostatic hyperplasia (BPH) and prostate cancer patients. METHODS In this case-control study, 63 patients were included in three groups; 21 with BPH as the control group, 21 with prostate cancer and good prognostic factors (based on prostate-specific antigen, Gleason score and stage) as good prognosis group, and 21 with prostate cancer and poor prognostic features as poor prognosis group. The prostate biopsy specimen of each individual was examined for hypermethylation of RARB and p16 promoters by methylation specific PCR (MSPCR). RESULTS Seven (33.3%) patients with good prognosis and 15 (71.4%) patients with poor prognosis were positive for RARB methylation, which were significantly higher than controls (P<0.0001). p16 promoter methylation was shown in 19.0% and 47.6% patients with good and poor prognosis, respectively. The RARB and p16 promoter methylation in the poor prognosis group was significantly higher than that in the good prognosis group (P =0.02 for RARB and P<0.0001 for p16). CONCLUSION Hypermethylation of RARB and p16 promoters may predict prognosis in prostate cancer.
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Bijron JG, Bol GM, Verheijen RH, van Diest PJ. Epigenetic biomarkers in the diagnosis of ovarian cancer. ACTA ACUST UNITED AC 2012; 6:421-38. [PMID: 23480807 DOI: 10.1517/17530059.2012.702105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Current diagnostic methods for ovarian cancer have limited performance. Recent advances within the field of epigenetics have shifted the clinical implementation of epigenetic biomarkers as a diagnostic approach from a dream for the future to a present-day consideration. Patients could potentially benefit greatly from this novel diagnostic approach. AREAS COVERED Epigenetic mechanisms in cancer are discussed, with a focus on potential diagnostic epigenetic biomarkers in ovarian cancer in tissue and body fluids. A literature search was undertaken (on 22-09-2011) for these subjects using the search syntax ((((((((((((((("ovarian") OR "ovary") OR "ovarian cancer") OR "ovarian cancers") OR "cancer of the ovary") OR "tumour of the ovary") OR "ovarian tumor") OR "ovarian tumors") OR "ovarian tumour") OR "ovarian tumours") OR "ovarian neoplasm") OR "ovarian neoplasms" OR "ovarian carcinoma") OR "ovarian carcinomas") OR "carcinoma of the ovary")) AND ((((((((("epigenetics") OR "epigenetic") OR "epigenome") OR "methylation") OR "hypermethylation") OR "chromatin modification") OR "histone") OR "histones") OR "acetylation") EXPERT OPINION To date no single epigenetic biomarker is able to accurately detect early ovarian cancer in either tissue or body fluids. A panel of epigenetic biomarkers based on aberrant DNA methylation in body fluids, especially blood, has the best chance of being implemented in clinical practice, as it is semi-invasive. However, progression toward clinical use is hampered by the lack of detection techniques combining high throughput and accuracy with low cost, by difficulties in establishing reliable reference values and by the heterogeneous nature of ovarian cancer. Until addressed, implementation as a diagnostic measure complimenting current techniques in select cases seems a far way to go, and implementation as a primary screening tool is yet even farther away.
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Affiliation(s)
- Jonathan G Bijron
- University Medical Center Utrecht, Department of Pathology , 3508 GA Utrecht , The Netherlands
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Huynh KT, Hoon DSB. Epigenetics of regional lymph node metastasis in solid tumors. Clin Exp Metastasis 2012; 29:747-56. [DOI: 10.1007/s10585-012-9491-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/20/2012] [Indexed: 01/01/2023]
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Woo HD, Kim J. Global DNA hypomethylation in peripheral blood leukocytes as a biomarker for cancer risk: a meta-analysis. PLoS One 2012; 7:e34615. [PMID: 22509334 PMCID: PMC3324531 DOI: 10.1371/journal.pone.0034615] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/02/2012] [Indexed: 12/25/2022] Open
Abstract
Background Good biomarkers for early detection of cancer lead to better prognosis. However, harvesting tumor tissue is invasive and cannot be routinely performed. Global DNA methylation of peripheral blood leukocyte DNA was evaluated as a biomarker for cancer risk. Methods We performed a meta-analysis to estimate overall cancer risk according to global DNA hypomethylation levels among studies with various cancer types and analytical methods used to measure DNA methylation. Studies were systemically searched via PubMed with no language limitation up to July 2011. Summary estimates were calculated using a fixed effects model. Results The subgroup analyses by experimental methods to determine DNA methylation level were performed due to heterogeneity within the selected studies (p<0.001, I2: 80%). Heterogeneity was not found in the subgroup of %5-mC (p = 0.393, I2: 0%) and LINE-1 used same target sequence (p = 0.097, I2: 49%), whereas considerable variance remained in LINE-1 (p<0.001, I2: 80%) and bladder cancer studies (p = 0.016, I2: 76%). These results suggest that experimental methods used to quantify global DNA methylation levels are important factors in the association study between hypomethylation levels and cancer risk. Overall, cancer risks of the group with the lowest DNA methylation levels were significantly higher compared to the group with the highest methylation levels [OR (95% CI): 1.48 (1.28–1.70)]. Conclusions Global DNA hypomethylation in peripheral blood leukocytes may be a suitable biomarker for cancer risk. However, the association between global DNA methylation and cancer risk may be different based on experimental methods, and region of DNA targeted for measuring global hypomethylation levels as well as the cancer type. Therefore, it is important to select a precise and accurate surrogate marker for global DNA methylation levels in the association studies between global DNA methylation levels in peripheral leukocyte and cancer risk.
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Affiliation(s)
- Hae Dong Woo
- Cancer Epidemiology Branch, National Cancer Center, Goyang-si, Korea
| | - Jeongseon Kim
- Cancer Epidemiology Branch, National Cancer Center, Goyang-si, Korea
- * E-mail:
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Shin SH, Lee K, Kim BH, Cho NY, Jang JY, Kim YT, Kim D, Jang JJ, Kang GH. Bile-based detection of extrahepatic cholangiocarcinoma with quantitative DNA methylation markers and its high sensitivity. J Mol Diagn 2012; 14:256-63. [PMID: 22446083 DOI: 10.1016/j.jmoldx.2012.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 11/15/2011] [Accepted: 01/04/2012] [Indexed: 12/15/2022] Open
Abstract
Extrahepatic cholangiocarcinoma (EHC) is usually difficult to diagnose by bile cytology because of cellular disintegration. However, DNA samples from bile fluid can provide sufficient materials to screen for the presence of EHC. We developed DNA methylation marker panels that can be used for MethyLight assay-based detection of EHC in bile fluid specimens. The methylation status of 59 DNA methylation markers was investigated in 20 EHC and 20 non-neoplastic gallbladder tissue samples with MethyLight assay to determine cancer-specific DNA methylation markers. Through assaying cancer-specific DNA methylation markers in a training set (n = 40) and validation set (n = 45) of bile fluid specimens from patients with EHC or those without cancer, we selected suitable marker panels that were assessed for their performance in a third set (test set; n = 40). Four marker panels showed a sensitivity of 60% or more and a specificity of 100% in both the training and validation sets, whereas bile cytology displayed a sensitivity of 40% to 46% and a specificity of 100%. In an independent test set of bile fluid samples, a five-gene panel (CCND2, CDH13, GRIN2B, RUNX3, and TWIST1) detected EHC at a sensitivity of 83%, which was far higher than that of bile cytology (46%, P = 0.004). Using bile fluids, a methylation assay consisting of a five-gene panel may be useful for detecting EHC and in helping to increase the sensitivity of preoperative diagnoses.
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Affiliation(s)
- So-Hyun Shin
- Laboratory of Epigenetics, Cancer Research Institute, Seoul, South Korea
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Abstract
Cancer patients' outcome and survival depends on the early diagnosis of malignant lesions. Several investigation methods used for the prevention and early detection strategies have specific limitations. More recently, epigenetic changes have been considered one of the most promising tools for the early diagnosis of cancer. Some of these epigenetic alterations including promoter hypermethylation of genes like P16INK4a, BRCA1, BRCA2, ERα and RARβ2, APC, and RASSF1A have been associated with early stages of mammary gland tumorigenesis and have been suggested to be included in the models that evaluate individual breast cancer risk. In lung cancer, P16INK4a and MGMT gene hypermethylation was observed in sputum years before clinical manifestation of the squamous cell carcinoma among smokers. Loss of GSTP1 function by DNA hypermethylation together with changes in the methylation levels of repetitive elements like LINE-1 and Sat2 was reported in prostatic preneoplastic lesions. Also, DNA hypermethylation for hMLH1 and MGMT DNA repair genes was reported in precursor lesions to colorectal cancer. These epigenetic alterations may be influenced by factors such as xenoestrogens, folate, and multivitamins. Detection of these changes may help determining cancer susceptibility and early diagnosis.
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Yang M, Park JY. DNA methylation in promoter region as biomarkers in prostate cancer. Methods Mol Biol 2012; 863:67-109. [PMID: 22359288 DOI: 10.1007/978-1-61779-612-8_5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The prostate gland is the most common site of cancer and the second leading cause of cancer death in American men. Recent emerging molecular biological technologies help us to know that epigenetic alterations such as DNA methylation within the regulatory (promoter) regions of genes are associated with transcriptional silencing in cancer. Promoter hypermethylation of critical pathway genes could be potential biomarkers and therapeutic targets for prostate cancer. In this chapter, we updated current information on methylated genes associated with the development and progression of prostate cancer. Over 40 genes have been investigated for methylation in promoter region in prostate cancer. These methylated genes are involved in critical pathways, such as DNA repair, metabolism, and invasion/metastasis. The role of hypermethylated genes in regulation of critical pathways in prostate cancer is discussed. These findings may provide new information of the pathogenesis, the exciting potential to be predictive and to provide personalized treatment of prostate cancer. Indeed, some epigenetic alterations in prostate tumors are being translated into clinical practice for therapeutic use.
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Affiliation(s)
- Mihi Yang
- Division of Cancer Prevention and Controls, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Bayani J, Diamandis EP. The physiology and pathobiology of human kallikrein-related peptidase 6 (KLK6). Clin Chem Lab Med 2011; 50:211-33. [PMID: 22047144 DOI: 10.1515/cclm.2011.750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 09/21/2011] [Indexed: 12/11/2022]
Abstract
The human kallikrein-related peptidase 6 (KLK6) gene belongs to the 15-member kallikrein (KLK) gene family mapping to chromosome 19q13.3-13.4. Encoding for an enzyme with trypsin-like properties, KLK6 can degrade components of the extracellular matrix. The successful utilisation of another KLK member (KLK3/PSA) for prostate cancer diagnosis has led many to evaluate KLK6 as a potential biomarker for other cancer and diseased states. The observed dysregulated expression in cancers, neurodegenerative diseases and skin conditions has led to the discovery that KLK6 participates in other cellular pathways including inflammation, receptor activation and regulation of apoptosis. Moreover, the improvements in high-throughput genomics have not only enabled the identification of sequence polymorphisms, but of transcript variants, whose functional significances have yet to be realised. This comprehensive review will summarise the current findings of KLK6 pathophysiology and discuss its potential as a viable biomarker.
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Affiliation(s)
- Jane Bayani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Sigalotti L, Fratta E, Bidoli E, Covre A, Parisi G, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M. Methylation levels of the "long interspersed nucleotide element-1" repetitive sequences predict survival of melanoma patients. J Transl Med 2011; 9:78. [PMID: 21615918 PMCID: PMC3123580 DOI: 10.1186/1479-5876-9-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Background The prognosis of cutaneous melanoma (CM) differs for patients with identical clinico-pathological stage, and no molecular markers discriminating the prognosis of stage III individuals have been established. Genome-wide alterations in DNA methylation are a common event in cancer. This study aimed to define the prognostic value of genomic DNA methylation levels in stage III CM patients. Methods Overall level of genomic DNA methylation was measured using bisulfite pyrosequencing at three CpG sites (CpG1, CpG2, CpG3) of the Long Interspersed Nucleotide Element-1 (LINE-1) sequences in short-term CM cultures from 42 stage IIIC patients. The impact of LINE-1 methylation on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analysis. Results Hypomethylation (i.e., methylation below median) at CpG2 and CpG3 sites significantly associated with improved prognosis of CM, CpG3 showing the strongest association. Patients with hypomethylated CpG3 had increased OS (P = 0.01, log-rank = 6.39) by Kaplan-Meyer analysis. Median OS of patients with hypomethylated or hypermethylated CpG3 were 31.9 and 11.5 months, respectively. The 5 year OS for patients with hypomethylated CpG3 was 48% compared to 7% for patients with hypermethylated sequences. Among the variables examined by Cox regression analysis, LINE-1 methylation at CpG2 and CpG3 was the only predictor of OS (Hazard Ratio = 2.63, for hypermethylated CpG3; 95% Confidence Interval: 1.21-5.69; P = 0.01). Conclusion LINE-1 methylation is identified as a molecular marker of prognosis for CM patients in stage IIIC. Evaluation of LINE-1 promises to represent a key tool for driving the most appropriate clinical management of stage III CM patients.
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Affiliation(s)
- Luca Sigalotti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
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DNA methylation profile during multistage progression of pulmonary adenocarcinomas. Virchows Arch 2011; 459:201-11. [PMID: 21494759 DOI: 10.1007/s00428-011-1079-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 12/31/2022]
Abstract
Multiple genetic and epigenetic alterations are known to be involved in the carcinogenesis of peripheral pulmonary adenocarcinoma (ADC). However, epigenetic abnormalities have not been extensively investigated in the following multistage progression sequence: atypical adenomatous hyperplasia (AAH) to adenocarcinoma in situ (AIS), to invasive ADC. To determine the potential role of promoter methylation during ADC development of the lung, we examined methylation status in 20 normal, 20 AAH, 30 AIS, and 60 ADC lung tissues and compared methylation status among the lesions. The MethyLight assay was used to determine the methylation status of 18 CpG island loci, which were hypermethylated in ADC compared to noncancerous lung tissues. The mean number of methylated CpG island loci was significantly higher in ADC than in AAH and AIS, (p < 0.003 between ADC and AAH, p < 0.005 between ADC and AIS). Aberrant methylation of HOXA1, TMEFF2, and RARB was frequently observed in preinvasive lesions, including AAH and AIS. Furthermore, methylation of PENK, BCL2, RUNX3, DLEC1, MT1G, GRIN2B, CDH13, CCND2, and HOXA10 was significantly more frequent in invasive ADC than AAH or AIS. Our results indicate that epigenetic alterations are involved in the multistep progression of pulmonary ADC development, and aberrant CpG island methylation accumulates during multistep carcinogenesis. In addition, aberrant methylation of HOXA1, TMEFF2, and RARB occurred in preinvasive lesions, which indicates that epigenetic alterations of these genes are involved in the early stages of pulmonary ADC development. In contrast, hypermethylation of PENK, BCL2, RUNX3, DLEC1, MT1G, GRIN2B, CDH13, CCND2, and HOXA10 was more frequent in invasive ADC than in preinvasive lesions, which indicates that methylation of these genes occurs later during tumor invasion in the AAH-AIS-ADC sequence.
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Liu L, Kron KJ, Pethe VV, Demetrashvili N, Nesbitt ME, Trachtenberg J, Ozcelik H, Fleshner NE, Briollais L, van der Kwast TH, Bapat B. Association of tissue promoter methylation levels of APC, TGFβ2, HOXD3 and RASSF1A with prostate cancer progression. Int J Cancer 2011; 129:2454-62. [PMID: 21207416 DOI: 10.1002/ijc.25908] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 11/26/2010] [Indexed: 11/12/2022]
Abstract
Aberrant promoter methylation is known to silence tumor-suppressor genes in prostate cancer (PCa). We correlated quantitative promoter methylation levels of APC, TGFβ2 and RASSF1A in 219 radical prostatectomies diagnosed between 1998 and 2001 with clinicopathological follow-up data available including Gleason Pattern (GP), Gleason Score (GS) and pathological stage and explored their potential in predicting biochemical recurrence using univariate and multivariate analyses. We observed that the average methylation levels of APC increased significantly from GS ≤ 6 to GS7, and pT2 to pT3a, and that of TGFβ2 increased from GS ≤ 6 to GS7, but not for RASSF1A. PCa samples were also stratified into high methylation (HM) and low methylation (LM) groups based on the PMR scores of all cases analyzed for each marker. The HM frequency of APC was greater in pT3a than pT2, and in GS ≥ 8 than GS ≤ 6. The HM frequency also increased significantly from GP3 to GP4 for APC, TGFβ2 and RASSF1A. APC methylation level was a significant predictor of biochemical recurrence in univariate analysis (p-value = 0.028). Finally, we combined methylation data of these three genes with the previously reported novel methylation biomarker HOXD3. Quantitative methylation assessment of a multiplex panel of markers, consisting of APC, HOXD3 and TGFβ2, outperforms any single marker for the prediction of biochemical recurrence (p-value = 0.017). Our study demonstrated that quantitative increase in promoter methylation levels of APC, HOXD3 and TGFβ2 are associated with PCa progression.
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Affiliation(s)
- Liyang Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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Kitkumthorn N, Mutirangura A. Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clin Epigenetics 2011; 2:315-30. [PMID: 22704344 PMCID: PMC3365388 DOI: 10.1007/s13148-011-0032-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/20/2011] [Indexed: 12/31/2022] Open
Abstract
Epigenetic changes in long interspersed nuclear element-1s (LINE-1s or L1s) occur early during the process of carcinogenesis. A lower methylation level (hypomethylation) of LINE-1 is common in most cancers, and the methylation level is further decreased in more advanced cancers. Consequently, several previous studies have suggested the use of LINE-1 hypomethylation levels in cancer screening, risk assessment, tumor staging, and prognostic prediction. Epigenomic changes are complex, and global hypomethylation influences LINE-1s in a generalized fashion. However, the methylation levels of some loci are dependent on their locations. The consequences of LINE-1 hypomethylation are genomic instability and alteration of gene expression. There are several mechanisms that promote both of these consequences in cis. Therefore, the methylation levels of different sets of LINE-1s may represent certain phenotypes. Furthermore, the methylation levels of specific sets of LINE-1s may indicate carcinogenesis-dependent hypomethylation. LINE-1 methylation pattern analysis can classify LINE-1s into one of three classes based on the number of methylated CpG dinucleotides. These classes include hypermethylation, partial methylation, and hypomethylation. The number of partial and hypermethylated loci, but not hypomethylated LINE-1s, is different among normal cell types. Consequently, the number of hypomethylated loci is a more promising marker than methylation level in the detection of cancer DNA. Further genome-wide studies to measure the methylation level of each LINE-1 locus may improve PCR-based methylation analysis to allow for a more specific and sensitive detection of cancer DNA or for an analysis of certain cancer phenotypes.
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Stanzer S, Balic M, Strutz J, Heitzer E, Obermair F, Hauser-Kronberger C, Samonigg H, Dandachi N. Rapid and reliable detection of LINE-1 hypomethylation using high-resolution melting analysis. Clin Biochem 2010; 43:1443-8. [PMID: 20883681 DOI: 10.1016/j.clinbiochem.2010.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 08/19/2010] [Accepted: 09/17/2010] [Indexed: 12/17/2022]
Abstract
OBJECTIVES The aim of the present study was to evaluate the precision and reproducibility of the LINE-1 high-resolution melting (HRM) assay to detect LINE-1 hypomethylation. DESIGN AND METHODS We first evaluated a methylated DNA dilution matrix and a panel of human cancer cell lines. We then applied this LINE-1 HRM assay to a set of 37 archival prostate cancer tissue samples. RESULTS Our LINE-1 HRM assay revealed small and reproducible run-to-run and bisulfite-to-bisulfite variations. As expected, we found a large variation in methylation levels between different cancer cell lines. All results were confirmed with MethyLight and pyrosequencing as indicated by the high correlation coefficient. Finally, we successfully applied the LINE-1 HRM assay to archival prostate cancer tissues. CONCLUSIONS The present LINE-1 HRM assay represents a novel, accurate, and cost-effective method to measure global hypomethylation, which makes it suitable for high- and low-throughput laboratories.
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Affiliation(s)
- Stefanie Stanzer
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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CpG island hypermethylation and repetitive DNA hypomethylation in premalignant lesion of extrahepatic cholangiocarcinoma. Virchows Arch 2009; 455:343-51. [PMID: 19763613 DOI: 10.1007/s00428-009-0829-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 08/05/2009] [Accepted: 08/24/2009] [Indexed: 12/13/2022]
Abstract
Biliary intraepithelial neoplasia (BilIN) is the premalignant lesion of extrahepatic cholangiocarcinoma (EHC), and there are no published data regarding epigenetic changes throughout disease progression from normal biliary epithelia to BilIN to EHC. The objective of this study was to identify the occurrence of CpG island hypermethylation and repetitive DNA hypomethylation in BilIN. A total of 50 EHCs, 31 BilINs, and 31 normal cystic duct samples were analyzed for their methylation status in seven genes and two repetitive DNA elements. The number of methylated genes increased with disease progression (normal bile duct, 0.6; BilIN, 2.0; EHC, 3.6; P < 0.001). The methylation level of examined genes was significantly higher in BilIN than in normal samples (TMEFF2, HOXA1, NEUROG1, and RUNX3, P < 0.05) and in EHC than in BilIN samples (TMEFF2, HOXA1, NEUROG1, RUNX3, RASSF1A, and APC, P < 0.05). Long interspersed nucleotide element-1 (LINE-1) and juxtacentromeric satellite 2 (SAT2) methylation levels were markedly lower in EHC than in normal duct and BilIN samples, and BilIN samples showed a decrease of SAT2 methylation levels but no decrease of LINE-1 methylation levels compared to normal samples. These findings suggest that most of cancer-specific CpG island hypermethylation occur in the stage of BilIN and that CpG island hypermethylation seems to occur earlier than repetitive DNA element hypomethylation.
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Tränkenschuh W, Puls F, Christgen M, Albat C, Heim A, Poczkaj J, Fleming P, Kreipe H, Lehmann U. Calcium influx and the Ca2+-calmodulin complex are involved in interferon-gamma-induced expression of HLA class II molecules on HL-60 cells. Proc Natl Acad Sci U S A 1988; 5:e13688. [PMID: 21060828 PMCID: PMC2966398 DOI: 10.1371/journal.pone.0013688] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 10/05/2010] [Indexed: 11/24/2022] Open
Abstract
Background Gene silencing due to aberrant DNA methylation is a frequent event in hepatocellular carcinoma (HCC) and also in hepatocellular adenoma (HCA). However, very little is known about epigenetic defects in fibrolamellar carcinoma (FLC), a rare variant of hepatocellular carcinoma that displays distinct clinical and morphological features. Methodology/Principal Findings We analyzed the methylation status of the APC, CDH1, cyclinD2, GSTπ1, hsa-mir-9-1, hsa-mir-9-2, and RASSF1A gene in a series of 15 FLC and paired normal liver tissue specimens by quantitative high-resolution pyrosequencing. Results were compared with common HCC arising in non-cirrhotic liver (n = 10). Frequent aberrant hypermethylation was found for the cyclinD2 (19%) and the RASSF1A (38%) gene as well as for the microRNA genes mir-9-1 (13%) and mir-9-2 (33%). In contrast to common HCC the APC and CDH1 (E-cadherin) genes were found devoid of any DNA methylation in FLC, whereas the GSTπ1 gene showed comparable DNA methylation in tumor and surrounding tissue at a moderate level. Changes in global DNA methylation level were measured by analyzing methylation status of the highly repetitive LINE-1 sequences. No evidence of global hypomethylation could be found in FLCs, whereas HCCs without cirrhosis showed a significant reduction in global methylation level as described previously. Conclusions FLCs display frequent and distinct gene-specific hypermethylation in the absence of significant global hypomethylation indicating that these two epigenetic aberrations are induced by different pathways and that full-blown malignancy can develop in the absence of global loss of DNA methylation. Only quantitative DNA methylation detection methodology was able to identify these differences.
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Affiliation(s)
| | - Florian Puls
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Matthias Christgen
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Cord Albat
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Albert Heim
- Institute of Virology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Jeanette Poczkaj
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Peer Fleming
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
- * E-mail:
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