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Habeshian TS, Cannavale KL, Slezak JM, Shu YH, Chien GW, Chen X, Shi F, Siegmund KD, Van Den Eeden SK, Huang J, Chao CR. DNA methylation markers for risk of metastasis in a cohort of men with localized prostate cancer. Epigenetics 2024; 19:2308920. [PMID: 38525786 DOI: 10.1080/15592294.2024.2308920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Accurately identifying life-threatening prostate cancer (PCa) at time of diagnosis remains an unsolved problem. We evaluated whether DNA methylation status of selected candidate genes can predict the risk of metastasis beyond clinical risk factors in men with untreated PCa. A nested case-control study was conducted among men diagnosed with localized PCa at Kaiser Permanente California between 01/01/1997-12/31/2006 who did not receive curative treatments. Cases were those who developed metastasis within 10 years from diagnosis. Controls were selected using density sampling. Ninety-eight candidate genes were selected from functional categories of cell cycle control, metastasis/tumour suppressors, cell signalling, cell adhesion/motility/invasion, angiogenesis, and immune function, and 41 from pluripotency genes. Cancer DNA from diagnostic biopsy blocks were extracted and analysed. Associations of methylation status were assessed using CpG site level and principal components-based analysis in conditional logistic regressions. In 215 cases and 404 controls, 27 candidate genes were found to be statistically significant in at least one of the two analytical approaches. The agreement between the methods was 25.9% (7 candidate genes, including 2 pluripotency markers). The DNA methylation status of several candidate genes was significantly associated with risk of metastasis in untreated localized PCa patients. These findings may inform future risk prediction models for PCa metastasis beyond clinical characteristics.
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Affiliation(s)
- Talar S Habeshian
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kimberly L Cannavale
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Jeff M Slezak
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Yu-Hsiang Shu
- Biostatistics and Innovations, Biostatistics and Programming, Clinical Affairs, Inari Medical, CA, USA
| | - Gary W Chien
- Department of Urology, Los Angeles Medical Center, Kaiser Permanente Southern California, Los Angeles, CA, USA
| | - XuFeng Chen
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Feng Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kimberly D Siegmund
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Chun R Chao
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, USA
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FitzGerald LM, Jung CH, Wong EM, Joo JE, Bassett JK, Dowty JG, Wang X, Dai JY, Stanford JL, O'Callaghan N, Nottle T, Pedersen J, Giles GG, Southey MC. Detection of differentially methylated CpGs between tumour and adjacent benign cells in diagnostic prostate cancer samples. Sci Rep 2024; 14:17877. [PMID: 39095452 PMCID: PMC11297152 DOI: 10.1038/s41598-024-66488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
Differentially methylated CpG sites (dmCpGs) that distinguish prostate tumour from adjacent benign tissue could aid in the diagnosis and prognosis of prostate cancer. Previously, the identification of such dmCpGs has only been undertaken in radical prostatectomy (RP) samples and not primary diagnostic tumour samples (needle biopsy or transurethral resection of the prostate). We interrogated an Australian dataset comprising 125 tumour and 43 adjacent histologically benign diagnostic tissue samples, including 41 paired samples, using the Infinium Human Methylation450 BeadChip. Regression analyses of paired tumour and adjacent benign samples identified 2,386 significant dmCpGs (Bonferroni p < 0.01; delta-β ≥ 40%), with LASSO regression selecting 16 dmCpGs that distinguished tumour samples in the full Australian diagnostic dataset (AUC = 0.99). Results were validated in independent North American (npaired = 19; AUC = 0.87) and The Cancer Genome Atlas (TCGA; npaired = 50; AUC = 0.94) RP datasets. Two of the 16 dmCpGs were in genes that were significantly down-regulated in Australian tumour samples (Bonferroni p < 0.01; GSTM2 and PRKCB). Ten additional dmCpGs distinguished low (n = 34) and high Gleason (n = 88) score tumours in the diagnostic Australian dataset (AUC = 0.95), but these performed poorly when applied to the RP datasets (North American: AUC = 0.66; TCGA: AUC = 0.62). The DNA methylation marks identified here could augment and improve current diagnostic tests and/or form the basis of future prognostic tests.
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Affiliation(s)
- Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - JiHoon E Joo
- Centre for Epidemiology and Biostatistics, School of Global and Population Health, University of Melbourne, Parkville, Australia
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James Y Dai
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Neil O'Callaghan
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Tim Nottle
- TissuPath, Mount Waverley, Melbourne, VIC, Australia
| | - John Pedersen
- TissuPath, Mount Waverley, Melbourne, VIC, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Global and Population Health, University of Melbourne, Parkville, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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Görtz M, Huber AK, Linz T, Schwab C, Stenzinger A, Goertz L, Bonekamp D, Schlemmer HP, Hohenfellner M. Detection Rate of Prostate Cancer in Repeat Biopsy after an Initial Negative Magnetic Resonance Imaging/Ultrasound-Guided Biopsy. Diagnostics (Basel) 2023; 13:diagnostics13101761. [PMID: 37238245 DOI: 10.3390/diagnostics13101761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
A negative multiparametric magnetic resonance imaging (mpMRI)-guided prostate biopsy in patients with suspected prostate cancer (PC) results in clinical uncertainty, as the biopsy can be false negative. The clinical challenge is to determine the optimal follow-up and to select patients who will benefit from repeat biopsy. In this study, we evaluated the rate of significant PC (sPC, Gleason score ≥7) and PC detection in patients who received a follow-up mpMRI/ultrasound-guided biopsy for persistent PC suspicion after a negative mpMRI/ultrasound-guided biopsy. We identified 58 patients at our institution that underwent repeat targeted biopsy in case of PI-RADS lesions and systematic saturation biopsy between 2014 and 2022. At the initial biopsy, the median age was 59 years, and the median prostate specific antigen level was 6.7 ng/mL. Repeat biopsy after a median of 18 months detected sPC in 3/58 (5%) patients and Gleason score 6 PC in 11/58 (19%). Among 19 patients with a downgraded PI-RADS score at the follow-up mpMRI, none had sPC. In conclusion, men with an initial negative mpMRI/ultrasound-guided biopsy had a high likelihood of not harboring sPC at repeat biopsy (95%). Due to the small size of the study, further research is recommended.
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Affiliation(s)
- Magdalena Görtz
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Junior Clinical Cooperation Unit 'Multiparametric Methods for Early Detection of Prostate Cancer', German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ann-Kathrin Huber
- Medical Faculty, Ruprecht-Karls University of Heidelberg, 69117 Heidelberg, Germany
| | - Tim Linz
- Medical Faculty, Ruprecht-Karls University of Heidelberg, 69117 Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, University of Heidelberg, 69120 Heidelberg, Germany
| | | | - Lukas Goertz
- Department of Radiology, Medical Faculty and University Hospital, University of Cologne, 50939 Cologne, Germany
| | - David Bonekamp
- Divison of Radiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Heinz-Peter Schlemmer
- Divison of Radiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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Kumari S, Mishra S, Anand N, Hadi R, Rastogi M, Husain N. Circulating free DNA integrity index and promoter methylation of tumor suppressor gene P16, DAPK and RASSF1A as a biomarker for oropharyngeal squamous cell carcinoma. Pathol Res Pract 2023; 246:154489. [PMID: 37150134 DOI: 10.1016/j.prp.2023.154489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
Circulating free DNA (cfDNA) is in use for the non-invasive diagnosis of tumors. Methylation of tumor suppressor genes (TSGs) is an early event in carcinogenesis and may serve as tumor biomarker. We have investigated cfDNA integrity and methylation of tumor suppressor genes P16, DAPK and RASSF1A in serum cfDNA of oropharyngeal squamous cell carcinoma (OPSCC) comparing paired serum and tumor tissue samples to evaluate their diagnostic use. Prospective case-control study, paired serum and tissue samples from 56 OPSCC, and 15 normal controls (NC). Sybr green Quantitate real time PCR was used for cfDNA quantification through amplification ALU 115 and 247 fragments. Promoter methylation of was analyzed in paired samples using methylation specific PCR. There was significantly high cfDNA integrity in OPSCC compared to normal control (p = < 0.0001). The cfDNA integrity values were significantly higher and associated with nodal status (p = 0.016). The AUC for cfDNA integrity was 0.967. The P16, DAPK and RASSF1 promoters were significantly hypermethylated in serum of OPSCC compared to NC with high concordance in tissue (up to 96.55 %). The gene promoter methylation of P16 was associated with smoking (p = 0.030), RASSF1A with stage (p = 0.011). The combination of ALU115 with cfDNA integrity and combination of gene methylation increases diagnostic sensitivity. In followup samples the cfDNA change was not different. Liquid biopsy approach including cfDNA integrity, methylation profiling in cfDNA, in combination or separately can assist in the diagnosis of OPSCC along with radio diagnostic scan. Serum changes represent changes in tissue with very high concordance.
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Affiliation(s)
- Swati Kumari
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nidhi Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Madhup Rastogi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Vibhuti Khand, Gomti Nagar, Lucknow, U.P. 226010, India.
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Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023; 13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Prostate cancer is the second most common cancer in men in the United States, and racial disparities are greatly observed in the disease. Specifically, African American (AA) patients have 60% higher incidence and mortality rates, in addition to higher grade and stage prostate tumors, than European American (EA) patients. In order to narrow the gap between clinical outcomes for these two populations, genetic and molecular signatures contributing to this disparity have been characterized. Over the past decade, profiles of prostate tumor samples from different ethnic groups have been developed using molecular and functional assays coupled with next generation sequencing or microarrays. Comparative genome-wide analyses of genomic, epigenomic, and transcriptomic profiles from prostate tumor samples have uncovered potential race-specific mutations, copy number alterations, DNA methylation, and gene expression patterns. In this study, we reviewed over 20 published studies that examined the aforementioned molecular contributions to racial disparities in AA and EA prostate cancer patients. The reviewed genomic studies revealed mutations, deletions, amplifications, duplications, or fusion genes differentially enriched in AA patients relative to EA patients. Commonly reported genomic alterations included mutations or copy number alterations of FOXA1, KMT2D, SPOP, MYC, PTEN, TP53, ZFHX3, and the TMPRSS2-ERG fusion. The reviewed epigenomic studies identified that CpG sites near the promoters of PMEPA1, RARB, SNRPN, and TIMP3 genes were differentially methylated between AA and EA patients. Lastly, the reviewed transcriptomic studies identified genes (e.g. CCL4, CHRM3, CRYBB2, CXCR4, GALR1, GSTM3, SPINK1) and signaling pathways dysregulated between AA and EA patients. The most frequently found dysregulated pathways were involved in immune and inflammatory responses and neuroactive ligand signaling. Overall, we observed that the genomic, epigenomic, and transcriptomic alterations evaluated between AA and EA prostate cancer patients varied between studies, highlighting the impact of using different methods and sample sizes. The reported genomic, epigenomic, and transcriptomic alterations do not only uncover molecular mechanisms of tumorigenesis but also provide researchers and clinicians valuable resources to identify novel biomarkers and treatment modalities to improve the disparity of clinical outcomes between AA and EA patients.
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Affiliation(s)
- Claire Stevens
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Alexandria Hightower
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Sarah G. Buxbaum
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Epidemiology and Biostatistics, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Sara M. Falzarano
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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Şeref C, Acar Ö, Kılıç M, Vural M, Sağlıcan Y, Saraç H, Coşkun B, İnce Ü, Esen T, Lack NA. Histologically benign PI-RADS 4 and 5 lesions contain cancer-associated epigenetic alterations. Prostate 2022; 82:145-153. [PMID: 34672371 DOI: 10.1002/pros.24255] [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: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND The detection rate of clinically significant prostate cancer has improved with the use of multiparametric magnetic resonance imaging (mpMRI). Yet, even with MRI-guided biopsy 15%-35% of high-risk lesions (Prostate Imaging-Reporting and Data System [PI-RADS] 4 and 5) are histologically benign. It is unclear if these false positives are due to diagnostic/sampling errors or pathophysiological alterations. To better understand this, we tested histologically benign PI-RAD 4 and 5 lesions for common malignant epigenetic alterations. MATERIALS AND METHODS MRI-guided in-bore biopsy samples were collected from 45 patients with PI-RADS 4 (n = 31) or 5 (n = 14) lesions. Patients had a median clinical follow-up of 3.8 years. High-risk mpMRI patients were grouped based on their histology into biopsy positive for tumor (BPT; n = 28) or biopsy negative for tumor (BNT; n = 17). From these biopsy samples, DNA methylation of well-known tumor suppressor genes (APC, GSTP1, and RARβ2) was quantified. RESULTS Similar to previous work we observed high rates of promoter methylation at GSTP1 (92.7%), RARβ2 (57.3%), and APC (37.8%) in malignant BPT samples but no methylation in benign TURP chips. Interestingly, similar to the malignant samples the BNT biopsies also had increased methylation at the promoter of GSTP1 (78.8%) and RARβ2 (34.6%). However, despite these epigenetic alterations none of these BNT patients developed prostate cancer, and those who underwent repeat mpMRI (n = 8) demonstrated either radiological regression or stability. CONCLUSIONS Histologically benign PI-RADS 4 and 5 lesions harbor prostate cancer-associated epigenetic alterations.
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Affiliation(s)
- Ceren Şeref
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Ömer Acar
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
| | - Mert Kılıç
- Department of Urology, VKF American Hospital, Istanbul, Turkey
| | - Metin Vural
- Department of Radiology, VKF American Hospital, Istanbul, Turkey
| | - Yeşim Sağlıcan
- Department of Pathology, Acıbadem University School of Medicine, Istanbul, Turkey
| | - Hilal Saraç
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Bilgen Coşkun
- Department of Radiology, VKF American Hospital, Istanbul, Turkey
| | - Ümit İnce
- Department of Pathology, Acıbadem University School of Medicine, Istanbul, Turkey
| | - Tarık Esen
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
- Department of Urology, VKF American Hospital, Istanbul, Turkey
| | - Nathan A Lack
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
- Department of Medical Pharmacology, Koç University School of Medicine, Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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Kim D, Kim Y, Kim Y. Effects of β-carotene on Expression of Selected MicroRNAs, Histone Acetylation, and DNA Methylation in Colon Cancer Stem Cells. J Cancer Prev 2019; 24:224-232. [PMID: 31950022 PMCID: PMC6951318 DOI: 10.15430/jcp.2019.24.4.224] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Background Beta-carotene (BC) is a carotenoid which exerts anti-cancer effects in several types of cancer, including colorectal cancer. Epigenetic modifications of genes, such as histone deacetylation and DNA hypermethylation, have also been detected in various types of cancer. To understand the molecular mechanism underlying cancer preventive and therapeutic effects of BC, microRNAs (miRNAs), histone acetylation, and global DNA methylation in colon cancer stem cells (CSCs) were investigated. Methods HCT116 colon cancer cells positive for expression of CD44 and CD133 were sorted by flow cytometry and used in subsequent experiments. Cell proliferation was examined by the MTT assay and self-renewal capacity was analyzed by the sphere formation assay. The miRNA sequencing array was used to detect miRNAs regulated by BC. Histone acetylation levels were measured by the Western blot analysis. mRNA expression of DNA methyltransferases (DNMTs) was examined by qPCR and global DNA methylation levels were determined by enzyme-linked immunosorbent assay. Results Treatment of CD44+CD133+ colon CSCs with BC caused a reduction in both cell proliferation and sphere formation. Analysis of the miRNA sequencing array showed that BC regulated expression of miRNAs associated with histone acetylation. Histone H3 and H4 acetylation levels were elevated by BC treatment. In addition, BC treatment down-regulated DNMT3A mRNA expression and global DNA methylation in colon CSCs. Conclusions These results suggest that BC regulates epigenetic modifications for its anti-cancer effects in colon CSCs.
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Affiliation(s)
- Daeun Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Korea
| | - Yerin Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Korea
| | - Yuri Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Korea
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Zhou X, Jiao D, Dou M, Chen J, Li Z, Li Y, Liu J, Han X. Association of glutathione-S-transferase p1 gene promoter methylation and the incidence of prostate cancer: a systematic review and meta-analysis. J Cancer Res Clin Oncol 2019; 145:1939-1948. [DOI: 10.1007/s00432-019-02962-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/28/2019] [Indexed: 02/05/2023]
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Kamińska K, Białkowska A, Kowalewski J, Huang S, Lewandowska MA. Differential gene methylation patterns in cancerous and non‑cancerous cells. Oncol Rep 2019; 42:43-54. [PMID: 31115550 PMCID: PMC6549081 DOI: 10.3892/or.2019.7159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022] Open
Abstract
Large-scale projects, such as The Cancer Genome Atlas (TCGA), Human Epigenome Project (HEP) and Human Epigenome Atlas (HEA), provide an insight into DNA methylation and histone modification markers. Changes in the epigenome significantly contribute to the initiation and progression of cancer. The goal of the present study was to characterize the prostate cancer malignant transformation model using the CpG island methylation pattern. The Human Prostate Cancer EpiTect Methyl II Signature PCR Array was used to evaluate the methylation status of 22 genes in prostate cancer cell lines: PC3, PC3M, PC3MPro4 and PC3MLN4, each representing different metastatic potential in vivo. Subsequently, it was ascertained whether DNA methylation plays a role in the expression of these genes in prostate cancer cells. Hypermethylation of APC, DKK3, GPX3, GSTP1, MGMT, PTGS2, RASSF1, TIMP2 and TNFRSF10D resulted in downregulation of their expression in prostate cancer cell lines as compared to WT fibroblasts. Mining of the TCGA data deposited in the MetHC database found increases in the methylation status of these 9 genes in prostate cancer patients, further supporting the role of methylation in altering the expression of these genes in prostate cancer. Future studies are warranted to investigate the role of these proteins in prostate cancer development.
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Affiliation(s)
- Katarzyna Kamińska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
| | - Aneta Białkowska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
| | - Janusz Kowalewski
- Department of Thoracic Surgery and Tumors, The Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85‑796 Bydgoszcz, Poland
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marzena A Lewandowska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
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Constâncio V, Barros-Silva D, Jerónimo C, Henrique R. Known epigenetic biomarkers for prostate cancer detection and management: exploring the potential of blood-based liquid biopsies. Expert Rev Mol Diagn 2019; 19:367-375. [PMID: 30961397 DOI: 10.1080/14737159.2019.1604224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Although prostate cancer (PCa) stands as an important cause of cancer-related deaths, a sizeable proportion of diagnosed cases are clinically insignificant. Hence, novel and more specific biomarkers to identify clinically significant PCa are needed. Liquid biopsies offer the potential to accurately identify cancer markers, including PCa. Epigenetic biomarkers such as cell-free DNA and circulating RNAs have emerged as minimally invasive cancer markers. Areas covered: Herein, we provide an overview of epigenetic biomarkers current state based on a comprehensive review of the relevant literature in blood-based liquid biopsies and challenges/limitations of this new and growing field of cancer biomarkers. Expert opinion: The epigenetic-based biomarkers characteristics make them attractive to the clinics and their minimally invasive assessment are a promising opportunity for PCa detection/management. The main limitations are the lack of robust validation studies and integrated approaches. Future studies would benefit from a change in focus to a 'selected PCa detection'.
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Affiliation(s)
- Vera Constâncio
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Daniela Barros-Silva
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Carmen Jerónimo
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal
| | - Rui Henrique
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal.,c Department of Pathology , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
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13
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Liyanage C, Wathupola A, Muraleetharan S, Perera K, Punyadeera C, Udagama P. Promoter Hypermethylation of Tumor-Suppressor Genes p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 in Salivary DNA as a Quadruple Biomarker Panel for Early Detection of Oral and Oropharyngeal Cancers. Biomolecules 2019; 9:biom9040148. [PMID: 31013839 PMCID: PMC6523930 DOI: 10.3390/biom9040148] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 01/01/2023] Open
Abstract
Silencing of tumor-suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis; hence, TSGs may serve as early tumor biomarkers. We determined the promoter methylation levels of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs in salivary DNA from oral cancer (OC) and oropharyngeal cancer (OPC) patients, using methylation-specific PCR coupled with densitometry analysis. We assessed the association between DNA methylation of individual TSGs with OC and OPC risk factors. The performance and the clinical validity of this quadruple-methylation marker panel were evaluated in discriminating OC and OPC patients from healthy controls using the CombiROC web tool. Our study reports that RASSF1A, TIMP3, and PCQAP/MED15 TSGs were significantly hypermethylated in OC and OPC cases compared to healthy controls. DNA methylation levels of TSGs were significantly augmented by smoking, alcohol use, and betel quid chewing, indicating the fact that frequent exposure to risk factors may drive oral and oropharyngeal carcinogenesis through TSG promoter hypermethylation. Also, this quadruple-methylation marker panel of p16INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs demonstrated excellent diagnostic accuracy in the early detection of OC at 91.7% sensitivity and 92.3% specificity and of OPC at 99.8% sensitivity and 92.1% specificity from healthy controls.
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Affiliation(s)
- Chamikara Liyanage
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Asanga Wathupola
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Sanjayan Muraleetharan
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
| | - Kanthi Perera
- National Cancer Institute of Sri Lanka, Maharagama, 10280, Sri Lanka.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, 37 Kent Street, Woolloongabba, Brisbane, QLD 4102, Australia.
| | - Preethi Udagama
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03 00300, Sri Lanka.
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14
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Izumchenko E, Shavit Grievink L, Rosenbaum E, Hoque MO. GSTP1 as a Potential Marker of Early Chemotherapy Response for Noninvasive Detection. Eur Urol 2019; 76:313-314. [PMID: 30642610 DOI: 10.1016/j.eururo.2018.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Evgeny Izumchenko
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liat Shavit Grievink
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel
| | - Eli Rosenbaum
- Institute of Oncology, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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15
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Smits M, Mehra N, Sedelaar M, Gerritsen W, Schalken JA. Molecular biomarkers to guide precision medicine in localized prostate cancer. Expert Rev Mol Diagn 2018. [PMID: 28635333 DOI: 10.1080/14737159.2017.1345627] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Major advances through tumor profiling technologies, that include next-generation sequencing, epigenetic, proteomic and transcriptomic methods, have been made in primary prostate cancer, providing novel biomarkers that may guide precision medicine in the near future. Areas covered: The authors provided an overview of novel molecular biomarkers in tissue, blood and urine that may be used as clinical tools to assess prognosis, improve selection criteria for active surveillance programs, and detect disease relapse early in localized prostate cancer. Expert commentary: Active surveillance (AS) in localized prostate cancer is an accepted strategy in patients with very low-risk prostate cancer. Many more patients may benefit from watchful waiting, and include patients of higher clinical stage and grade, however selection criteria have to be optimized and early recognition of transformation from localized to lethal disease has to be improved by addition of molecular biomarkers. The role of non-invasive biomarkers is challenging the need for repeat biopsies, commonly performed at 1 and 4 years in men under AS programs.
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Affiliation(s)
- Minke Smits
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Niven Mehra
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Michiel Sedelaar
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Winald Gerritsen
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
| | - Jack A Schalken
- a Department of Urology and Oncology , Radboud Universiteit , Nijmegen , The Netherlands
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16
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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17
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Zhao S, Geybels MS, Leonardson A, Rubicz R, Kolb S, Yan Q, Klotzle B, Bibikova M, Hurtado-Coll A, Troyer D, Lance R, Lin DW, Wright JL, Ostrander EA, Fan JB, Feng Z, Stanford JL. Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer. Clin Cancer Res 2017; 23:311-319. [PMID: 27358489 PMCID: PMC5199634 DOI: 10.1158/1078-0432.ccr-16-0549] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/08/2016] [Accepted: 06/11/2016] [Indexed: 01/22/2023]
Abstract
PURPOSE Aside from Gleason sum, few factors accurately identify the subset of prostate cancer patients at high risk for metastatic progression. We hypothesized that epigenetic alterations could distinguish prostate tumors with life-threatening potential. EXPERIMENTAL DESIGN Epigenome-wide DNA methylation profiling was performed in surgically resected primary tumor tissues from a population-based (n = 430) and a replication (n = 80) cohort of prostate cancer patients followed prospectively for at least 5 years. Metastasis was confirmed by positive bone scan, MRI, CT, or biopsy, and death certificates confirmed cause of death. AUC, partial AUC (pAUC, 95% specificity), and P value criteria were used to select differentially methylated CpG sites that robustly stratify patients with metastatic-lethal from nonrecurrent tumors, and which were complementary to Gleason sum. RESULTS Forty-two CpG biomarkers stratified patients with metastatic-lethal versus nonrecurrent prostate cancer in the discovery cohort, and eight of these CpGs replicated in the validation cohort based on a significant (P < 0.05) AUC (range, 0.66-0.75) or pAUC (range, 0.007-0.009). The biomarkers that improved discrimination of patients with metastatic-lethal prostate cancer include CpGs in five genes (ALKBH5, ATP11A, FHAD1, KLHL8, and PI15) and three intergenic regions. In the validation dataset, the AUC for Gleason sum alone (0.82) significantly increased with the addition of four individual CpGs (range, 0.86-0.89; all P <0.05). CONCLUSIONS Eight differentially methylated CpGs that distinguish patients with metastatic-lethal from nonrecurrent tumors were validated. These novel epigenetic biomarkers warrant further investigation as they may improve prognostic classification of patients with clinically localized prostate cancer and provide new insights on tumor aggressiveness. Clin Cancer Res; 23(1); 311-9. ©2016 AACR.
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Affiliation(s)
- Shanshan Zhao
- National Institute of Environmental Health Sciences, Biostatistics and Computational Biology Branch, Research Triangle Park, Durham, North Carolina
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Amy Leonardson
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Qingxiang Yan
- MD Anderson Cancer Center, Department of Biostatistics, Houston, Texas
| | | | | | - Antonio Hurtado-Coll
- Department of Urologic Sciences, University of British Columbia, and the Prostate Center, Vancouver General Hospital, Vancouver, Canada
| | - Dean Troyer
- Departments of Pathology, Microbiology, and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia
| | - Raymond Lance
- Department of Urology, Eastern Virginia Medical School, Norfolk, Virginia
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
- Department of Urology, University of Washington School of Medicine, Seattle, Washington
| | - Jonathan L Wright
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
- Department of Urology, University of Washington School of Medicine, Seattle, Washington
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | - Ziding Feng
- MD Anderson Cancer Center, Department of Biostatistics, Houston, Texas
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington.
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
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18
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Han Y, He X. Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights 2016; 10:267-289. [PMID: 27980397 PMCID: PMC5138066 DOI: 10.4137/bbi.s38427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.; Present address: Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ximiao He
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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19
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Angulo JC, Lopez JI, Dorado JF, Sanchez-Chapado M, Colas B, Ropero S. A DNA Hypermethylation Profile Independently Predicts Biochemical Recurrence Following Radical Prostatectomy. Urol Int 2016; 97:16-25. [DOI: 10.1159/000446446] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/25/2016] [Indexed: 11/19/2022]
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20
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Rybicki BA, Rundle A, Kryvenko ON, Mitrache N, Do KC, Jankowski M, Chitale DA, Trudeau S, Belinsky SA, Tang D. Methylation in benign prostate and risk of disease progression in men subsequently diagnosed with prostate cancer. Int J Cancer 2016; 138:2884-93. [PMID: 26860439 DOI: 10.1002/ijc.30038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/25/2016] [Indexed: 12/31/2022]
Abstract
In DNA from prostate tumors, methylation patterns in gene promoter regions can be a biomarker for disease progression. It remains unclear whether methylation patterns in benign prostate tissue--prior to malignant transformation--may provide similar prognostic information. To determine whether early methylation events predict prostate cancer outcomes, we evaluated histologically benign prostate specimens from 353 men who eventually developed prostate cancer and received "definitive" treatment [radical prostatectomy (58%) or radiation therapy (42%)]. Cases were drawn from a large hospital-based cohort of men with benign prostate biopsy specimens collected between 1990 and 2002. Risk of disease progression associated with methylation was estimated using time-to-event analyses. Average follow-up was over 5 years; biochemical recurrence (BCR) occurred in 91 cases (26%). In White men, methylation of the APC gene was associated with increased risk of BCR, even after adjusting for standard clinical risk factors for prostate cancer progression (adjusted hazard ratio (aHR) = 2.26; 95%CI 1.23-4.16). APC methylation was most strongly associated with a significant increased risk of BCR in White men with low prostate specific antigen at cohort entry (HR = 3.66; 95%CI 1.51-8.85). In additional stratified analyses, we found that methylation of the RARB gene significantly increased risk of BCR in African American cases who demonstrated methylation of at least one of the other four genes under study (HR = 3.80; 95%CI 1.07-13.53). These findings may have implications in the early identification of aggressive prostate cancer as well as reducing unnecessary medical procedures and emotional distress for men who present with markers of indolent disease.
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Affiliation(s)
- Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI.,Josephine Ford Cancer Institute, Henry Ford Hospital, Detroit, MI
| | - Andrew Rundle
- Department of Epidemiology, Columbia University, New York, NY
| | - Oleksandr N Kryvenko
- Department of Pathology and Urology, University of Miami Miller School of Medicine, Miami, FL
| | - Nicoleta Mitrache
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI
| | - Kieu C Do
- Lung Cancer Division, Lovelace Respiratory Research Institute, Albuquerque, NM
| | | | - Dhananjay A Chitale
- Josephine Ford Cancer Institute, Henry Ford Hospital, Detroit, MI.,Department of Surgical Pathology, Henry Ford Hospital, Detroit, MI
| | - Sheri Trudeau
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI
| | - Steven A Belinsky
- Lung Cancer Division, Lovelace Respiratory Research Institute, Albuquerque, NM
| | - Deliang Tang
- Department of Environmental Health Sciences, Columbia University, New York, NY
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DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer. PLoS One 2015; 10:e0130651. [PMID: 26086362 PMCID: PMC4472347 DOI: 10.1371/journal.pone.0130651] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 05/25/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is a very heterogeneous disease with respect to clinical outcome. This study explored differential DNA methylation in a priori selected genes to diagnose PCa and predict clinical failure (CF) in high-risk patients. METHODS A quantitative multiplex, methylation-specific PCR assay was developed to assess promoter methylation of the APC, CCND2, GSTP1, PTGS2 and RARB genes in formalin-fixed, paraffin-embedded tissue samples from 42 patients with benign prostatic hyperplasia and radical prostatectomy specimens of patients with high-risk PCa, encompassing training and validation cohorts of 147 and 71 patients, respectively. Log-rank tests, univariate and multivariate Cox models were used to investigate the prognostic value of the DNA methylation. RESULTS Hypermethylation of APC, CCND2, GSTP1, PTGS2 and RARB was highly cancer-specific. However, only GSTP1 methylation was significantly associated with CF in both independent high-risk PCa cohorts. Importantly, trichotomization into low, moderate and high GSTP1 methylation level subgroups was highly predictive for CF. Patients with either a low or high GSTP1 methylation level, as compared to the moderate methylation groups, were at a higher risk for CF in both the training (Hazard ratio [HR], 3.65; 95% CI, 1.65 to 8.07) and validation sets (HR, 4.27; 95% CI, 1.03 to 17.72) as well as in the combined cohort (HR, 2.74; 95% CI, 1.42 to 5.27) in multivariate analysis. CONCLUSIONS Classification of primary high-risk tumors into three subtypes based on DNA methylation can be combined with clinico-pathological parameters for a more informative risk-stratification of these PCa patients.
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Abstract
Most recent investigations into cancer etiology have identified a key role played by epigenetics. Specifically, aberrant DNA and histone modifications which silence tumor suppressor genes or promote oncogenes have been demonstrated in multiple cancer models. While the role of epigenetics in several solid tumor cancers such as colorectal cancer are well established, there is emerging evidence that epigenetics also plays a critical role in breast and prostate cancer. In breast cancer, DNA methylation profiles have been linked to hormone receptor status and tumor progression. Similarly in prostate cancer, epigenetic patterns have been associated with androgen receptor status and response to therapy. The regulation of key receptor pathways and activities which affect clinical therapy treatment options by epigenetics renders this field high priority for elucidating mechanisms and potential targets. A new set of methylation arrays are now available to screen epigenetic changes and provide the cutting-edge tools needed to perform such investigations. The role of nutritional interventions affecting epigenetic changes particularly holds promise. Ultimately, determining the causes and outcomes from epigenetic changes will inform translational applications for utilization as biomarkers for risk and prognosis as well as candidates for therapy.
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Affiliation(s)
- Yanyuan Wu
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
- Corresponding Author Contact Information: Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, 1731 East 120th Street, Los Angeles, CA 90059, USA. Tele: 323-563-4853. Fax: 323-563-4859 ;
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23
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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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24
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Maldonado L, Brait M, Loyo M, Sullenberger L, Wang K, Peskoe SB, Rosenbaum E, Howard R, Toubaji A, Albadine R, Netto GJ, Hoque MO, Platz EA, Sidransky D. GSTP1 promoter methylation is associated with recurrence in early stage prostate cancer. J Urol 2014; 192:1542-8. [PMID: 24769028 PMCID: PMC4390043 DOI: 10.1016/j.juro.2014.04.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2014] [Indexed: 12/31/2022]
Abstract
PURPOSE Recurrent prostate cancer remains a major problem. Staging, grading and prostate specific antigen level at surgery are helpful but still imperfect predictors of recurrence. For this reason there is an imperative need for additional biomarkers that add to the prediction of currently used prognostic factors. MATERIALS AND METHODS We evaluated the extent of promoter methylation of genes previously reported as aberrantly methylated in prostate cancer (AIM1, APC, CCND2, GPX3, GSTP1, MCAM, RARβ2, SSBP2 and TIMP3) by quantitative fluorogenic methylation-specific polymerase chain reaction. We used cancer tissue from a nested case-control study of 452 patients surgically treated for prostate cancer. Recurrence cases and controls were compared and the association between methylation extent and recurrence risk was estimated by logistic regression adjusting for patient age at prostatectomy, prostatectomy year, stage, grade, surgical margins and preprostatectomy prostate specific antigen. All statistical tests were 2-sided with p ≤0.05 considered statistically significant. RESULTS The extent of GSTP1 methylation was higher in patients with recurrence than in controls (p = 0.01), especially patients with early disease, ie organ confined or limited extraprostatic extension (p = 0.001). After multivariate adjustment GSTP1 promoter methylation at or above the median was associated with an increased risk of recurrence, including in men with early disease (each p = 0.05). CONCLUSIONS Greater GSTP1 promoter methylation in cancer tissue was independently associated with the risk of recurrence in patients with early prostate cancer. This suggests that GSTP1 promoter methylation may be a potential tissue based recurrence marker.
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Affiliation(s)
- Leonel Maldonado
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Myriam Loyo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lauren Sullenberger
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kevin Wang
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah B Peskoe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eli Rosenbaum
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Roslyn Howard
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Antoun Toubaji
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Roula Albadine
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - George J Netto
- James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Mohammad O Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth A Platz
- James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland.
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25
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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: 82] [Impact Index Per Article: 8.2] [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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Vasiljević N, Ahmad AS, Thorat MA, Fisher G, Berney DM, Møller H, Foster CS, Cuzick J, Lorincz AT. DNA methylation gene-based models indicating independent poor outcome in prostate cancer. BMC Cancer 2014; 14:655. [PMID: 25193387 PMCID: PMC4162944 DOI: 10.1186/1471-2407-14-655] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/30/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Prostate cancer has a variable clinical behaviour with frequently unpredictable outcome. DNA methylation plays an important role in determining the biology of cancer but prognostic information is scanty. We assessed the potential of gene-specific DNA methylation changes to predict death from prostate cancer in a cohort of untreated men in the UK. METHODS This was a population-based study in which cases were identified from six cancer registries in Great Britain. DNA was extracted from formalin-fixed paraffin wax-embedded transurethral prostate resection tissues collected during 1990-96 from men with clinically-localised cancer who chose not to be treated for at least 6 months following diagnosis. The primary end point was death from prostate cancer. Outcomes were determined through medical records and cancer registry records. Pyrosequencing was used to quantify methylation in 13 candidate genes with established or suggested roles in cancer. Univariate and multivariate Cox models were used to identify possible predictors for prostate cancer-related death. RESULTS Of 367 men, 99 died from prostate cancer during a median of 9.5 years follow-up (max = 20). Univariately, 12 genes were significantly associated with prostate cancer mortality, hazard ratios ranged between 1.09 and 1.28 per decile increase in methylation. Stepwise Cox regression modelling suggested that the methylation of genes HSPB1, CCND2 and DPYS contributed objective prognostic information to Gleason score and PSA with respect to cancer-related death during follow-up (p = 0.006). CONCLUSION Methylation of 13 genes was analysed in 367 men with localised prostate cancer who were conservatively treated and stratified with respect to death from prostate cancer and those who survived or died of other causes. Of the 13 genes analysed, differential methylation of HSPB1, CCND2 and DPYS provided independent prognostic information. Assessment of gene-methylation may provide independent objective information that can be used to segregate prostate cancers at diagnosis into predicted behavioural groups.
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Affiliation(s)
- Nataša Vasiljević
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
| | - Amar S Ahmad
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
| | - Mangesh A Thorat
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
| | - Gabrielle Fisher
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
| | - Daniel M Berney
- />Molecular Oncology Centre, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Henrik Møller
- />King’s College London, Cancer Epidemiology and Population Health, London, SE1 9RT UK
| | - Christopher S Foster
- />HCA International Pathology Laboratories, 2-22 Capper Street, London, WC1E 6JA UK
| | - Jack Cuzick
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
| | - Attila T Lorincz
- />Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, London, EC1M 6BQ UK
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Ovchinnikov DA, Wan Y, Coman WB, Pandit P, Cooper-White JJ, Herman JG, Punyadeera C. DNA Methylation at the Novel CpG Sites in the Promoter of MED15/PCQAP Gene as a Biomarker for Head and Neck Cancers. Biomark Insights 2014; 9:53-60. [PMID: 25057238 PMCID: PMC4085102 DOI: 10.4137/bmi.s16199] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/19/2014] [Accepted: 05/21/2014] [Indexed: 01/07/2023] Open
Abstract
Head and neck cancers (HNCs) represent a significant and ever-growing burden to the modern society, mainly due to the lack of early diagnostic methods. A significant number of HNCs is often associated with drinking, smoking, chewing beetle nut, and human papilloma virus (HPV) infections. We have analyzed DNA methylation patterns in tumor and normal tissue samples collected from head and neck squamous cell carcinoma (HNSCC) patients who were smokers. We have identified novel methylation sites in the promoter of the mediator complex subunit 15 (MED15/PCQAP) gene (encoing a co-factor important for regulation of transcription initiation for promoters of many genes), hypermethylated specifically in tumor cells. Two clusters of CpG dinucleotides methylated in tumors, but not in normal tissue from the same patients, were identified. These CpG methylation events in saliva samples were further validated in a separate cohort of HNSCC patients (who developed cancer due to smoking or HPV infections) and healthy controls using methylation-specific PCR (MSP). We used saliva as a biological medium because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option for large-scale screening studies. The methylation levels for the two identified CpG clusters were significantly different between the saliva samples collected from healthy controls and HNSCC individuals (Welch’s t-test returning P < 0.05 and Mann–Whitney test P < 0.01 for both). The developed MSP assays also provided a good discriminative ability with AUC values of 0.70 (P < 0.01) and 0.63 (P < 0.05). The identified novel CpG methylation sites may serve as potential non-invasive biomarkers for detecting HNSCC.
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Affiliation(s)
- Dmitry A Ovchinnikov
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Old Coopers Road, St Lucia, Queensland, Australia
| | - Yunxia Wan
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
| | - William B Coman
- The School of Medicine, University of Queensland, Queensland, Australia
| | - Pratibala Pandit
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
| | - Justin J Cooper-White
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Old Coopers Road, St Lucia, Queensland, Australia. ; The School of Chemical Engineering, The University of Queensland, St Lucia, Queensland, Australia
| | - James G Herman
- The Sidney Kimmel Comprehensive Cancer Centre, School of Medicine, Johns Hopkins University, Baltimore, USA
| | - Chamindie Punyadeera
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Old Coopers Road, St Lucia, Queensland, Australia. ; University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Brisbane, Australia
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28
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Stott-Miller M, Zhao S, Wright JL, Kolb S, Bibikova M, Klotzle B, Ostrander EA, Fan JB, Feng Z, Stanford JL. Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence. Cancer Epidemiol Biomarkers Prev 2014; 23:1331-9. [PMID: 24718283 PMCID: PMC4082437 DOI: 10.1158/1055-9965.epi-13-1000] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND One challenge in prostate cancer is distinguishing indolent from aggressive disease at diagnosis. DNA promoter hypermethylation is a frequent epigenetic event in prostate cancer, but few studies of DNA methylation in relation to features of more aggressive tumors or prostate cancer recurrence have been completed. METHODS We used the Infinium HumanMethylation450 BeadChip to assess DNA methylation in tumor tissue from 407 patients with clinically localized prostate cancer who underwent radical prostatectomy. Recurrence status was determined by follow-up patient surveys, medical record review, and linkage with the Surveillance, Epidemiology, and End Results (SEER) registry. The methylation status of 14 genes for which promoter hypermethylation was previously correlated with advanced disease or biochemical recurrence was evaluated. Average methylation level for promoter region CpGs in patients who recurred compared with those with no evidence of recurrence was analyzed. For two genes with differential methylation, time to recurrence was examined. RESULTS During an average follow-up of 11.7 years, 104 (26%) patients recurred. Significant promoter hypermethylation in at least 50% of CpG sites in two genes, ABHD9 and HOXD3, was found in tumors from patients who recurred compared with those without recurrence. Evidence was strongest for HOXD3 (lowest P = 9.46 × 10(-6)), with higher average methylation across promoter region CpGs associated with reduced recurrence-free survival (P = 2 × 10(-4)). DNA methylation profiles did not differ by recurrence status for the other genes. CONCLUSIONS These results validate the association between promoter hypermethylation of ADHB9 and HOXD3 and prostate cancer recurrence. IMPACT Tumor DNA methylation profiling may help to distinguish patients with prostate cancer at higher risk for disease recurrence.
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Affiliation(s)
- Marni Stott-Miller
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Shanshan Zhao
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Jonathan L Wright
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Department of Urology, University of Washington School of Medicine; Departments of
| | - Suzanne Kolb
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | | | | | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | - Ziding Feng
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Biostatistics and
| | - Janet L Stanford
- Authors' Affiliations: Division of Public Health Sciences, Fred Hutchinson Cancer Research Center; Epidemiology, University of Washington, Seattle, Washington;
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29
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Daniunaite K, Jarmalaite S, Kalinauskaite N, Petroska D, Laurinavicius A, Lazutka JR, Jankevicius F. Prognostic value of RASSF1 promoter methylation in prostate cancer. J Urol 2014; 192:1849-55. [PMID: 24980613 DOI: 10.1016/j.juro.2014.06.075] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 01/02/2023]
Abstract
PURPOSE Patients with prostate cancer who have biochemical recurrence after curative therapy are at higher risk for distant metastasis and cancer specific death. Assessment of aberrant DNA methylation in urine might complement currently used clinical prognostic factors and serve as a noninvasive tool for early prediction of biochemical recurrence after radical prostatectomy. MATERIALS AND METHODS Promoter methylation of 7 genes was evaluated by methylation sensitive polymerase chain reaction in 149 prostate cancer tissues, 37 noncancerous prostate tissues and 17 benign prostatic hyperplasia samples. Quantitative polymerase chain reaction was used for DNA methylation analysis of the urine of 253 patients with prostate cancer and 32 with benign prostatic hyperplasia. RESULTS In prostate cancer tissue the most frequently methylated genes were RASSF1, GSTP1 and RARB, which combined were positively identified in 85% of cases. These genes were also methylated in the urine of 60% of patients with prostate cancer. RASSF1 was methylated in 45% of prostate cancer urine samples with methylation intensity significantly higher in prostate cancer than in benign prostatic hyperplasia cases (p = 0.018). In a univariate model RASSF1 methylation and the total number of methylated genes in prostate cancer tissue were predictive of time to biochemical recurrence (p = 0.019 and 0.043, respectively). On multivariate analysis RASSF1 methylation together with pathological stage was the most significant predictor of biochemical recurrence in patients with Gleason score 6 tumors when analyzed in tissue and urine (p ≤0.001). CONCLUSIONS Hypermethylation of RASSF1 in cancerous tissue and urine from patients with prostate cancer correlated with biochemical recurrence after radical prostatectomy. The prognostic potential of this biomarker deserves further investigation.
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Affiliation(s)
| | - Sonata Jarmalaite
- Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania.
| | | | - Donatas Petroska
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania; National Centre of Pathology, Vilnius, Lithuania
| | - Arvydas Laurinavicius
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania; National Centre of Pathology, Vilnius, Lithuania
| | - Juozas R Lazutka
- Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania
| | - Feliksas Jankevicius
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Urology Centre, Vilnius University, Vilnius, Lithuania
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30
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Methylation markers for prostate cancer prognosis: a systematic review. Cancer Causes Control 2014; 24:1615-41. [PMID: 23797237 DOI: 10.1007/s10552-013-0249-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 06/07/2013] [Indexed: 12/31/2022]
Abstract
PURPOSE We conducted a systematic review to summarize current evidence on the prognostic utility of DNA methylation markers in prostate cancer and ascertain knowledge gaps to inform future research. METHODS We identified relevant studies using combined key search against PubMed database. Inclusion criteria were studies of human subjects that examined the association between DNA methylation markers and prostate cancer disease outcomes. The methodological quality of each study was systematically evaluated. Findings were qualitatively summarized. Due to heterogeneity and concerns of internal validity, no meta-analysis was performed. RESULTS Twenty studies were reviewed; sample size ranged from 35 to 605 men in the prognostic analyses. Sixteen studies examined methylation markers in prostate cancer tissue and four examined circulating DNA methylation markers. Of all genes reviewed, paired-like homeodomain transcription factor 2 (PITX2) methylation was examined in two more rigorously designed studies and was found to be associated with biochemical recurrence. Common limitations in current literature included small sample sizes,lack of adequate adjustment for established prognostic factors, and poor reporting quality. CONCLUSION Evidence on the prognostic utility of methylation markers in prostate cancer is inconclusive. Future research should ascertain large samples with adequate follow-up and include patients of racial/ethnic minority and those treated with modalities other than prostatectomy(e.g., using prostate cancer diagnostic biopsy as tissue source).
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Abstract
Epigenetic change is part of the carcinogenic process and a deep reservoir for biomarker discovery. Reversible methylation of cytosines is noteworthy because it can be measured accurately and easily by various molecular methods and DNA methylation patterns are linked to important tumourigenic pathways. Clinically relevant methylation changes are known in common human cancers such as cervix, prostate, breast, colon, bladder, stomach and lung. Differential methylation may have a central role in the development and outcome of most if not all human malignancies. The advent of deep sequencing holds great promise for epigenomics, with bioinformatics tools ready to reveal large numbers of new targets for prognosis and therapeutic intervention. This review focuses on two selected cancers, namely cervix and prostate, which illustrate the more general themes of epigenetic diagnostics in cancer. Also discussed is differential methylation of specific human and viral DNA targets and laboratory methods for measuring methylation biomarkers.
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Affiliation(s)
- Attila T Lorincz
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, EC1M 6BQ, UK
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32
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Schiano C, Casamassimi A, Rienzo M, de Nigris F, Sommese L, Napoli C. Involvement of Mediator complex in malignancy. Biochim Biophys Acta Rev Cancer 2013; 1845:66-83. [PMID: 24342527 DOI: 10.1016/j.bbcan.2013.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/28/2013] [Accepted: 12/09/2013] [Indexed: 12/22/2022]
Abstract
Mediator complex (MED) is an evolutionarily conserved multiprotein, fundamental for growth and survival of all cells. In eukaryotes, the mRNA transcription is dependent on RNA polymerase II that is associated to various molecules like general transcription factors, MED subunits and chromatin regulators. To date, transcriptional machinery dysfunction has been shown to elicit broad effects on cell proliferation, development, differentiation, and pathologic disease induction, including cancer. Indeed, in malignant cells, the improper activation of specific genes is usually ascribed to aberrant transcription machinery. Here, we focus our attention on the correlation of MED subunits with carcinogenesis. To date, many subunits are mutated or display altered expression in human cancers. Particularly, the role of MED1, MED28, MED12, CDK8 and Cyclin C in cancer is well documented, although several studies have recently reported a possible association of other subunits with malignancy. Definitely, a major comprehension of the involvement of the whole complex in cancer may lead to the identification of MED subunits as novel diagnostic/prognostic tumour markers to be used in combination with imaging technique in clinical oncology, and to develop novel anti-cancer targets for molecular-targeted therapy.
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Affiliation(s)
- Concetta Schiano
- Institute of Diagnostic and Nuclear Development (SDN), IRCCS, Via E. Gianturco 113, 80143 Naples, Italy
| | - Amelia Casamassimi
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Monica Rienzo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Filomena de Nigris
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Linda Sommese
- U.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology [SIMT], Regional Reference Laboratory of Transplant Immunology [LIT], Azienda Universitaria Policlinico (AOU), 1st School of Medicine, Second University of Naples, Piazza Miraglia 2, 80138 Naples, Italy
| | - Claudio Napoli
- Institute of Diagnostic and Nuclear Development (SDN), IRCCS, Via E. Gianturco 113, 80143 Naples, Italy; Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy; U.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology [SIMT], Regional Reference Laboratory of Transplant Immunology [LIT], Azienda Universitaria Policlinico (AOU), 1st School of Medicine, Second University of Naples, Piazza Miraglia 2, 80138 Naples, Italy
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Fukushige S, Horii A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. TOHOKU J EXP MED 2013; 229:173-85. [PMID: 23419314 DOI: 10.1620/tjem.229.173] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Initiation and progression of human cancer not only depends on genetic alterations but also on epigenetic changes such as DNA methylation and histone modifications. Aberrant DNA hypermethylation in the promoter regions of genes is the most well-defined epigenetic change in tumors and is associated with inappropriate gene silencing. This feature can be utilized to search for tumor-specific DNA methylation biomarkers and to examine candidate DNA biomarkers for clinical use. DNA methylation biomarker is defined as a molecular target that undergoes DNA methylation changes in carcinogenesis. Such a biomarker is useful for early detection of cancer, predicting and/or monitoring the therapeutic response, and detection of recurrent cancer. In this review, we describe the mechanism that establishes and maintains DNA methylation patterns as well as the mechanism of aberrant gene silencing in cancer, and then we introduce methods to isolate the DNA methylation biomarkers. We also summarize the current status of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including tissue factor pathway inhibitor 2 (TFPI2), septin 9 (SEPT9), glutathione S-transferase pi 1 (GSTP1), and O(6)-methylguanine-DNA methyltransferase (MGMT), and assess the clinical potential of these biomarkers for risk assessment, early diagnosis, prognosis, treatment, and the prevention of cancer. Finally we describe the possible involvement of 5-hydroxymethylcytosine in cancer; this is a recently discovered 5-methylcytosine oxidation derivative and might have a diagnostic potential in certain cancers. Abnormal DNA methylations are leading candidates for the development of specific markers for cancer diagnosis and therapy.
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Affiliation(s)
- Shinichi Fukushige
- Department of Molecular Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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Chen R, Ren S, Meng T, Aguilar J, Sun Y. Impact of glutathione-S-transferases (GST) polymorphisms and hypermethylation of relevant genes on risk of prostate cancer biochemical recurrence: a meta-analysis. PLoS One 2013; 8:e74775. [PMID: 24086370 PMCID: PMC3781159 DOI: 10.1371/journal.pone.0074775] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 08/06/2013] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Accurate prediction of the biochemical recurrence (BCR) is critical for patients after intended curative therapy like radical prostatectomy (RP) or definitive radiotherapy for prostate cancer. Glutathione-S-transferases polymorphisms as well as hypermethylation of GSTP1 and functional genes in carcinogenesis, including tumor suppression gene (APC), hormone receptor that regulates cell growth and differentiation gene (RARbeta) were reported to be associated with BCR. Nevertheless, the reported results are inconsistent. To evaluate the relationship between glutathione-S-transferases polymorphisms and hypermethylation of these genes and the risk of prostate cancer BCR, we carried out a meta-analysis of the published studies. METHODS AND MATERIALS We performed a search in Medline, Embase and CNKI database with GST, APC, RARbeta in combination with single nucleotide polymorphism, hypermethylation, prostate cancer and recurrence. Languages were restricted to English and Chinese. RESULTS Our study included 4 case-control studies and 7 cohort studies including 12 data sets and 3,037 prostate cancer patients. We confirmed that APC hypermethylation is associated with a modest hazard for biochemical recurrence after RP (HR = 1.85, 95%CI = 1.12-3.06). We also suggest GSTP1 polymorphism and CpG hypermethylation tested in serum are associated with BCR (HR = 1.94, 95%CI = 1.13-3.34). We also identified a possible association between GSTM1 null polymorphism and prostate cancer biochemical recurrence risk with borderline significance (HR = 1.29, 95%CI = 0.97-1.71). CONCLUSION To our knowledge, this is the first meta-analysis evaluating the relationship of polymorphisms and hypermethylation in GSTs and biochemical recurrence. GSTM1, GSTP1 polymorphisms and hypermethylation of GSTP1, APC may be potential biomarkers for the evaluation of the probability of BCR. Further studies are warranted to validate these findings in larger cohorts with longer follow-up.
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Affiliation(s)
- Rui Chen
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tong Meng
- Department of Orthopedics, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Josephine Aguilar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, United States of America
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
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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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Lin J, Wang C, Kelly WK. Targeting epigenetics for the treatment of prostate cancer: recent progress and future directions. Semin Oncol 2013; 40:393-401. [PMID: 23806502 DOI: 10.1053/j.seminoncol.2013.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Epigenetic aberrations contribute to prostate cancer carcinogenesis and disease progression. Efforts have been made to target DNA methyltransferase and histone deacetylases (HDACs) in prostate cancer and other solid tumors but have not had the success that was seen in the hematologic malignancies. Oral, less toxic, and more specific agents are being developed in solid tumors including prostate cancer. Combinations of epigenetic agents alone or with a targeted agent such as androgen receptor signaling inhibitors are promising approaches and will be discussed further.
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Affiliation(s)
- Jianqing Lin
- Department of Medical Oncology, Jefferson Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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Chen J, Zhang D, Yan W, Yang D, Shen B. Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era. BIOMED RESEARCH INTERNATIONAL 2013; 2013:901578. [PMID: 23957008 PMCID: PMC3727129 DOI: 10.1155/2013/901578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/22/2013] [Indexed: 01/13/2023]
Abstract
The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS) technologies. Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer. Here we review the recent developments in prostate cancer biomarkers by high throughput sequencing technologies. We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.
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Affiliation(s)
- Jiajia Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Daqing Zhang
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Wenying Yan
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
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Richiardi L, Fiano V, Grasso C, Zugna D, Delsedime L, Gillio-Tos A, Merletti F. Methylation of APC and GSTP1 in non-neoplastic tissue adjacent to prostate tumour and mortality from prostate cancer. PLoS One 2013; 8:e68162. [PMID: 23874531 PMCID: PMC3706543 DOI: 10.1371/journal.pone.0068162] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 05/29/2013] [Indexed: 12/22/2022] Open
Abstract
Background Markers that can discriminate between indolent and aggressive prostate tumours are needed. We studied gene methylation in non-neoplastic tissue adjacent to prostate tumour (NTAT) in association with prostate cancer mortality. Methods From two cohorts of consecutive prostate cancer patients diagnosed at one pathology ward in Turin, Italy, we selected 157 patients with available NTAT and followed them up for more than 14 years. We obtained DNA from NTAT in paraffin-embedded prostate tumour tissues and used probe real-time PCR to analyse methylation of the glutathione S-transferase (GSTP1) and adenomatous polyposis coli (APC) gene promoters. Results Prevalence of APC and GSTP1 methylation in the NTAT was between 40 and 45%. It was associated with methylation in prostate tumour tissue for the same two genes as well as with a high Gleason score. The hazard ratio (HR) of prostate cancer mortality was 2.38 (95% confidence interval: 1.23–4.61) for APC methylation, and 2.92 (1.49–5.74) for GSTP1 methylation in NTAT. It changed to 1.91 (1.03–3.56) and 1.60 (0.80–3.19) after adjusting for Gleason score and methylation in prostate tumour tissue. Comparison of 2 vs. 0 methylated genes in NTAT revealed a HR of 4.30 (2.00–9.22), which decreased to 2.40 (1.15–5.01) after adjustment. Results were stronger in the first 5 years of follow-up (adjusted HR: 3.29, 95% CI: 1.27–8.52). Conclusions Changes in gene methylation are an early event in prostate carcinogenesis and may play a role in cancer progression. Gene methylation in NTAT is a possible prognostic marker to be evaluated in clinical studies.
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Affiliation(s)
- Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, and CPO-Piemonte, Turin, Italy.
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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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Augello MA, Ostrander WF, Knudsen KE. Beyond the Cell Cycle: Implications of D-type Cyclin Deregulation in Prostate Cancer. Prostate Cancer 2013. [DOI: 10.1007/978-1-4614-6828-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Abstract
The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development have led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter critiques and describes the major approaches to analyzing DNA methylation.
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Mahapatra S, Klee EW, Young CYF, Sun Z, Jimenez RE, Klee GG, Tindall DJ, Donkena KV. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res 2012; 18:2882-95. [PMID: 22589488 DOI: 10.1158/1078-0432.ccr-11-2090] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The aim of this study was to investigate the promoter hypermethylation as diagnostic markers to detect malignant prostate cells and as prognostic markers to predict the clinical recurrence of prostate cancer. EXPERIMENTAL DESIGN DNA was isolated from prostate cancer and normal adjacent tissues. After bisulfite conversion, methylation of 14,495 genes was evaluated using the Methylation27 microarrays in 238 prostate tissues. We analyzed methylation profiles in four different groups: (i) tumor (n = 198) versus matched normal tissues (n = 40), (ii) recurrence (n = 123) versus nonrecurrence (n = 75), (iii) clinical recurrence (n = 80) versus biochemical recurrence (n = 43), and (iv) systemic recurrence (n = 36) versus local recurrence (n = 44). Group 1, 2, 3, and 4 genes signifying biomarkers for diagnosis, prediction of recurrence, clinical recurrence, and systemic progression were determined. Univariate and multivariate analyses were conducted to predict risk of recurrence. We validated the methylation of genes in 20 independent tissues representing each group by pyrosequencing. RESULTS Microarray analysis revealed significant methylation of genes in four different groups of prostate cancer tissues. The sensitivity and specificity of methylation for 25 genes from 1, 2, and 4 groups and 7 from group 3 were shown. Validation of genes by pyrosequencing from group 1 (GSTP1, HIF3A, HAAO, and RARβ), group 2 (CRIP1, FLNC, RASGRF2, RUNX3, and HS3ST2), group 3 (PHLDA3, RASGRF2, and TNFRSF10D), and group 4 (BCL11B, POU3F3, and RASGRF2) confirmed the microarray results. CONCLUSIONS Our study provides a global assessment of DNA methylation in prostate cancer and identifies the significance of genes as diagnostic and progression biomarkers of prostate cancer.
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Affiliation(s)
- Saswati Mahapatra
- Department of Urology and Laboratory Medicine and Pathology, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
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Ribeiro da Silva M, Tobias-Machado M, Lima-Pompeo A, Reis L, da Silva Pinhal M. [Prostate cancer: promising biomarkers related to aggressive disease]. Actas Urol Esp 2012; 36:484-90. [PMID: 22520043 DOI: 10.1016/j.acuro.2011.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 11/21/2011] [Accepted: 11/24/2011] [Indexed: 12/25/2022]
Abstract
BACKGROUND Although a rapidly growing number of candidate biological markers of prognosis and/or response to specific treatments in prostate cancer, none have to date showed ability to completely prognosticate prostate cancer on evidence based urology. OBJECTIVE To review the pertinent literature on the issue. ACQUISITION OF EVIDENCE A comprehensive review of the current literature was done focusing on promising biomarkers related to aggressive prostate cancer. SUMMARY OF EVIDENCE Combined with the heterogeneous nature of the disease, mixed case series are the most common study design, impeding robust results and the development of an effective therapeutic strategy. Improvement in prostate cancer patient survival requires not only the identification of new therapeutic target based on detailed understanding of the biological mechanisms involved in metastatic dissemination and tumor growth but strong clinical studies as well. CONCLUSION Better study design involving potential markers and including well-classified and staged patients with robust methodology and adequate outcomes (mainly survival) are necessary to the field evolution.
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Olkhov-Mitsel E, Van der Kwast T, Kron KJ, Ozcelik H, Briollais L, Massey C, Recker F, Kwiatkowski M, Fleshner NE, Diamandis EP, Zlotta AR, Bapat B. Quantitative DNA methylation analysis of genes coding for kallikrein-related peptidases 6 and 10 as biomarkers for prostate cancer. Epigenetics 2012; 7:1037-45. [PMID: 22874102 DOI: 10.4161/epi.21524] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays an important role in carcinogenesis and is being recognized as a promising diagnostic and prognostic biomarker for a variety of malignancies including Prostate cancer (PCa). The human kallikrein-related peptidases (KLKs) have emerged as an important family of cancer biomarkers, with KLK3, encoding for Prostate Specific Antigen, being most recognized. However, few studies have examined the epigenetic regulation of KLKs and its implications to PCa. To assess the biological effect of DNA methylation on KLK6 and KLK10 expression, we treated PC3 and 22RV1 PCa cells with a demethylating drug, 5-aza-2'deoxycytidine, and observed increased expression of both KLKs, establishing that DNA methylation plays a role in regulating gene expression. Subsequently, we have quantified KLK6 and KLK10 DNA methylation levels in two independent cohorts of PCa patients operated by radical prostatectomy between 2007-2011 (Cohort I, n = 150) and 1998-2001 (Cohort II, n = 124). In Cohort I, DNA methylation levels of both KLKs were significantly higher in cancerous tissue vs. normal. Further, we evaluated the relationship between DNA methylation and clinicopathological parameters. KLK6 DNA methylation was significantly associated with pathological stage only in Cohort I while KLK10 DNA methylation was significantly associated with pathological stage in both cohorts. In Cohort II, low KLK10 DNA methylation was associated with biochemical recurrence in univariate and multivariate analyses. A similar trend for KLK6 DNA methylation was observed. The results suggest that KLK6 and KLK10 DNA methylation distinguishes organ confined from locally invasive PCa and may have prognostic value.
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Van Neste L, Herman JG, Otto G, Bigley JW, Epstein JI, Van Criekinge W. The epigenetic promise for prostate cancer diagnosis. Prostate 2012; 72:1248-61. [PMID: 22161815 DOI: 10.1002/pros.22459] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 10/31/2011] [Indexed: 01/01/2023]
Abstract
BACKGROUND Prostate cancer is the most common cancer diagnosis in men and a leading cause of death. Improvements in disease management would have a significant impact and could be facilitated by the development of biomarkers, whether for diagnostic, prognostic, or predictive purposes. The blood-based prostate biomarker PSA has been part of clinical practice for over two decades, although it is surrounded by controversy. While debates of usefulness are ongoing, alternatives should be explored. Particularly with recent recommendations against routine PSA-testing, the time is ripe to explore promising biomarkers to yield a more efficient and accurate screening for detection and management of prostate cancer. Epigenetic changes, more specifically DNA methylation, are amongst the most common alterations in human cancer. These changes are associated with transcriptional silencing of genes, leading to an altered cellular biology. METHODS One gene in particular, GSTP1, has been widely studied in prostate cancer. Therefore a meta-analysis has been conducted to examine the role of this and other genes and the potential contribution to prostate cancer management and screening refinement. RESULTS More than 30 independent, peer reviewed studies have reported a consistently high sensitivity and specificity of GSTP1 hypermethylation in prostatectomy or biopsy tissue. The meta-analysis combined and compared these results. CONCLUSIONS GSTP1 methylation detection can serve an important role in prostate cancer managment. The meta-analysis clearly confirmed a link between tissue DNA hypermethylation of this and other genes and prostate cancer. Detection of DNA methylation in genes, including GSTP1, could serve an important role in clinical practice.
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Rosenbaum E, Begum S, Brait M, Zahurak M, Maldonado L, Mangold LA, Eisenberger MA, Epstein JI, Partin AW, Sidransky D, Hoque MO. AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy. Prostate 2012; 72:1133-9. [PMID: 22127895 PMCID: PMC3360823 DOI: 10.1002/pros.22461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 10/27/2011] [Indexed: 11/09/2022]
Abstract
PURPOSE To evaluate the prognostic significance of six epigenetic biomarkers (AIM1, CDH1, KIF1A, MT1G, PAK3, and RBM6 promoter hypermethlation) in a homogeneous group of prostate cancer patients, following radical prostatectomy (RP). PATIENTS AND METHODS Biomarker analyses were performed retrospectively on tumors from 95 prostate cancer patients all with a Gleason score of 3 + 4 = 7 and a minimum follow-up period of 8 years. Using Quantitative Methylation Specific PCR (QMSP), we analyzed the promoter region of six genes in primary prostate tumor tissues. Time to any progression was the primary endpoint and development of metastatic disease and/or death from prostate cancer was a secondary endpoint. The association of clinicopathological and biomolecular risk factors to recurrence was performed using the Log-rank test and Cox proportional hazards model for multivariate analysis. To identify independent prognostic factors, a stepwise selection method was used. RESULTS At a median follow-up time of 10 years, 48 patients (50.5%) had evidence of recurrence: Biochemical/PSA relapse, metastases, or death from prostate cancer. In the final multivariate analysis for time to progression, the significant factors were: Older age, HR = 0.95 (95% CI: 0.91, 1.0) (P = 0.03), positive lymph nodes HR = 2.11 (95% CI: 1.05, 4.26) (P = 0.04), and decreased hypermethylation of AIM1 HR = 0.45 (95% CI: 0.2, 1.0) (P = 0.05). CONCLUSIONS Methylation status of AIM1 in the prostate cancer specimen may predict for time to recurrence in Gleason 3 + 4 = 7 patients undergoing prostatectomy. These results should be validated in a larger and unselected cohort.
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Affiliation(s)
- Eli Rosenbaum
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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Kloth M, Goering W, Ribarska T, Arsov C, Sorensen KD, Schulz WA. The SNP rs6441224 influences transcriptional activity and prognostically relevant hypermethylation of RARRES1 in prostate cancer. Int J Cancer 2012; 131:E897-904. [PMID: 22573467 DOI: 10.1002/ijc.27628] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/23/2012] [Indexed: 02/03/2023]
Abstract
Epigenetic aberrations are frequent in prostate cancer and could be useful for detection and prognostication. However, the underlying mechanisms and the sequence of these changes remain to be fully elucidated. The tumor suppressor gene RARRES1 (TIG1) is frequently hypermethylated in several cancers. Having noted changes in the expression of its paralogous neighbor gene LXN at 3q25.32, we used pyrosequencing to quantify DNA methylation at both genes and determine its relationship with clinicopathological parameters in 86 prostate cancer tissues from radical prostatectomies. Methylation at LXN and RARRES1 was highly correlated. Increasing methylation was associated with worse clinical features, including biochemical recurrence, and decreased expression of both genes. However, expression of three neighboring genes was unaffected. Intriguingly, RARRES1 methylation was influenced by the genotype of the rs6441224 single-nucleotide polymorphism (SNP) in its promoter. We found that this SNP is located within an ETS-family-response element and that the more strongly methylated allele confers lower activity in reporter assays. Concomitant methylation of RARRES1 and LXN in cancerous tissues was also detected in prostate cancer cell lines and was shown to be associated with repressive histone modifications and transcriptional downregulation. In conclusion, we found that genotype-associated hypermethylation of the ETS-family target gene RARRES1 influences methylation at its neighbor gene LXN and could be useful as a prognostic biomarker.
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Affiliation(s)
- Michael Kloth
- Department of Urology, Heinrich Heine University, Duesseldorf, Germany
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Schiewer MJ, Augello MA, Knudsen KE. The AR dependent cell cycle: mechanisms and cancer relevance. Mol Cell Endocrinol 2012; 352:34-45. [PMID: 21782001 PMCID: PMC3641823 DOI: 10.1016/j.mce.2011.06.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 06/08/2011] [Accepted: 06/27/2011] [Indexed: 01/04/2023]
Abstract
Prostate cancer cells are exquisitely dependent on androgen receptor (AR) activity for proliferation and survival. As these functions are critical targets of therapeutic intervention for human disease, it is imperative to delineate the mechanisms by which AR engages the cell cycle engine. More than a decade of research has revealed that elegant intercommunication between AR and the cell cycle machinery governs receptor-dependent cellular proliferation, and that perturbations in this process occur frequently in human disease. Here, AR-cell cycle interplay and associated cancer relevance will be reviewed.
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Affiliation(s)
- Matthew J. Schiewer
- Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Department of Cancer Biology, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
| | - Michael A. Augello
- Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Department of Cancer Biology, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
| | - Karen E. Knudsen
- Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Department of Cancer Biology, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Department of Urology, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Department of Radiation Oncology, Thomas Jefferson University, 233 S 10th St., Philadelphia, PA 19107, USA
- Corresponding author at: Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th St., BLSB 1008, Philadelphia, PA 19107, USA. Tel.: +1 215 503 8574 (office)/+1 215 503 8573 (lab). (K.E. Knudsen)
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Epigenetic biomarkers in prostate cancer: Current and future uses. Cancer Lett 2012; 342:248-56. [PMID: 22391123 DOI: 10.1016/j.canlet.2012.02.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 02/10/2012] [Accepted: 02/11/2012] [Indexed: 12/18/2022]
Abstract
Epigenome alterations are characteristic of nearly all human malignancies and include changes in DNA methylation, histone modifications and microRNAs (miRNAs). However, what induces these epigenetic alterations in cancer is largely unknown and their mechanistic role in prostate tumorigenesis is just beginning to be evaluated. Identification of the epigenetic modifications involved in the development and progression of prostate cancer will not only identify novel therapeutic targets but also prognostic and diagnostic markers. This review will focus on the use of epigenetic modifications as biomarkers for prostate cancer.
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