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Albuquerque-Castro Â, Macedo-Silva C, Oliveira-Sousa R, Constâncio V, Lobo J, Carneiro I, Henrique R, Jerónimo C. Redefining prostate cancer risk stratification: a pioneering strategy to estimate outcome based on Ki67 immunoscoring. Biomark Res 2024; 12:75. [PMID: 39090707 PMCID: PMC11295892 DOI: 10.1186/s40364-024-00627-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024] Open
Abstract
Accurate prostate cancer (PCa) patient diagnosis and risk assessment are key to ensure the best outcome. Currently, low- and favorable intermediate-risk PCa patients may be offered AS due to the indolent nature of the disease. Nonetheless, deciding between active surveillance and curative-intent treatment remains an intricate task, as a subset of these patients may eventually progress, enduring poorer prognosis. Herein, we sought to construct risk calculators based on cancer biomarkers, enabling more accurate discrimination among patients which may benefit from active interventions.Ki67 immunoscore, GSTP1 and KLF8 promoter methylation levels (me) were assessed in PCa tissues. Study endpoints included overall and biochemical recurrence-free (BCR) survival. Combination with relevant clinicopathological parameters allowed for construction of graphical calculating tools (nomograms).Higher Ki67 index correlated with worse BCR-free survival, whereas higher KLF8me levels were associated with improved overall survival, especially in patients with lower-grade tumors. GSTP1me levels had no prognostic value. Among prognostic models tested, a BCR-risk calculator - ProstARK (including Ki67 and clinicopathologic parameters) - disclosed 79.17% specificity, 66.67% sensitivity, 55% positive predictive value, 86% negative predictive value, and 75.76% accuracy. Similar results were found using an independent PCa biopsy cohort, validating its prognostication ability.Combining clinicopathologic features and Ki67 index into a risk calculator enables easy and accurate implementation of a novel PCa prognostication tool. This nomogram may be useful for a more accurate selection of patients for active surveillance protocols. Nonetheless, validation in a larger, multicentric, set of diagnostic PCa biopsies is mandatory for further confirmation of these results.
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Affiliation(s)
- Ângela Albuquerque-Castro
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Masters' in Oncology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rúben Oliveira-Sousa
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Masters' in Oncology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - Vera Constâncio
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Doctoral Program in Biomedical Sciences, ICBAS-School of Medicine and Biomedical Sciences, ICBAS-UP), University of Porto, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr António Bernardino de Almeida, Porto, 4200-072, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Isa Carneiro
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Masters' in Oncology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr António Bernardino de Almeida, Porto, 4200-072, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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Mecca M, Picerno S, Cortellino S. The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer. Int J Mol Sci 2024; 25:2750. [PMID: 38473997 DOI: 10.3390/ijms25052750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.
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Affiliation(s)
- Marisabel Mecca
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Simona Picerno
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Salvatore Cortellino
- Laboratory of Preclinical and Translational Research, Responsible Research Hospital, 86100 Campobasso, CB, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, 80138 Naples, NA, Italy
- S.H.R.O. Italia Foundation ETS, 10060 Candiolo, TO, Italy
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3
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Khan S, Baligar P, Tandon C, Nayyar J, Tandon S. Molecular heterogeneity in prostate cancer and the role of targeted therapy. Life Sci 2024; 336:122270. [PMID: 37979833 DOI: 10.1016/j.lfs.2023.122270] [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: 07/31/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
Data collected from large-scale studies has shown that the incidence of prostate cancer globally is on the rise, which could be attributed to an overall increase in lifespan. So, the question is how has modern science with all its new technologies and clinical breakthroughs mitigated or managed this disease? The answer is not a simple one as prostate cancer exhibits various subtypes, each with its unique characteristics or signatures which creates challenges in treatment. To understand the complexity of prostate cancer these signatures must be deciphered. Molecular studies of prostate cancer samples have identified certain genetic and epigenetic alterations, which are instrumental in tumorigenesis. Some of these candidates include the androgen receptor (AR), various oncogenes, tumor suppressor genes, and the tumor microenvironment, which serve as major drivers that lead to cancer progression. These aberrant genes and their products can give an insight into prostate cancer development and progression by acting as potent markers to guide future therapeutic approaches. Thus, understanding the complexity of prostate cancer is crucial for targeting specific markers and tailoring treatments accordingly.
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Affiliation(s)
- Sabiha Khan
- Amity Institute of Molecular Medicine, Amity University Uttar Pradesh, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine, Amity University Uttar Pradesh, India
| | - Chanderdeep Tandon
- Amity School of Biological Sciences, Amity University Punjab, Mohali, India
| | - Jasamrit Nayyar
- Department of Chemistry, Goswami Ganesh Dutt Sanatan Dharam College, Chandigarh, India
| | - Simran Tandon
- Amity School of Health Sciences, Amity University Punjab, Mohali, India.
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4
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Creighton CJ, Zhang F, Zhang Y, Castro P, Hu R, Islam M, Ghosh S, Ittmann M, Kwabi-Addo B. Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer. Epigenetics 2023; 18:2180585. [PMID: 37279148 PMCID: PMC9980641 DOI: 10.1080/15592294.2023.2180585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
African American (AA) men have the highest incidence and mortality rate from Prostate cancer (PCa) than any other racial/ethnic group. To date, PCa genomic studies have largely under-represented tumour samples from AA men. We measured genome-wide DNA methylation in benign and tumor prostate tissues from AA men using the Illumina Infunium 850 K EPIC array. mRNA expression database from a subset of the AA biospecimen were used to assess correlation of transcriptome and methylation datasets. Genome-wide methylation analysis identified 11,460 probes that were significant (p < 0.01) and differentially methylated in AA PCa compared to normal prostate tissues and showed significant (p < 0.01) inverse-correlation with mRNA expression. Ingenuity pathway analysis and Gene Ontology analysis in our AA dataset compared with TCGA dataset showed similarities in methylation patterns: top candidate genes with significant hypermethylation and corresponding down-regulated gene expression were associated with biological pathways in hemidesmosome assembly, mammary gland development, epidermis development, hormone biosynthesis, and cell communication. In addition, top candidate genes with significant hypomethylation and corresponding up-regulated gene expression were associated with biological pathways in macrophage differentiation, cAMP-dependent protein kinase activity, protein destabilization, transcription co-repression, and fatty acid biosynthesis. In contrast, differences in genome-wide methylation in our AA dataset compared with TCGA dataset were enriched for genes in steroid signalling, immune signalling, chromatin structure remodelling and RNA processing. Overall, differential methylation of AMIGO3, IER3, UPB1, GRM7, TFAP2C, TOX2, PLSCR2, ZNF292, ESR2, MIXL1, BOLL, and FGF6 were significant and uniquely associated with PCa progression in our AA cohort.
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Affiliation(s)
- Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Flora Zhang
- Center for Women’s Studies, Colgate University, Hamilton, New York, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Castro
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Rong Hu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Somiranjan Ghosh
- Department of Biology, Howard University, Washington, Columbia, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University, Washington, Columbia, USA
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Rehman K, Iqbal Z, Zhiqin D, Ayub H, Saba N, Khan MA, Yujie L, Duan L. Analysis of genetic biomarkers, polymorphisms in ADME-related genes and their impact on pharmacotherapy for prostate cancer. Cancer Cell Int 2023; 23:247. [PMID: 37858151 PMCID: PMC10585889 DOI: 10.1186/s12935-023-03084-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
Prostate cancer (PCa) is a non-cutaneous malignancy in males with wide variation in incidence rates across the globe. It is the second most reported cause of cancer death. Its etiology may have been linked to genetic polymorphisms, which are not only dominating cause of malignancy casualties but also exerts significant effects on pharmacotherapy outcomes. Although many therapeutic options are available, but suitable candidates identified by useful biomarkers can exhibit maximum therapeutic efficacy. The single-nucleotide polymorphisms (SNPs) reported in androgen receptor signaling genes influence the effectiveness of androgen receptor pathway inhibitors and androgen deprivation therapy. Furthermore, SNPs located in genes involved in transport, drug metabolism, and efflux pumps also influence the efficacy of pharmacotherapy. Hence, SNPs biomarkers provide the basis for individualized pharmacotherapy. The pharmacotherapeutic options for PCa include hormonal therapy, chemotherapy (Docetaxel, Mitoxantrone, Cabazitaxel, and Estramustine, etc.), and radiotherapy. Here, we overview the impact of SNPs reported in various genes on the pharmacotherapy for PCa and evaluate current genetic biomarkers with an emphasis on early diagnosis and individualized treatment strategy in PCa.
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Affiliation(s)
- Khurram Rehman
- Faculty of Pharmacy, Gomal University, D.I.Khan, Pakistan
| | - Zoya Iqbal
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Deng Zhiqin
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Hina Ayub
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | - Naseem Saba
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | | | - Liang Yujie
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518035, Guangdong, China.
| | - Li Duan
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China.
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
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6
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Eismann L, von Walter P, Jung A, Chaloupka M, Rodler S, Westhofen T, Buchner A, Stief CG, Stadler T, Schlenker B. Methylation status of various gene loci in localized prostate cancer: Novel biomarkers for diagnostics and biochemical recurrence. Urol Oncol 2023; 41:325.e1-325.e8. [PMID: 37179150 DOI: 10.1016/j.urolonc.2023.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Oncologic outcomes for patients with localized prostate cancer (PCa) undergoing radical prostatectomy (RP) can vary widely. Hypermethylation of tumor-associated genes has potential as a novel diagnostic tool and predictive biomarker in PCa. We investigated the methylation status of tumor-associated genes in patients who underwent RP. METHODS Patients who underwent RP during 2004 to 2008 were matched retrospectively based on post-operative D'Amico risk stratification. Quantitative pyrosequencing was used to analyze methylation status of 10 gene loci in cancerous and adjacent benign tissue from histological specimen. Follow-up was performed according to EAU guideline recommendations. Statistical analyses were performed to correlate methylation levels in cancerous and benign tissue with risk profiles and biochemical recurrence (BCR). RESULTS The cohort included 71 patients: 22 low-risk, 22 intermediate-risk, and 27 high-risk. Mean follow-up time was 74 months. Methylation status differed significantly between cancerous and adjacent benign tissue for the 5 gene loci GSTP1, APC, RASSF1, TNFRFS10c, and RUNX3 (each P < 0.001). Also, the methylation level was significantly higher in high-risk than in low-risk patients for Endoglin2 and APC (P = 0.026; P = 0.032). Using ROC analysis, hypermethylation of APC in PCa tissue was associated with higher risk of BCR (P = 0.005). CONCLUSION Methylation status of various gene loci holds diagnostic and predictive potential in PCa. Hypermethylation of APC, RASSF1, TNFRFS10c and RUNX3 were identified as novel PCa-specific biomarkers. Furthermore, increased methylation levels of APC and Endoglin2 were associated with high-risk PCa. Additionally, hypermethylation of APC was associated with increased risk of BCR after RP.
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Affiliation(s)
- Lennert Eismann
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany.
| | - Philipp von Walter
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Andreas Jung
- Pathologisches Institut, Ludwig-Maximilians-Universität, München, Germany; German Cancer Consortium (DKTK) Partner Site Munich, Germany
| | - Michael Chaloupka
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Severin Rodler
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Thilo Westhofen
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Alexander Buchner
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Christian G Stief
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Thomas Stadler
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
| | - Boris Schlenker
- Klinik und Poliklinik für Urologie, Klinikum der Universität München, München, Germany
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Xu C, Zhao S, Cai L. Epigenetic (De)regulation in Prostate Cancer. Cancer Treat Res 2023; 190:321-360. [PMID: 38113006 DOI: 10.1007/978-3-031-45654-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Prostate cancer (PCa) is a heterogeneous disease exhibiting both genetic and epigenetic deregulations. Epigenetic alterations are defined as changes not based on DNA sequence, which include those of DNA methylation, histone modification, and chromatin remodeling. Androgen receptor (AR) is the main driver for PCa and androgen deprivation therapy (ADT) remains a backbone treatment for patients with PCa; however, ADT resistance almost inevitably occurs and advanced diseases develop termed castration-resistant PCa (CRPC), due to both genetic and epigenetic changes. Due to the reversible nature of epigenetic modifications, inhibitors targeting epigenetic factors have become promising anti-cancer agents. In this chapter, we focus on recent studies about the dysregulation of epigenetic regulators crucially involved in the initiation, development, and progression of PCa and discuss the potential use of inhibitors targeting epigenetic modifiers for treatment of advanced PCa.
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Affiliation(s)
- Chenxi Xu
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Shuai Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ling Cai
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
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Tonmoy MIQ, Fariha A, Hami I, Kar K, Reza HA, Bahadur NM, Hossain MS. Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. Sci Rep 2022; 12:10260. [PMID: 35715447 PMCID: PMC9205881 DOI: 10.1038/s41598-022-13381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs), caused by alterations in DNA methylation, is a driving factor in several cancers. Interplay between lncRNAs’ aberrant methylation and expression in prostate cancer (PC) progression still remains largely elusive. Therefore, this study characterized the genome-wide epigenetic landscape and expression profiles of lncRNAs and their clinical impact by integrating multi-omics data implementing bioinformatics approaches. We identified 62 differentially methylated CpG-sites (DMCs) and 199 differentially expressed lncRNAs (DElncRNAs), where 32 DElncRNAs contain 32 corresponding DMCs within promoter regions. Significant negative correlation was observed between 8 DElncRNAs-DMCs pairs. 3 (cg23614229, cg23957912, and cg11052780) DMCs and 4 (CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1) DElncRNAs were identified as high-risk factors for poor prognosis of PC patients. Overexpression of hypo-methylated CACNA1G-AS1, F11-AS1, and NNT-AS1 and down-regulation of hyper-methylated MSC-AS1 significantly lower the survival of PC patients and could be a potential prognostic and therapeutic biomarker. These DElncRNAs were found to be associated with several molecular functions whose deregulation can lead to cancer. Involvement of these epigenetically deregulated DElncRNAs in cancer-related biological processes was also noticed. These findings provide new insights into the understanding of lncRNA regulation by aberrant DNA methylation which will help to clarify the epigenetic mechanisms underlying PC.
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Affiliation(s)
- Mahafujul Islam Quadery Tonmoy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh. .,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh.
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9
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Moreira-Silva F, Henrique R, Jerónimo C. From Therapy Resistance to Targeted Therapies in Prostate Cancer. Front Oncol 2022; 12:877379. [PMID: 35686097 PMCID: PMC9170957 DOI: 10.3389/fonc.2022.877379] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is the second most common malignancy among men worldwide. Although early-stage disease is curable, advanced stage PCa is mostly incurable and eventually becomes resistant to standard therapeutic options. Different genetic and epigenetic alterations are associated with the development of therapy resistant PCa, with specific players being particularly involved in this process. Therefore, identification and targeting of these molecules with selective inhibitors might result in anti-tumoral effects. Herein, we describe the mechanisms underlying therapy resistance in PCa, focusing on the most relevant molecules, aiming to enlighten the current state of targeted therapies in PCa. We suggest that selective drug targeting, either alone or in combination with standard treatment options, might improve therapeutic sensitivity of resistant PCa. Moreover, an individualized analysis of tumor biology in each PCa patient might improve treatment selection and therapeutic response, enabling better disease management.
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Affiliation(s)
- Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences of the University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (He-alth Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences of the University of Porto (ICBAS-UP), Porto, Portugal
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10
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Xia T, Liu S, Xu G, Zhou S, Luo Z. Dihydroartemisinin induces cell apoptosis through repression of UHRF1 in prostate cancer cells. Anticancer Drugs 2022; 33:e113-e124. [PMID: 34387595 DOI: 10.1097/cad.0000000000001156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Prostate cancer (PCa) seriously jeopardizes men's health worldwide. Dihydroartemisinin, which is an effective antimalarial agent, has shown potential anticancer effects in various human cancer cell lines, including PCa cells. However, the mechanisms underlying the anticancer activity of dihydroartemisinin are not fully understood. Ubiquitin-like with plant homeodomain and ring finger domain 1 (UHRF1) is highly expressed in a variety of tumors and is negatively correlated with the prognosis of various tumors. We reported previously that UHRF1 is downregulated during apoptosis induced by dihydroartemisinin in PC-3 PCa cells. In this study, we transfected PC-3 cells with lentiviruses containing UHRF1 or shRNA-UHRF1. Then, the cells were treated with dihydroartemisinin at different concentrations. Our data showed that overexpression of UHRF1 promoted cell proliferation and migration in PC-3 cells, inhibited cell apoptosis, increased cell proportion in G2 phase, increased DNA methyltransferase 1 and decreased p16INK4A expression at mRNA and protein levels. Downregulation of UHRF1 produces the opposite results. Moreover, the phenomena caused by overexpression of UHRF1 were inhibited after dihydroartemisinin treatment. Compared with control cells, cells overexpressing UHRF1 can resist the proapoptotic and antiproliferative effects of dihydroartemisinin to a certain extent. The effects of UHRF1 knockdown were further aggravated by dihydroartemisinin treatment, but no statistically significant effect was observed with increasing drug concentration. Our results suggested that dihydroartemisinin decreases proliferation and migration but enhances apoptosis of PCa cells, likely by downregulating UHRF1 and upregulating p16INK4A.
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Affiliation(s)
- Tong Xia
- Laboratory of Medical Experiment Technology, Institute of Life Science, Chongqing Medical University, Chongqing, China
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11
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Farah E, Zhang Z, Utturkar SM, Liu J, Ratliff TL, Liu X. Targeting DNMTs to overcome enzalutamide resistance in prostate cancer. Mol Cancer Ther 2021; 21:193-205. [PMID: 34728570 DOI: 10.1158/1535-7163.mct-21-0581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is a FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment. After a short positive response period to enzalutamide, tumors will develop drug resistance. In this study, we uncovered that DNA methylation was deregulated in enzalutamide-resistant cells. DNMT activity and DNMT3B expression were upregulated in resistant cell lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role of p53 and pRB in this process. The overexpression of DNMT3B3, a DNMT3B variant, promoted an enzalutamide-resistant phenotype in C4-2B cell lines. Inhibition of DNA methylation and DNMT3B knockdown induced a re-sensitization to enzalutamide. Decitabine treatment in enzalutamide-resistant cells induced a decrease of the expression of AR-V7 and changes of genes for apoptosis, DNA repair and mRNA splicing. Combination treatment of Decitabine and enzalutamide induced a decrease of tumor weight, Ki-67 and AR-V7 expression and an increase of cleaved-caspase3 levels in 22Rv1 xenografts. The collective results suggest that DNA methylation pathway is deregulated after enzalutamide resistance onset and that targeting DNA methyltransferases restores the sensitivity to enzalutamide in prostate cancer cells.
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Affiliation(s)
| | | | - Sagar M Utturkar
- Purdue University Center for Cancer Research, Purdue University West Lafayette
| | - Jinpeng Liu
- Markey Cancer Center, Department of Biostatistics, University of Kentucky
| | - Timothy L Ratliff
- Comparative Pathobiology and the Center for Cancer Research, Purdue University West Lafayette
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky
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12
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Cheng H, Wang Y, Liu C, Wu T, Chen S, Chen M. Development and Verification of a Prostate Cancer Prognostic Signature Based on an Immunogenomic Landscape Analysis. Front Oncol 2021; 11:711258. [PMID: 34568039 PMCID: PMC8459614 DOI: 10.3389/fonc.2021.711258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose Prostate cancer (PCa) has a high incidence among older men. Until now, there are no immunological markers available to predict PCa patients’ survival. Therefore, it is necessary to explore the immunological characteristics of PCa. Methods First, we retrieved RNA-seq and clinical data of 499 PCa and 52 normal prostate tissue samples from the Cancer Genome Atlas (TCGA). We identified 193 differentially expressed immune-related genes (IRGs) between PCa and normal prostate tissues. Functional enrichment analyses showed that the immune system can participate in PCa initiation. Then, we constructed a correlation network between transcription factors (TFs) and IRGs. We performed univariate and multivariate Cox regression analyses and identified five key prognostic IRGs (S100A2, NOX1, IGHV7-81, AMH, and AGTR1). Finally, a predictive nomogram was established and verified by the C-index. Results We successfully constructed and validated an immune-related PCa prediction model. The signature could independently predict PCa patients’ survival. Results showed that high-immune-risk patients were correlated with advanced stage. We also validated the S100A2 expression in vitro using PCa and normal prostate tissues. We found that higher S100A2 expressions were related to lower biochemical recurrences. Additionally, higher AMH expressions were related to higher Gleason score, lymph node metastasis and positive rate, and tumor stages, and higher ATGR1 expressions were related to lower PSA value. Conclusion Overall, we detected five IRGs (S100A2, NOX1, IGHV7-81, AMH, and AGTR1) that can be used as independent PCa prognostic factors.
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Affiliation(s)
- Hong Cheng
- Department of Urology, Zhongda Hospital Affiliated to Southestern China University, Nanjing, China
| | - Yi Wang
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
| | - Chunhui Liu
- Department of Urology, Zhongda Hospital Affiliated to Southestern China University, Nanjing, China
| | - Tiange Wu
- Department of Urology, Zhongda Hospital Affiliated to Southestern China University, Nanjing, China
| | - Shuqiu Chen
- Department of Urology, Zhongda Hospital Affiliated to Southestern China University, Nanjing, China
| | - Ming Chen
- Department of Urology, Zhongda Hospital Affiliated to Southestern China University, Nanjing, China
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13
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Machado OAS, Diniz VLS, Passos MEP, de Oliveira HH, Santos-Oliveira LC, Alecrim AL, Bertola Lobato T, Manoel R, Correa I, Silva EB, de Oliveira Poma S, Mendes de Almeida M, Pithon-Curi TC, Diniz S, Levada-Pires AC, Curi R, Masi LN, Hirabara SM, Gorjão R. Physical exercise increases global and gene-specific (interleukin-17 and interferon-γ) DNA methylation in lymphocytes from aged women. Exp Physiol 2021; 106:1878-1885. [PMID: 34229361 DOI: 10.1113/ep089673] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/05/2021] [Indexed: 12/22/2022]
Abstract
NEW FINDINGS What is the central question of this study? Is lymphocyte DNA methylation differentially modulated by resistance training and aerobic exercise in older women? What is the main finding and its importance? The practice of resistance training led to an increased global DNA methylation in lymphocytes. The exercise-induced increase of inflammatory genes methylation may be associated with immune function impairment during ageing. ABSTRACT Ageing-induced increase in inflammatory gene expression through a reduction in DNA methylation might contribute to chronic diseases. Regular physical exercise practices, in turn, are associated with a decrease in the incidence of inflammatory diseases. We herein evaluated the effects of three exercise modalities on lymphocyte global and gene-specific (interferon γ (IFN-γ) and interleukin 17A (IL-17A) DNA methylation in aged women (68 ± 7.5 years). This cross-sectional study included 86 women, divided into four groups according to the physical exercise practice: 20 were practicing resistance training (RT); 24 were practicing water aerobics exercise (W); 22 were practicing water aerobics and resistance exercise (RWT), and 20 did not practice any physical exercise (CON). We evaluated volunteer functional capability using the Timed Up and Go (TUG) test, global lymphocyte DNA methylation by enzyme-linked immunosorbent assay, IFN-γ and IL-17A methylation by qPCR and CD4+ IFN-γ+ and CD4+ IL-17+ cell percentage by flow cytometry. The three physically exercised groups performed functional capability tests in a shorter period and showed a higher global lymphocyte DNA methylation and methylated CpGs of IL-17A and IFN-γ promoter regions than the control group. The practice of resistance training (RT and RWT groups) lead to high global DNA methylation. The combination of resistance training and aerobic exercise led to the increase of lymphocyte IL-17A and IFN-γ gene methylation induced by each separately. However, the percentage of IFN-γ+ and IL-17+ cells was lower only in the RT group. The exercise-induced increase of inflammatory-gene methylation may be associated with gene expression changes and immune function impairment during ageing.
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Affiliation(s)
- Otávio A S Machado
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil.,Physiology and Metabolism Study Center, Physical Education Faculty of Sorocaba YMCA, Sorocaba, Brazil
| | - Vinicius L S Diniz
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Maria E P Passos
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Heloisa H de Oliveira
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Laiane C Santos-Oliveira
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Amanda L Alecrim
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Tiago Bertola Lobato
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Richelieau Manoel
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Ilana Correa
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Eliane B Silva
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Sarah de Oliveira Poma
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Mariana Mendes de Almeida
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Tania C Pithon-Curi
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | | | - Adriana C Levada-Pires
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Rui Curi
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Laureane Nunes Masi
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Sandro M Hirabara
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
| | - Renata Gorjão
- Interdisciplinary Post-Graduate Program in Health Sciences, Health Sciences department, Cruzeiro do Sul University, São Paulo, Brazil
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14
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The Role of the Metzincin Superfamily in Prostate Cancer Progression: A Systematic-Like Review. Int J Mol Sci 2021; 22:ijms22073608. [PMID: 33808504 PMCID: PMC8036576 DOI: 10.3390/ijms22073608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/21/2021] [Accepted: 03/26/2021] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer remains a leading cause of cancer-related morbidity in men. Potentially important regulators of prostate cancer progression are members of the metzincin superfamily of proteases, principally through their regulation of the extracellular matrix. It is therefore timely to review the role of the metzincin superfamily in prostate cancer and its progression to better understand their involvement in this disease. A systematic-like search strategy was conducted. Articles that investigated the roles of members of the metzincin superfamily and their key regulators in prostate cancer were included. The extracted articles were synthesized and data presented in tabular and narrative forms. Two hundred and five studies met the inclusion criteria. Of these, 138 investigated the role of the Matrix Metalloproteinase (MMP) subgroup, 34 the Membrane-Tethered Matrix Metalloproteinase (MT-MMP) subgroup, 22 the A Disintegrin and Metalloproteinase (ADAM) subgroup, 8 the A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) subgroup and 53 the Tissue Inhibitor of Metalloproteinases (TIMP) family of regulators, noting that several studies investigated multiple family members. There was clear evidence that specific members of the metzincin superfamily are involved in prostate cancer progression, which can be either in a positive or negative manner. However, further understanding of their mechanisms of action and how they may be used as prognostic indicators or molecular targets is required.
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15
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Sugiura M, Sato H, Kanesaka M, Imamura Y, Sakamoto S, Ichikawa T, Kaneda A. Epigenetic modifications in prostate cancer. Int J Urol 2020; 28:140-149. [PMID: 33111429 DOI: 10.1111/iju.14406] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Prostate cancer is a major cause of cancer-related deaths among men worldwide. In addition to genomic alterations, epigenetic alterations accumulated in prostate cancer have been elucidated. While aberrant deoxyribonucleic acid hypermethylation in promoter CpG islands inactivates crucial genes associated with deoxyribonucleic acid repair, cell cycle, apoptosis or cell adhesion, aberrant deoxyribonucleic acid hypomethylation can lead to oncogene activation. Acetylation of histone is also deregulated in prostate cancer, which could cause aberrant super-enhancer formation and activation of genes associated with cancer development. Deregulations of histone methylation, such as an increase of trimethylation at position 27 of histone H3 by enhancer of zeste homolog2 overexpression, or other modifications, such as phosphorylation and ubiquitination, are also involved in prostate cancer development, and inhibitors targeting these epigenomic aberrations might be novel therapeutic strategies. In this review, we provide an overview of epigenetic alterations in the development and progression of prostate cancer, focusing on deoxyribonucleic acid methylation and histone modifications.
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Affiliation(s)
- Masahiro Sugiura
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hiroaki Sato
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Manato Kanesaka
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan.,Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yusuke Imamura
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shinichi Sakamoto
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Tomohiko Ichikawa
- Departments of, Department of, Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Atsushi Kaneda
- Department of, Molecular Oncology, Chiba University Graduate School of Medicine, Chiba, Japan
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16
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Autoencoded DNA methylation data to predict breast cancer recurrence: Machine learning models and gene-weight significance. Artif Intell Med 2020; 110:101976. [PMID: 33250148 DOI: 10.1016/j.artmed.2020.101976] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 08/05/2020] [Accepted: 10/18/2020] [Indexed: 12/29/2022]
Abstract
Breast cancer is the most frequent cancer in women and the second most frequent overall after lung cancer. Although the 5-year survival rate of breast cancer is relatively high, recurrence is also common which often involves metastasis with its consequent threat for patients. DNA methylation-derived databases have become an interesting primary source for supervised knowledge extraction regarding breast cancer. Unfortunately, the study of DNA methylation involves the processing of hundreds of thousands of features for every patient. DNA methylation is featured by High Dimension Low Sample Size which has shown well-known issues regarding feature selection and generation. Autoencoders (AEs) appear as a specific technique for conducting nonlinear feature fusion. Our main objective in this work is to design a procedure to summarize DNA methylation by taking advantage of AEs. Our proposal is able to generate new features from the values of CpG sites of patients with and without recurrence. Then, a limited set of relevant genes to characterize breast cancer recurrence is proposed by the application of survival analysis and a pondered ranking of genes according to the distribution of their CpG sites. To test our proposal we have selected a dataset from The Cancer Genome Atlas data portal and an AE with a single-hidden layer. The literature and enrichment analysis (based on genomic context and functional annotation) conducted regarding the genes obtained with our experiment confirmed that all of these genes were related to breast cancer recurrence.
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17
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Demircan Tan B, Turan T, Yucel B, Altundag Kara S, Salman Yilmaz S, Yildirim A. Aberrant SOCS3 Promoter Methylation as a Noninvasive Diagnostic Biomarker for Locally Advanced Prostate Cancer. Medeni Med J 2020; 35:99-105. [PMID: 32733758 PMCID: PMC7384502 DOI: 10.5222/mmj.2020.58708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/12/2020] [Indexed: 11/05/2022] Open
Abstract
Objective The aim of this study was to investigate the promoter methylation status of Rasassociated domain family 1A (RASSF1A), O-6-methylguanine-DNA methyltransferase (MGMT), Phosphatase with tensin homology (PTEN) and Suppressor of cytokine signaling 3 (SOCS3) tumor suppressor genes and evaluate the clinical utility of these genes as noninvasive, blood-based epigenetic biomarkers for the diagnosis of Prostate Cancer (PCa). Method A total of 41 consecutive patients and 10 healthy control groups were enrolled in the study. Pyrosequencing was performed to analyze the methylation levels of the promoter regions of the four tumor suppressor genes in patients compared to healthy controls. Results The promoter methylation levels of RASSF1A, MGMT, PTEN and SOCS3 did not differ between the patient and control groups. However, SOCS3 promoter methylation level was significantly higher for patients having locally advanced PCa compared to those having localizedPCa (p<0.05). Conclusion Our results indicated that SOCS3 could be a useful, noninvasive blood-based epigenetic biomarker for the diagnosis of locally advanced PCa.
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Affiliation(s)
- Berna Demircan Tan
- Istanbul Medeniyet University, Faculty of Medicine Department of Medical Biology, Istanbul, Turkey
| | - Turgay Turan
- Istanbul Medeniyet University, Faculty of Medicine, Department of Urology, Istanbul, Turkey
| | - Burcu Yucel
- Istanbul Medeniyet University, Faculty of Medicine, Department of Medical Biology, Istanbul, Turkey
| | - Sedef Altundag Kara
- Istanbul Okan University, Faculty of Medicine, Department of Histology, Istanbul, Turkey
| | - Seda Salman Yilmaz
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Medical Genetics, Istanbul, Turkey
| | - Asif Yildirim
- Istanbul Medeniyet University, Faculty of Medicine, Department of Urology, Istanbul, Turkey
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18
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Multinu F, Chen J, Madison JD, Torres M, Casarin J, Visscher D, Shridhar V, Bakkum-Gamez J, Sherman M, Wentzensen N, Mariani A, Walther-Antonio M. Analysis of DNA methylation in endometrial biopsies to predict risk of endometrial cancer. Gynecol Oncol 2020; 156:682-688. [PMID: 31902687 DOI: 10.1016/j.ygyno.2019.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine whether analysis of methylated DNA in benign endometrial biopsy (EB) specimens is associated with risk of endometrial cancer (EC). METHODS We identified 23 women with EBs performed at Mayo Clinic diagnosed as normal (n = 14) or hyperplasia (n = 9) and who later developed endometrial cancer after a median interval of 1 year. Cases were matched 1:1 with patients with benign EBs who did not develop EC (controls) by histology of benign EB (normal endometrium vs. endometrial hyperplasia without atypia), date of EB, age at EB, and length of post-biopsy follow-up. DNA extracted from formalin-fixed paraffin-embedded tissues underwent pyrosequencing to determine percent methylation of promoter region CpGs at 26 loci in 4 genes (ADCYAP1, HAND2, MME, RASSF1A) previously reported as methylated in EC. RESULTS After pathologic review, 23 matched pairs of cases and controls were identified (14 normal, 9 hyperplasia without atypia per group). Among cases, median time from benign EB to EC was 1 year (range 2 days - 9.2 years). We evaluated 26 CpG sites within 4 genes and found a consistent trend of increasing percentage of methylation from control to case to EC for all CpGs. At the gene-level, mean methylation events of ADCYAP1 and HAND2 in cases were significantly higher than control (p = 0.015 and p = 0.021, respectively). Though the other genes did not reach statistical significance, we observed an increased methylation trend among all genes. Area-under-curve (AUC) calculations (predicting future development of EC in the setting of benign EB) for ADCYAP1 and HAND2 were 0.71 (95% CI 0.55-0.88) and 0.83 (95% CI 0.64-1, respectively). CONCLUSIONS This proof-of-principle study provides evidence that specific methylation patterns in benign EB correlate with future development of EC.
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Affiliation(s)
- Francesco Multinu
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States of America
| | - Joseph D Madison
- Department of Surgery, Mayo Clinic, Rochester, MN, United States of America; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Michelle Torres
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Jvan Casarin
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Daniel Visscher
- Department of Laboratory Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Viji Shridhar
- Department of Laboratory Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Jamie Bakkum-Gamez
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Mark Sherman
- Department of Health Sciences Research and Division of Epidemiology, Mayo Clinic, Jacksonville, FL, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Andrea Mariani
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Marina Walther-Antonio
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America; Department of Surgery, Mayo Clinic, Rochester, MN, United States of America; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America.
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Badal S, Aiken W, Morrison B, Valentine H, Bryan S, Gachi A, Ragin C. Disparities in prostate cancer incidence and mortality rates: Solvable or not? Prostate 2020; 80:3-16. [PMID: 31702061 PMCID: PMC8378246 DOI: 10.1002/pros.23923] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/18/2019] [Indexed: 12/21/2022]
Abstract
Prostate cancer (PCa) is recognized as a disease possessing not only great variation in its geographic and racial distribution but also tremendous variation in its potential to cause morbidity and death and it, therefore, ought not to be considered a homogenous disease entity. Morbidity and death from PCa are disproportionately higher in men of African ancestry (MAA) who are generally observed to have more aggressive disease and worse outcomes following treatment compared to men of European ancestry (MEA). The higher rates of PCa among MAA relative to MEA appear to be multifactorial and related to inherent differences in biological aggressiveness; a continued lack of awareness of the disease and methods of prevention; a lower prevalence of screen-detected PCa; comparatively lower access to quality healthcare as well as systemic and institutionalized disparities in the administration of optimal care to MAA in developed countries such as the United States of America where high-quality care is available. Even when access to quality healthcare is assured in equal access settings, it appears that MAA still have worse outcomes after PCa treatment stage-for-stage and grade-for-grade compared to MEA, suggesting that, inherent racial, ethnic and biological differences are paramount in predicting poor outcomes. This review has explored the different contributing factors to the current disparities in PCa incidence and mortality rates with emphasis on the incongruence in how research has been conducted in understanding the disease towards developing therapies.
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Affiliation(s)
- Simone Badal
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - William Aiken
- Department of Surgery, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Belinda Morrison
- Department of Surgery, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Henkel Valentine
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Sophia Bryan
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - Andrew Gachi
- Department of pathology, Aga Khan University Hospital, 3 Avenue, Parklands, Nairobi, Kenya
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- African Caribbean Cancer Consortium
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20
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Xu S, Wu X, Tao Z, Li H, Fan C, Chen S, Guo J, Ning Y, Hu X. Effect of aberrantly methylated androgen receptor target gene PCDH7 on the development of androgen-independent prostate cancer cells. Genes Genomics 2019; 42:299-307. [PMID: 31872382 DOI: 10.1007/s13258-019-00903-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/04/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Androgen-independent prostate cancer (AIPC) is an extremely malignant tumor developed from the androgen dependent (ADPC). However, the mechanism of transition process from ADPC to AIPC remains unknown. OBJECTIVE Here we aimed to identify the androgen receptor (AR) target gene and its roles in AIPC. METHODS Target genes of AR were identified by ChIP-seq in AIPC cells. AR target gene PCDH7 was detected by real time PCR and western blot. Methylation of PCDH7 was measured by bisulfite sequencing and bisulfite amplicon sequencing. Cell growth, invasion and apoptosis were measured by CCK-8, transwell and flow cytometry, respectively. RESULTS AR was significantly enriched in the upstream of PCDH7 gene. The expression of PCDH7 was significantly decreased, while the methylation of PCDH7 was increased in the AIPC cells compared to the ADPC cells. DNA methyltransferase inhibitor significantly suppressed the methylation and increased the mRNA and protein level of PCDH7. Moreover, overexpression of DNMT1 remarkably reduced the mRNA and protein level of PCDH7. DNA methyltransferase inhibitor decreased the cell growth and invasion while promote the cell apoptosis in the AIPC cells. AR significantly target PCDH7, whose hypermethylation may repress cell growth and invasion, and promote apoptosis in AIPC. CONCLUSIONS This study might provide a novel potential target for the treatment of AIPC.
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Affiliation(s)
- Siqi Xu
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Xiaoyan Wu
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Zhihua Tao
- The Clinical Laboratory of the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Hongsheng Li
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Chenliang Fan
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Songjin Chen
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Jianwei Guo
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Yao Ning
- The Clinical Laboratory of the Second Hospital of Jiaxing, Jiaxing, 314000, China
| | - Xuqi Hu
- The Orthopaedics Department of the Second Hospital of Jiaxing, No. 1518, Huancheng North Road, Nanhu District, Jiaxing, 314000, Zhejiang, China.
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21
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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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22
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Xu J, Tsai CW, Chang WS, Han Y, Bau DT, Pettaway CA, Gu J. Methylation of global DNA repeat LINE-1 and subtelomeric DNA repeats D4Z4 in leukocytes is associated with biochemical recurrence in African American prostate cancer patients. Carcinogenesis 2019; 40:1055-1060. [PMID: 30874286 DOI: 10.1093/carcin/bgz061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
Global DNA methylation may play important roles in cancer etiology and prognosis. The goal of this study is to investigate whether the methylation of long interspersed nucleotide elements (LINE-1) and subtelomeric DNA repeats D4Z4 in leukocyte DNA is associated with aggressive prostate cancer (PCa) in African Americans. We measured DNA methylation levels of LINE-1 and D4Z4 in 306 African American (AA) PCa patients using pyrosequencing and compared their methylation levels among clinical variables. We further applied multivariate Cox proportional hazards model and Kaplan-Meier survival function and log-rank tests to assess the association between DNA methylation and biochemical recurrence (BCR). Overall, there was no significant difference of the methylation levels of LINE-1 and D4Z4 among patients with different clinical and epidemiological characteristics. However, the methylation of LINE-1 and D4Z4 was associated with BCR. Patients with lower LINE-1 methylation and higher D4Z4 methylation exhibited markedly increased risks of BCR with adjusted hazard ratios of 3.34 (95% confidence interval, 1.32-8.45) and 4.12 (95% confidence interval, 1.32-12.86), respectively, and significantly shorter BCR-free survival times. Our results suggest that lower global DNA methylation and higher subtelomeric region methylation may predict worse prognosis in localized AA PCa patients.
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Affiliation(s)
- Junfeng Xu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Wen Tsai
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Shin Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung, Taiwan
| | - Yuyan Han
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Da-Tian Bau
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung, Taiwan
| | - Curtis A Pettaway
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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23
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Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B. Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression. Clin Epigenetics 2019; 11:54. [PMID: 30917865 PMCID: PMC6438015 DOI: 10.1186/s13148-019-0651-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background Global DNA methylation alterations are hallmarks of cancer. The tumor-suppressive TET enzymes, which are involved in DNA demethylation, are decreased in prostate cancer (PCa); in particular, TET2 is specifically targeted by androgen-dependent mechanisms of repression in PCa and may play a central role in carcinogenesis. Thus, the identification of key genes targeted by TET2 dysregulation may provide further insight into cancer biology. Results Using a CRISPR/Cas9-derived TET2-knockout prostate cell line, and through whole-transcriptome and whole-methylome sequencing, we identified seven candidate genes—ASB2, ETNK2, MEIS2, NRG1, NTN1, NUDT10, and SRPX—exhibiting reduced expression and increased promoter methylation, a pattern characteristic of tumor suppressors. Decreased expression of these genes significantly discriminates between recurrent and non-recurrent prostate tumors from the Cancer Genome Atlas (TCGA) cohort (n = 423), and ASB2, NUDT10, and SRPX were significantly correlated with lower recurrence-free survival in patients by Kaplan-Meier analysis. ASB2, MEIS2, and SRPX also showed significantly lower expression in high-risk Gleason score 8 tumors as compared to low or intermediate risk tumors, suggesting that these genes may be particularly useful as indicators of PCa progression. Furthermore, methylation array probes in the TCGA dataset, which were proximal to the highly conserved, differentially methylated sites identified in our TET2-knockout cells, were able to significantly distinguish between matched prostate tumor and normal prostate tissues (n = 50 pairs). Except ASB2, all genes exhibited significantly increased methylation at these probes, and methylation status of at least one probe for each of these genes showed association with measures of PCa progression such as recurrence, stage, or Gleason score. Since ASB2 did not have any probes within the TET2-knockout differentially methylated region, we validated ASB2 methylation in an independent series of matched tumor-normal samples (n = 19) by methylation-specific qPCR, which revealed concordant and significant increases in promoter methylation within the TET2-knockout site. Conclusions Our study identifies seven genes governed by TET2 loss in PCa which exhibit an association between their methylation and expression status and measures of PCa progression. As differential methylation profiles and TET2 expression are associated with advanced PCa, further investigation of these specialized TET2 targets may provide important insights into patterns of carcinogenic gene dysregulation. Electronic supplementary material The online version of this article (10.1186/s13148-019-0651-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shivani Kamdar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Ruth Isserlin
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
| | - Theodorus Van der Kwast
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.,Department of Pathology, University Health Network, University of Toronto, 200 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Alexandre R Zlotta
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada.,Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON, M5S 3E1, Canada
| | - Neil E Fleshner
- Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada
| | - Bharati Bapat
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building (6th floor), 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. .,Department of Pathology, University Health Network, University of Toronto, 200 Elizabeth St, Toronto, ON, M5G 2C4, Canada. .,Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, 190 Elizabeth St, Toronto, ON, M5G 2C4, Canada.
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24
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Lin C, Salzillo TC, Bader DA, Wilkenfeld SR, Awad D, Pulliam TL, Dutta P, Pudakalakatti S, Titus M, McGuire SE, Bhattacharya PK, Frigo DE. Prostate Cancer Energetics and Biosynthesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:185-237. [PMID: 31900911 PMCID: PMC8096614 DOI: 10.1007/978-3-030-32656-2_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancers must alter their metabolism to satisfy the increased demand for energy and to produce building blocks that are required to create a rapidly growing tumor. Further, for cancer cells to thrive, they must also adapt to an often changing tumor microenvironment, which can present new metabolic challenges (ex. hypoxia) that are unfavorable for most other cells. As such, altered metabolism is now considered an emerging hallmark of cancer. Like many other malignancies, the metabolism of prostate cancer is considerably different compared to matched benign tissue. However, prostate cancers exhibit distinct metabolic characteristics that set them apart from many other tumor types. In this chapter, we will describe the known alterations in prostate cancer metabolism that occur during initial tumorigenesis and throughout disease progression. In addition, we will highlight upstream regulators that control these metabolic changes. Finally, we will discuss how this new knowledge is being leveraged to improve patient care through the development of novel biomarkers and metabolically targeted therapies.
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Affiliation(s)
- Chenchu Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Travis C Salzillo
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - David A Bader
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sandi R Wilkenfeld
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dominik Awad
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Thomas L Pulliam
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Prasanta Dutta
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shivanand Pudakalakatti
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Titus
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sean E McGuire
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pratip K Bhattacharya
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel E Frigo
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Molecular Medicine Program, The Houston Methodist Research Institute, Houston, TX, USA.
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25
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Sharma B, Kanwar SS. Phosphatidylserine: A cancer cell targeting biomarker. Semin Cancer Biol 2018; 52:17-25. [DOI: 10.1016/j.semcancer.2017.08.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/12/2017] [Accepted: 08/30/2017] [Indexed: 12/11/2022]
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26
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Köseoğlu H. Genetics in the Prostate Cancer. Prostate Cancer 2018. [DOI: 10.5772/intechopen.77259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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27
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Marques-Magalhães Â, Graça I, Henrique R, Jerónimo C. Targeting DNA Methyltranferases in Urological Tumors. Front Pharmacol 2018; 9:366. [PMID: 29706891 PMCID: PMC5909196 DOI: 10.3389/fphar.2018.00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
Urological cancers are a heterogeneous group of malignancies accounting for a considerable proportion of cancer-related morbidity and mortality worldwide. Aberrant epigenetic traits, especially altered DNA methylation patterns constitute a hallmark of these tumors. Nonetheless, these alterations are reversible, and several efforts have been carried out to design and test several epigenetic compounds that might reprogram tumor cell phenotype back to a normal state. Indeed, several DNMT inhibitors are currently under evaluation for therapeutic efficacy in clinical trials. This review highlights the critical role of DNA methylation in urological cancers and summarizes the available data on pre-clinical assays and clinical trials with DNMT inhibitors in bladder, kidney, prostate, and testicular germ cell cancers.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
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28
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Cao Z, Wei L, Zhu W, Yao X. Meta-analysis of CDKN2A methylation to find its role in prostate cancer development and progression, and also to find the effect of CDKN2A expression on disease-free survival (PRISMA). Medicine (Baltimore) 2018; 97:e0182. [PMID: 29561434 PMCID: PMC5895353 DOI: 10.1097/md.0000000000010182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Reduction of cyclin-dependent kinase inhibitor 2A (CDKN2A) (p16 and p14) expression through DNA methylation has been reported in prostate cancer (PCa). This meta-analysis was conducted to assess the difference of p16 and p14 methylation between PCa and different histological types of nonmalignant controls and the correlation of p16 or p14 methylation with clinicopathological features of PCa. METHODS According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement criteria, articles were searched in PubMed, Embase, EBSCO, Wanfang, and CNKI databases. The strength of correlation was calculated by the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). Trial sequential analysis (TSA) was used to estimate the required population information for significant results. RESULTS A total of 20 studies published from 1997 to 2017 were identified in this meta-analysis, including 1140 PCa patients and 530 cases without cancer. Only p16 methylation in PCa was significantly higher than in benign prostatic lesions (OR = 4.72, P = .011), but had a similar level in PCa and adjacent tissues or high-grade prostatic intraepithelial neoplasias (HGPIN). TSA revealed that this analysis on p16 methylation is a false positive result in cancer versus benign prostatic lesions (the estimated required information size of 5116 participants). p16 methylation was not correlated with PCa in the urine and blood. Besides, p16 methylation was not linked to clinical stage, prostate-specific antigen (PSA) level, and Gleason score (GS) of patients with PCa. p14 methylation was not correlated with PCa in tissue and urine samples. No correlation was observed between p14 methylation and clinical stage or GS. CDKN2A mutation and copy number alteration were not associated with prognosis of PCa in overall survival and disease-free survival. CDKN2A expression was not correlated with the prognosis of PCa in overall survival (492 cases) (P > .1), while CDKN2A expression was significantly associated with a poor disease-free survival (P < .01). CONCLUSION CDKN2A methylation may not be significantly associated with the development, progression of PCa. Although CDKN2A expression had an unfavorable prognosis in disease-free survival. More studies are needed to confirm our results.
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Affiliation(s)
| | - Lijuan Wei
- Department of Respiratory Medicine, Ningbo Urology and Nephrology Hospital, Ningbo, Zhejiang, China
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29
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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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30
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Han Y, Xu J, Kim J, Wu X, Gu J. Methylation of subtelomeric repeat D4Z4 in peripheral blood leukocytes is associated with biochemical recurrence in localized prostate cancer patients. Carcinogenesis 2017; 38:821-826. [PMID: 28854562 DOI: 10.1093/carcin/bgx064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/28/2017] [Indexed: 01/06/2023] Open
Abstract
Global DNA methylation may affect chromosome structure and genomic stability and is involved in carcinogenesis. In this study, we aimed to investigate whether methylation of pericentromeric repeat NBL2 and subtelomeric repeat D4Z4 in peripheral blood was associated with the aggressiveness of prostate cancer (PCa). We measured the methylation status of different CpG sites of NBL2 and D4Z4 in 795 PCa patients and compared their methylation levels among patients with different Gleason Score at diagnosis. We then analyzed the association of the NBL2 and D4Z4 methylation with the risk of biochemical recurrence (BCR) in patients receiving radical prostatectomy or radiotherapy using a multivariate Cox proportional hazards model. In addition, we used the Kaplan-Meier survival function and log-rank tests to assess BCR-free survival associated with D4Z4 methylation. There was no significant difference in methylation level of NBL2 and D4Z4 between clinically defined aggressive and non-aggressive PCa at diagnosis. However, the methylation of D4Z4 was associated with BCR, while the methylation of NBL2 was not. In tertile analysis, patients in the highest tertile of D4Z4 methylation had an increased risk of BCR (HR = 2.17, 95% CI 1.36-3.48) compared to patients in the lower tertiles after adjustment of age, body mass index, smoking status, pack year, D'Amico risk groups and treatments. Among the four CpG sites in this region, the association was mostly attributable to the methylation of the second CpG site of D4Z4. These data suggest that higher methylation in D4Z4 was associated with worse prognosis of localized PCa patients.
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Affiliation(s)
- Yuyan Han
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Junfeng Xu
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeri Kim
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xifeng Wu
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jian Gu
- To whom correspondence should be addressed. Tel: +713 7928016; Fax: +713 7922145;
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31
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Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM. Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer 2017; 17:273. [PMID: 28412973 PMCID: PMC5392915 DOI: 10.1186/s12885-017-3252-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. METHODS We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. RESULTS We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. CONCLUSIONS DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.
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Affiliation(s)
- Marie K. Kirby
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: TRM Oncology, 5901-C Peachtree Dunwoody Rd, Suite 200, Atlanta, GA 30328 USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Genetics, Kaul Human Genetics Building, Suite 230, 720 20th Street South, Birmingham, AL 35294 USA
| | - Brian S. Roberts
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | | | - David S. Gunther
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: University of Southern California, University Park, Los Angeles, CA 90089 USA
| | - Todd C. Burwell
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Boeing Co., 499 Boeing Blvd, SW, Huntsville, AL 35824 USA
| | - Nicholas S. Davis
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Duke University, 101 Science Drive, Durham, NC 27708 USA
| | - Zulfiqar G. Gulzar
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
- Present Address: NuGEN technologies, 201 Industrial Rd #310, San Carlos, CA 94070 USA
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - James D. Brooks
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
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32
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Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients. Sci Rep 2017; 7:40636. [PMID: 28084441 PMCID: PMC5233981 DOI: 10.1038/srep40636] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer (PC) diagnosis is based on histological evaluation of prostate needle biopsies, which have high false negative rates. Here, we investigated if cancer-associated epigenetic field effects in histologically normal prostate tissue may be used to increase sensitivity for PC. We focused on nine genes (AOX1, CCDC181 (C1orf114), GABRE, GAS6, HAPLN3, KLF8, MOB3B, SLC18A2, and GSTP1) known to be hypermethylated in PC. Using quantitative methylation-specific PCR, we analysed 66 malignant and 134 non-malignant tissue samples from 107 patients, who underwent ultrasound-guided prostate biopsy (67 patients had at least one cancer-positive biopsy, 40 had exclusively cancer-negative biopsies). Hypermethylation was detectable for all genes in malignant needle biopsy samples (AUC: 0.80 to 0.98), confirming previous findings in prostatectomy specimens. Furthermore, we identified a four-gene methylation signature (AOX1xGSTP1xHAPLN3xSLC18A2) that distinguished histologically non-malignant biopsies from patients with vs. without PC in other biopsies (AUC = 0.65; sensitivity = 30.8%; specificity = 100%). This signature was validated in an independent patient set (59 PC, 36 adjacent non-malignant, and 9 normal prostate tissue samples) analysed on Illumina 450 K methylation arrays (AUC = 0.70; sensitivity = 40.6%; specificity = 100%). Our results suggest that a novel four-gene signature may be used to increase sensitivity for PC diagnosis through detection of epigenetic field effects in histologically non-malignant prostate tissue samples.
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33
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Rodrigues MFSD, Esteves CM, Xavier FCA, Nunes FD. Methylation status of homeobox genes in common human cancers. Genomics 2016; 108:185-193. [PMID: 27826049 DOI: 10.1016/j.ygeno.2016.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/27/2016] [Accepted: 11/01/2016] [Indexed: 02/06/2023]
Abstract
Approximately 300 homeobox loci were identified in the euchromatic regions of the human genome, of which 235 are probable functional genes and 65 are likely pseudogenes. Many of these genes play important roles in embryonic development and cell differentiation. Dysregulation of homeobox gene expression is a frequent occurrence in cancer. Accumulating evidence suggests that as genetics disorders, epigenetic modifications alter the expression of oncogenes and tumor suppressor genes driving tumorigenesis and perhaps play a more central role in the evolution and progression of this disease. Here, we described the current knowledge regarding homeobox gene DNA methylation in human cancer and describe its relevance in the diagnosis, therapeutic response and prognosis of different types of human cancers.
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Affiliation(s)
| | | | | | - Fabio Daumas Nunes
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil.
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34
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Graça I, Pereira-Silva E, Henrique R, Packham G, Crabb SJ, Jerónimo C. Epigenetic modulators as therapeutic targets in prostate cancer. Clin Epigenetics 2016; 8:98. [PMID: 27651838 PMCID: PMC5025578 DOI: 10.1186/s13148-016-0264-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/07/2016] [Indexed: 01/24/2023] Open
Abstract
Prostate cancer is one of the most common non-cutaneous malignancies among men worldwide. Epigenetic aberrations, including changes in DNA methylation patterns and/or histone modifications, are key drivers of prostate carcinogenesis. These epigenetic defects might be due to deregulated function and/or expression of the epigenetic machinery, affecting the expression of several important genes. Remarkably, epigenetic modifications are reversible and numerous compounds that target the epigenetic enzymes and regulatory proteins were reported to be effective in cancer growth control. In fact, some of these drugs are already being tested in clinical trials. This review discusses the most important epigenetic alterations in prostate cancer, highlighting the role of epigenetic modulating compounds in pre-clinical and clinical trials as potential therapeutic agents for prostate cancer management.
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Affiliation(s)
- Inês Graça
- Cancer Biology and Epigenetics Group-Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal ; School of Allied Health Sciences (ESTSP), Polytechnic of Porto, Porto, Portugal
| | - Eva Pereira-Silva
- Cancer Biology and Epigenetics Group-Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group-Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal ; Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal ; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, The Somers Cancer Research Building, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, S016 6YD UK
| | - Simon J Crabb
- Cancer Research UK Centre, Cancer Sciences, The Somers Cancer Research Building, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, S016 6YD UK
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group-Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Research Center-LAB 3, F Bdg, 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal ; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
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35
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Corbin JM, Ruiz-Echevarría MJ. One-Carbon Metabolism in Prostate Cancer: The Role of Androgen Signaling. Int J Mol Sci 2016; 17:E1208. [PMID: 27472325 PMCID: PMC5000606 DOI: 10.3390/ijms17081208] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 01/06/2023] Open
Abstract
Cancer cell metabolism differs significantly from the metabolism of non-transformed cells. This altered metabolic reprogramming mediates changes in the uptake and use of nutrients that permit high rates of proliferation, growth, and survival. The androgen receptor (AR) plays an essential role in the establishment and progression of prostate cancer (PCa), and in the metabolic adaptation that takes place during this progression. In its role as a transcription factor, the AR directly affects the expression of several effectors and regulators of essential catabolic and biosynthetic pathways. Indirectly, as a modulator of the one-carbon metabolism, the AR can affect epigenetic processes, DNA metabolism, and redox balance, all of which are important factors in tumorigenesis. In this review, we focus on the role of AR-signaling on one-carbon metabolism in tumorigenesis. Clinical implications of one-carbon metabolism and AR-targeted therapies for PCa are discussed in this context.
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Affiliation(s)
- Joshua M Corbin
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Maria J Ruiz-Echevarría
- Department of Pathology, Oklahoma University Health Sciences Center and Stephenson Cancer Center, Oklahoma City, OK 73104, USA.
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36
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p16 upregulation is linked to poor prognosis in ERG negative prostate cancer. Tumour Biol 2016; 37:12655-12663. [PMID: 27444279 DOI: 10.1007/s13277-016-5167-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/12/2016] [Indexed: 10/21/2022] Open
Abstract
Altered expression of the p16 tumor suppressor is frequently found in prostate cancer, but its role for tumor development and patient prognosis is disputed. In order to clarify the prognostic role of p16 and to draw conclusions on interactions with key molecular features of prostate cancer, we studied p16 expression in a tissue microarray (TMA) with more than 12,400 prostate cancers and attached clinical, pathological, and molecular data such as ERG status and deletions of 3p13, 5q21, 6q15, and PTEN. p16 immunostaining was absent in non-neoplastic prostate cells but was found in 37 % of 9627 interpretable prostate cancers. Finding p16 expression in 58 % of ERG positive but in only 22 % of ERG negative cancers (p < 0.0001), highlights the known androgen-dependence of both genes. Significant associations between p16 upregulation and tumor phenotype or patient prognosis were strictly limited to the subset of ERG negative cancers. For example, p16 positivity increased from 15 % in Gleason ≤3 + 3 to 38 % in Gleason ≥4 + 4 cancers (p < 0.0001) and was associated with early PSA recurrence (p < 0.0001). p16 upregulation was strongly linked to deletions of PTEN (p < 0.0001), highlighting the interaction of both genes in growth control. In conclusion, p16 upregulation is a strong prognostic factor in ERG negative cancers. The strict limitation of its prognostic impact to a molecularly defined subgroup challenges the concept of molecular prognosis testing without considering molecular subtypes.
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37
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Amacher DE. A 2015 survey of established or potential epigenetic biomarkers for the accurate detection of human cancers. Biomarkers 2016; 21:387-403. [PMID: 26983778 DOI: 10.3109/1354750x.2016.1153724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Context The silencing or activation of cancer-associated genes by epigenetic mechanisms can ultimately lead to the clonal expansion of cancer cells. Objective The aim of this review is to summarize all relevant epigenetic biomarkers that have been proposed to date for the diagnosis of some prevalent human cancers. Methods A Medline search for the terms epigenetic biomarkers, human cancers, DNA methylation, histone modifications and microRNAs was performed. Results One hundred fifty-seven relevant publications were found and reviewed. Conclusion To date, a significant number of potential epigenetic cancer biomarkers of human cancer have been investigated, and some have advanced to clinical implementation.
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38
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Kamdar SN, Ho LT, Kron KJ, Isserlin R, van der Kwast T, Zlotta AR, Fleshner NE, Bader G, Bapat B. Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis. Clin Epigenetics 2016; 8:32. [PMID: 26981160 PMCID: PMC4791926 DOI: 10.1186/s13148-016-0195-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/02/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation marks by performing whole-genome next-generation sequencing in representative normal and prostate cancer-derived cell lines in order to determine functional pathways and key genes regulated by these epigenomic modifications in cancer. RESULTS Our cell line model shows disruption of hydroxymethylation distribution in cancer, with global loss and highly specific gain in promoter and CpG island regions. Significantly, we observed locus-specific retention of hydroxymethylation marks in specific intronic and intergenic regions which may play a novel role in the regulation of gene expression in critical functional pathways, such as BARD1 signaling and steroid hormone receptor signaling in cancer. We confirm a modest correlation of hydroxymethylation with expression in intragenic regions in prostate cancer, while identifying an original role for intergenic hydroxymethylation in differentially expressed regulatory pathways in cancer. We also demonstrate a successful strategy for the identification and validation of key candidate genes from differentially regulated biological pathways in prostate cancer. CONCLUSIONS Our results indicate a distinct function for aberrant hydroxymethylation within each genomic feature in cancer, suggesting a specific and complex role for the deregulation of hydroxymethylation in tumorigenesis, similar to methylation. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for methylation and hydroxymethylation marks may allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis.
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Affiliation(s)
- Shivani N. Kamdar
- />Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- />Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON Canada
| | - Linh T. Ho
- />Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Ken J. Kron
- />Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Ruth Isserlin
- />The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON Canada
| | - Theodorus van der Kwast
- />Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- />Department of Pathology, University Health Network, University of Toronto, Toronto, ON Canada
| | - Alexandre R. Zlotta
- />Department of Surgery and Surgical Oncology, Division of Urology, University Health Network, University of Toronto, Toronto, ON Canada
| | - Neil E. Fleshner
- />Division of Urology, University Health Network, Toronto, ON Canada
| | - Gary Bader
- />The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON Canada
| | - Bharati Bapat
- />Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- />Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON Canada
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39
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Biomarkers for prostate cancer: present challenges and future opportunities. Future Sci OA 2015; 2:FSO72. [PMID: 28031932 PMCID: PMC5137959 DOI: 10.4155/fso.15.72] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 01/30/2023] Open
Abstract
Prostate cancer (PCa) has variable biological potential with multiple treatment options. A more personalized approach, therefore, is needed to better define men at higher risk of developing PCa, discriminate indolent from aggressive disease and improve risk stratification after treatment by predicting the likelihood of progression. This may improve clinical decision-making regarding management, improve selection for active surveillance protocols and minimize morbidity from treatment. Discovery of new biomarkers associated with prostate carcinogenesis present an opportunity to provide patients with novel genetic signatures to better understand their risk of developing PCa and help forecast their clinical course. In this review, we examine the current literature evaluating biomarkers in PCa. We also address current limitations and present several ideas for future studies.
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40
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Chen X, McClelland M, Jia Z, Rahmatpanah FB, Sawyers A, Trent J, Duggan D, Mercola D. The identification of trans-associations between prostate cancer GWAS SNPs and RNA expression differences in tumor-adjacent stroma. Oncotarget 2015; 6:1865-73. [PMID: 25638161 PMCID: PMC4359337 DOI: 10.18632/oncotarget.2763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/17/2014] [Indexed: 11/25/2022] Open
Abstract
Here we tested the hypothesis that SNPs associated with prostate cancer risk, might differentially affect RNA expression in prostate cancer stroma. The most significant 35 SNP loci were selected from Genome Wide Association (GWA) studies of ~40,000 patients. We also selected 4030 transcripts previously associated with prostate cancer diagnosis and prognosis. eQTL analysis was carried out by a modified BAYES method to analyze the associations between the risk variants and expressed transcripts jointly in a single model. We observed 47 significant associations between eight risk variants and the expression patterns of 46 genes. This is the first study to identify associations between multiple SNPs and multiple in trans gene expression differences in cancer stroma. Potentially, a combination of SNPs and associated expression differences in prostate stroma may increase the power of risk assessment for individuals, and for cancer progression.
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Affiliation(s)
- Xin Chen
- Genomics Center, Loma Linda University, Loma Linda, California, 92354, United States of America
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, 92697, United States of America.,Department of Microbiology and Molecular Genetics, University of California, Irvine, California, 92697, United States of America
| | - Zhenyu Jia
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, 92697, United States of America.,Department of Statistics, The University of Akron, Akron, Ohio, 44325, United States of America.,Department of Family & Community Medicine, Northeast Ohio Medical University, Rootstown, Ohio, 44272, United States of America
| | - Farah B Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, 92697, United States of America
| | - Anne Sawyers
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, 92697, United States of America
| | - Jeffrey Trent
- Genetic Basis of Human Disease Division, The Translational Genomics Research Institute, Phoenix, Arizona, 85004, United States of America
| | - David Duggan
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, 85004, United States of America
| | - Dan Mercola
- Department of Pathology and Laboratory Medicine, University of California, Irvine, California, 92697, United States of America
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41
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Costa-Pinheiro P, Montezuma D, Henrique R, Jerónimo C. Diagnostic and prognostic epigenetic biomarkers in cancer. Epigenomics 2015; 7:1003-15. [PMID: 26479312 DOI: 10.2217/epi.15.56] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Growing cancer incidence and mortality worldwide demands development of accurate biomarkers to perfect detection, diagnosis, prognostication and monitoring. Urologic (prostate, bladder, kidney), lung, breast and colorectal cancers are the most common and despite major advances in their characterization, this has seldom translated into biomarkers amenable for clinical practice. Epigenetic alterations are innovative cancer biomarkers owing to stability, frequency, reversibility and accessibility in body fluids, entailing great potential of assay development to assist in patient management. Several studies identified putative epigenetic cancer biomarkers, some of which have been commercialized. However, large multicenter validation studies are required to foster translation to the clinics. Herein we review the most promising epigenetic detection, diagnostic, prognostic and predictive biomarkers for the most common cancers.
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Affiliation(s)
- Pedro Costa-Pinheiro
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal
| | - Diana Montezuma
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute - Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute - Porto, Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) - University of Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group - Research Center of Portuguese Oncology Institute - Porto (CI-IPOP), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) - University of Porto, Portugal
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42
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Labbé DP, Zadra G, Ebot EM, Mucci LA, Kantoff PW, Loda M, Brown M. Role of diet in prostate cancer: the epigenetic link. Oncogene 2015; 34:4683-91. [PMID: 25531313 PMCID: PMC4476943 DOI: 10.1038/onc.2014.422] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 12/12/2022]
Abstract
Diet is hypothesized to be a critical environmentally related risk factor for prostate cancer (PCa) development, and specific diets and dietary components can also affect PCa progression; however, the mechanisms underlying these associations remain elusive. As for a maturing organism, PCa's epigenome is plastic and evolves from the pre-neoplastic to the metastatic stage. In particular, epigenetic remodeling relies on substrates or cofactors obtained from the diet. Here we review the evidence that bridges dietary modulation to alterations in the prostate epigenome. We propose that such diet-related effects offer a mechanistic link between the impact of different diets and the course of PCa development and progression.
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Affiliation(s)
- D P Labbé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - G Zadra
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - E M Ebot
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - L A Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - P W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - M Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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43
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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44
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Sorokin I, Mian BM. Risk calculators and updated tools to select and plan a repeat biopsy for prostate cancer detection. Asian J Androl 2015; 17:864-9. [PMID: 26112489 PMCID: PMC4814963 DOI: 10.4103/1008-682x.156859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Millions of men each year are faced with a clinical suspicion of prostate cancer (PCa) but the prostate biopsy fails to detect the disease. For the urologists, how to select the appropriate candidate for repeat biopsy is a significant clinical dilemma. Traditional risk-stratification tools in this setting such as prostate-specific antigen (PSA) related markers and histopathology findings have met with limited correlation with cancer diagnosis or with significant disease. Thus, an individualized approach using predictive models such as an online risk calculator (RC) or updated biomarkers is more suitable in counseling men about their risk of harboring clinically significant prostate cancer. This review will focus on the available risk-stratification tools in the population of men with prior negative biopsies and persistent suspicion of PCa. The underlying methodology and platforms of the available tools are reviewed to better understand the development and validation of these models. The index patient is then assessed with different RCs to determine the range of heterogeneity among various RCs. This should allow the urologists to better incorporate these various risk-stratification tools into their clinical practice and improve patient counseling.
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Affiliation(s)
| | - Badar M Mian
- Department of Urology, Albany Medical College, Albany, NY, USA
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45
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Changes of protein expression in prostate cancer having lost its androgen sensitivity. Int Urol Nephrol 2015; 47:1149-54. [PMID: 25953123 DOI: 10.1007/s11255-015-0985-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE The majority of prostate cancers require androgen hormones for growth, and androgen ablation is an important part of the systemic treatment of advanced prostate cancer. Nevertheless, most of these cancers eventually relapse as they become less sensitive to androgen ablation and anti-androgen treatment. Elucidating the molecular events that are responsible for the conversion of androgen-sensitive cancers to androgen-refractory tumors may reveal new therapeutic opportunities. METHODS In the present study, we investigated nine androgen-sensitive and nine androgen-refractory prostate cancer samples to evaluate the expression levels of 10 selected proteins that have been implicated in oncogenesis and cancer progression. RESULTS Our immunohistochemical data show that three of the investigated proteins (i.e., minichromosome maintenance-2, methylguanine-DNA methyltransferase, and androgen receptor) are expressed at significantly different levels in the androgen-refractory cancer samples than in the androgen-sensitive tumors, whereas the expression levels of the seven other studied proteins (i.e., β-catenin, p27, p21, p16, Ki67, hypoxia-inducible factor 1 alpha, and geminin) are not significantly different regarding the two groups. CONCLUSIONS Our data suggest that the increased expression of minichromosome maintenance-2 and decreased expression of methylguanine-DNA methyltransferase related to androgen receptor are indicative of the androgen-refractory stage in prostate cancer. Further studies are required to determine whether these expression changes play a causative role in the transition of androgen-sensitive to androgen-refractory prostate cancer.
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46
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Basu S, Majumder S, Bhowal A, Ghosh A, Naskar S, Nandy S, Mukherjee S, Sinha RK, Basu K, Karmakar D, Banerjee S, Sengupta S. A study of molecular signals deregulating mismatch repair genes in prostate cancer compared to benign prostatic hyperplasia. PLoS One 2015; 10:e0125560. [PMID: 25938433 PMCID: PMC4418837 DOI: 10.1371/journal.pone.0125560] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/24/2015] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer is one of the leading causes of mortality among aging males. There is an unmet requirement of clinically useful biomarkers for early detection of prostate cancer to reduce the liabilities of overtreatment and accompanying morbidity. The present population-based study investigates the factors disrupting expression of multiple functionally related genes of DNA mismatch repair pathway in prostate cancer patients to identify molecular attributes distinguishing adenocarcinoma from benign hyperplasia of prostate. Gene expression was compared between tissue samples from prostate cancer and benign prostatic hyperplasia using real-time-PCR, western blot and immunohistochemistry. Assessment of genotypes of seven single-nucleotide-polymorphisms of three MMR genes was conducted using PCR-coupled RFLP and sequencing. Promoter methylation was interrogated by methylation-specific-PCR and bisulfite-sequencing. Interaction between microRNAs and MMR genes was verified by 3'UTR-based dual luciferase assays. Concurrent reduction of three MMR genes namely hMLH1, hMSH6 and hMSH2 (34-85%, P<0.05) was observed in prostate cancer tissues. hMSH6 polymorphism rs1800932(Pro92Pro) conferred a borderline protection in cancer patients (OR = 0.33, 95% CI = 0.15-0.75). Relative transcript level of hMLH1 was inversely related (r = -0.59, P<0.05) with methylation quotient of its promoter which showed a significantly higher methylation density (P = 0.008, Z = -2.649) in cancer patients. hsa-miR-155, hsa-miR-141 and hsa-miR-21 gene expressions were significantly elevated (66-85%, P<0.05) in tumor specimens and negatively correlated (r = -0.602 to -0.527, P<0.05) with that of MMR genes. hsa-miR-155 & hsa-miR-141 and hsa-miR-155 & hsa-miR-21 were demonstrated to bind to their putative seed sequences in hMLH1 and hMSH6 3'UTRs respectively. Relatively higher expression of DNA methyl-transferases (DNMT1 and DNMT3b) and HIF-1α genes (34-50%, P<0.05) were also detected in tumor tissues. This study provides statistical evidence that MMR deficiency is correlated with hypermethylation of hMLH1 promoter and upregulation of hsa-miR-155, hsa-miR-141 and hsa-miR-21 in prostate cancer. This comparative study reflects that microRNA expression level, particularly hsa-miR-155, exhibits predictive signature of prostate adenocarcinoma.
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Affiliation(s)
- Sanmitra Basu
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Subhadipa Majumder
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Ankur Bhowal
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Alip Ghosh
- Centre for Liver Research, Institute of Post-Graduate Medical Education & Research, Kolkata, West Bengal, India
| | - Sukla Naskar
- Department of Pathology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Sumit Nandy
- Department of Pathology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Subhabrata Mukherjee
- Department of Urology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Rajan Kumar Sinha
- Department of Urology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Keya Basu
- Department of Pathology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Dilip Karmakar
- Department of Urology, Calcutta National Medical College & Hospital, Kolkata, West Bengal, India
| | - Soma Banerjee
- Centre for Liver Research, Institute of Post-Graduate Medical Education & Research, Kolkata, West Bengal, India
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Abstract
Malignancies of the genitourinary system have some of the highest cancer incidence and mortality rates. For example prostate cancer is the second most common cancer in men and ovarian cancer mortality and incidence are near equal. In addition to genetic changes modulation of the epigenome is critical to cancer development and progression. In this regard epigenetic changes in DNA methylation state and DNA hypermethylation in particular has garnered a great deal of attention. While hypomethylation occurs mostly in repeated sequence such as tandem and interspersed repeats and segment duplications, hypermethylation is associated with CpG islands. Hypomethylation leads to activation of cancer-causing genes with global DNA hypomethylation being commonly associated with metastatic disease. Hypermethylation-mediated silencing of tumor suppressive genes is commonly associated with cancer development. Bioactive phytochemicals such as flavonoids present in fruits, vegetables, beverages etc. have the ability to modulate DNA methylation status and are therefore very valuable agents for cancer prevention. In this review we discuss several commonly methylated genes and flavonoids used to modulate DNA methylation in the prevention of genitourinary cancers.
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Heerboth S, Housman G, Leary M, Longacre M, Byler S, Lapinska K, Willbanks A, Sarkar S. EMT and tumor metastasis. Clin Transl Med 2015; 4:6. [PMID: 25852822 PMCID: PMC4385028 DOI: 10.1186/s40169-015-0048-3] [Citation(s) in RCA: 532] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/26/2015] [Indexed: 02/07/2023] Open
Abstract
EMT and MET comprise the processes by which cells transit between epithelial and mesenchymal states, and they play integral roles in both normal development and cancer metastasis. This article reviews these processes and the molecular pathways that contribute to them. First, we compare embryogenesis and development with cancer metastasis. We then discuss the signaling pathways and the differential expression and down-regulation of receptors in both tumor cells and stromal cells, which play a role in EMT and metastasis. We further delve into the clinical implications of EMT and MET in several types of tumors, and lastly, we discuss the role of epigenetic events that regulate EMT/MET processes. We hypothesize that reversible epigenetic events regulate both EMT and MET, and thus, also regulate the development of different types of metastatic cancers.
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Affiliation(s)
- Sarah Heerboth
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Genevieve Housman
- />School of Human Evolution and Social Change, Arizona State University, Tempe, AZ USA
| | - Meghan Leary
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | | | - Shannon Byler
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Karolina Lapinska
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Amber Willbanks
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Sibaji Sarkar
- />Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA USA
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A urine-based methylation signature for risk stratification within low-risk prostate cancer. Br J Cancer 2015; 112:802-8. [PMID: 25695483 PMCID: PMC4453961 DOI: 10.1038/bjc.2015.7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/12/2014] [Accepted: 12/21/2014] [Indexed: 11/30/2022] Open
Abstract
Background: Prostate cancer overdiagnosis and overtreatment represents a major problem. Many men with low-grade disease on biopsy are undergraded and they harbour high-grade disease at prostatectomy with no reliable way to identify these men. We used a novel urine-based 2-gene methylation test to identify prostate cancers with aggressive features. Methods: Following a proof of concept study in 100 post-radical prostatectomy tissue samples, urine samples were tested from 665 men at multiple U.S. centers undergoing prostate needle biopsy for elevated prostate-specific antigen (2–10 ng ml−1). A prediction model was then developed from a combination of clinical factors and the urine-based markers. It was then prospectively tested for accurate prediction of adverse disease (surgical Gleason score ⩾7 and/or a pathological stage ⩾T3a) using urine from a separate cohort of 96 men before radical prostatectomy. Results: Among pre-prostatectomy men with a biopsy Gleason score <7, 41% had adverse disease of which 100% were correctly identified by the test with a negative predictive value of 100% (95% confidence interval, 86–100%). Conclusions: This urine-based test accurately identifies men with clinical low-risk disease who do not have adverse pathology in their prostates and would be excellent candidates for active surveillance.
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50
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Global DNA hypomethylation in prostate cancer development and progression: a systematic review. Prostate Cancer Prostatic Dis 2014; 18:1-12. [PMID: 25384337 DOI: 10.1038/pcan.2014.45] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/10/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND The role of global DNA methylation in prostate cancer (PCa) remains largely unknown. Our aim was to summarize evidence on the role of global DNA hypomethylation in PCa development and progression. METHODS We searched PubMed through December 2013 for all studies containing information on global methylation levels in PCa tissue and at least one non-tumor comparison tissue and/or studies reporting association between global methylation levels in PCa tissue and survival, disease recurrence or at least one clinicopathological prognostic factor. We summarized results using non-parametric comparisons and P-value summary methods. RESULTS We included 15 studies in the review: 6 studies with both diagnostic and prognostic information, 5 studies with only diagnostic information and 4 studies with only prognostic information. Quantitative meta-analysis was not possible because of the large heterogeneity in molecular techniques, types of tissues analyzed, aims and study designs. Summary statistical tests showed association of DNA hypomethylation with PCa diagnosis (P<0.006) and prognosis (P<0.001). Restriction to studies assessing 5-methylcytosine or long interspersed nucleotide element-1 revealed results in the same direction. Analyses restricted to specific clinicopathological features showed association with the presence of metastasis and tumor stage in all tests with P<0.03, and no association with Gleason score (all tests P>0.1 except for the weighted Z-test, P=0.05). CONCLUSION DNA hypomethylation was associated with PCa development and progression. However, due to the heterogeneity and small sample sizes of the included studies, along with the possibility of publication bias, this association requires additional assessment.
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