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Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [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: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
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Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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Namous H, Braz CU, Wang Y, Khatib H. The Activation of Protamine 1 Using Epigenome Editing Decreases the Proliferation of Tumorigenic Cells. Front Genome Ed 2022; 4:844904. [PMID: 35783678 PMCID: PMC9244402 DOI: 10.3389/fgeed.2022.844904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methyltransferases (DNMT) and histone deacetylases (HDAC) inhibitors are used as cancer epigenome drugs. However, these epigenetic drugs lack targeting specificity and could risk inducing genome instability and the expression of oncogenes. Therefore, there is a need to develop new therapeutic strategies where specific cancer genes can be targeted for silencing or activation. The CRISPR/dCas9 system represents a promising, powerful therapeutic tool because of its simplicity and specificity. Protamine 1 (PRM1) is exclusively expressed in sperm and has a vital role in the tight packaging of DNA, thus inducing transcriptional silencing in sperm cells. We hypothesized that the activation of the PRM1 gene in tumorigenic cells would lead to DNA condensation and reduce the proliferation of these cells. To test our hypothesis, we transfected human embryonic kidney cells 293T with a dCas9-P300 plasmid that adds acetyl groups to the promoter region of PRM1 via specific gRNAs plasmids. RNA-Seq analysis of transfected cells revealed high specificity of targeted gene activation. PRM1 expression resulted in a significant decrease in cell proliferation as measured by the BrdU ELISA assay. To confirm that the activation of PRM1 was due to acetyl groups deposited to H3K27, a ChIP-qPCR was performed. The acetylation of the PRM1 promoter region targeted by dCas9-p300 in transfected cells was higher than that of the control cells. Interestingly, the targeted promoter region for acetylation showed reduced DNA methylation. These findings demonstrate the efficacy of epigenome editing in activating PRM1 in non-expressing tumorigenic cells, which could be used as a promising therapeutic strategy in cancer treatment.
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Ishizaki T, Yamazaki J, Meagawa S, Yokoyama N, Aoshima K, Takiguchi M, Kimura T. Long interspersed nucleotide element-1 hypomethylation in canine malignant mucosal melanoma. Vet Comp Oncol 2020; 18:854-860. [PMID: 32187810 DOI: 10.1111/vco.12591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 01/01/2023]
Abstract
Canine malignant melanoma is a common cancer with a high mortality rate and is a clinically important disease. DNA methylation has been considered to be a potential tumorigenic mechanism through aberrant DNA methylation at promoter region which represses gene transcription. Global hypomethylation could also facilitate chromosome instability. There are few reports regarding DNA methylation in canine malignant melanoma; therefore, the purpose of this study was to examine DNA methylation status of long interspersed nucleotide element-1 (LINE-1) to be a surrogate marker of genome-wide methylation changes in this disease. We measured levels of DNA methylation of two adjacent cytosine-guanine sites on CpG island (CGI) at the putative promoter of canine LINE-1 sequence by bisulphite-pyrosequencing in 41 canine melanoma patient samples as well as six cell lines compared with normal mucosae. The survival rates were obtained from owners or medical records. We found DNA methylation levels of LINE-1 in normal mucosae were methylated. Interestingly, both melanoma cell lines and clinical melanoma samples showed remarkable hypomethylation. In addition, patients with lower LINE-1 methylation showed worse prognosis than those with higher LINE-1 methylation, though the difference did not reach statistical significance (P = .09). Here, we demonstrate that hypomethylation of LINE-1 is an epigenetically aberrant feature in canine melanoma with possible prognostic value.
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Affiliation(s)
- Teita Ishizaki
- Laboratory of Comparative Pathology, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Jumpei Yamazaki
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Shinji Meagawa
- Department of Pediatrics, MD Anderson Cancer Center, Houston, Texas, USA
| | - Nozomu Yokoyama
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Keisuke Aoshima
- Laboratory of Comparative Pathology, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi Kimura
- Laboratory of Comparative Pathology, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
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Sarkisjan D, Julsing JR, El Hassouni B, Honeywell RJ, Kathmann I, Matherly LH, Lee YB, Kim DJ, Peters GJ. RX-3117 (Fluorocyclopentenyl-Cytosine)-Mediated Down-Regulation of DNA Methyltransferase 1 Leads to Protein Expression of Tumor-Suppressor Genes and Increased Functionality of the Proton-Coupled Folate Carrier. Int J Mol Sci 2020; 21:ijms21082717. [PMID: 32295203 PMCID: PMC7215832 DOI: 10.3390/ijms21082717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/31/2020] [Accepted: 04/10/2020] [Indexed: 12/31/2022] Open
Abstract
(1) Background: RX-3117 (fluorocyclopentenyl-cytosine) is a cytidine analog that inhibits DNA methyltransferase 1 (DNMT1). We investigated the mechanism and potential of RX-3117 as a demethylating agent in several in vitro models. (2) Methods: we used western blotting to measure expression of several proteins known to be down-regulated by DNA methylation: O6-methylguanine-DNA methyltransferase (MGMT) and the tumor-suppressor genes, p16 and E-cadherin. Transport of methotrexate (MTX) mediated by the proton-coupled folate transporter (PCFT) was used as a functional assay. (3) Results: RX-3117 treatment decreased total DNA-cytosine-methylation in A549 non-small cell lung cancer (NSCLC) cells, and induced protein expression of MGMT, p16 and E-cadherin in A549 and SW1573 NSCLC cells. Leukemic CCRF-CEM cells and the MTX-resistant variant (CEM/MTX, with a deficient reduced folate carrier) have a very low expression of PCFT due to promoter hypermethylation. In CEM/MTX cells, pre-treatment with RX-3117 increased PCFT-mediated MTX uptake 8-fold, and in CEM cells 4-fold. With the reference hypomethylating agent 5-aza-2′-deoxycytidine similar values were obtained. RX-3117 also increased PCFT gene expression and PCFT protein. (4) Conclusion: RX-3117 down-regulates DNMT1, leading to hypomethylation of DNA. From the increased protein expression of tumor-suppressor genes and functional activation of PCFT, we concluded that RX-3117 might have induced hypomethylation of the promotor.
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Affiliation(s)
- Dzjemma Sarkisjan
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Joris R. Julsing
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Btissame El Hassouni
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Richard J. Honeywell
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Ietje Kathmann
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
| | - Larry H. Matherly
- Department of Oncology, Wayne State University School of Medicine, Detroit, and Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201-1976, USA;
| | - Young B. Lee
- Rexahn Pharmaceuticals, Inc., Rockville, MD 20850, USA; (Y.B.L.); (D.J.K.)
| | - Deog J. Kim
- Rexahn Pharmaceuticals, Inc., Rockville, MD 20850, USA; (Y.B.L.); (D.J.K.)
| | - Godefridus J. Peters
- Laboratory Medical Oncology, Amsterdam UMC, location VU University Medical Center, 1081 HV Amsterdam, The Netherlands; (D.S.); (J.R.J.); (B.E.H.); (R.J.H.); (I.K.)
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdansk, Poland
- Correspondence: ; Tel.: +31-20-4442633
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Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:51-60. [DOI: 10.1016/j.mrrev.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]
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Chen M, Nie J, Liu Y, Li X, Zhang Y, Brock MV, Feng K, Wu Z, Li X, Shi L, Li S, Guo M, Mei Q, Han W. Phase Ib/II study of safety and efficacy of low-dose decitabine-primed chemoimmunotherapy in patients with drug-resistant relapsed/refractory alimentary tract cancer. Int J Cancer 2018; 143:1530-1540. [PMID: 29663379 PMCID: PMC6099263 DOI: 10.1002/ijc.31531] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/19/2018] [Accepted: 03/29/2018] [Indexed: 12/15/2022]
Abstract
The pressing need for improved therapeutic outcomes provides a good rationale for identifying effective strategies for alimentary tract (AT) cancer treatment. The potential re-sensitivity property to chemo- and immunotherapy of low-dose decitabine has been evident both preclinically and in previous phase I trials. We conducted a phase Ib/II trial evaluating low-dose decitabine-primed chemoimmunotherapy in patients with drug-resistant relapsed/refractory (R/R) esophageal, gastric or colorectal cancers. Forty-five patients received either the 5-day decitabine treatment with subsequent readministration of the previously resistant chemotherapy (decitabine-primed chemotherapy, D-C cohort) or the aforementioned regimen followed by cytokine-induced killer cells therapy (D-C and cytokine-induced killer [CIK] cell treatment, D-C + CIK cohort) based on their treatment history. Grade 3 to 4 adverse events (AEs) were reported in 11 (24.4%) of 45 patients. All AEs were controllable, and no patient experienced a treatment-related death. The objective response rate (ORR) and disease control rate (DCR) were 24.44% and 82.22%, respectively, including two patients who achieved durable complete responses. Clinical response could be associated with treatment-free interval and initial surgical resection history. ORR and DCR reached 28% and 92%, respectively, in the D-C + CIK cohort. Consistently, the progression-free survival (PFS) of the D-C + CIK cohort compared favorably to the best PFS of the pre-resistant unprimed therapy (p = 0.0001). The toxicity and ORRs exhibited were non-significantly different between cancer types and treatment cohort. The safety and efficacy of decitabine-primed re-sensitization to chemoimmunotherapy is attractive and promising. These data warrant further large-scale evaluation of drug-resistant R/R AT cancer patients with advanced stage disease.
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MESH Headings
- Adenocarcinoma/drug therapy
- Adenocarcinoma/immunology
- Adenocarcinoma/secondary
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/secondary
- Cells, Cultured
- Cohort Studies
- Cytokine-Induced Killer Cells/drug effects
- Cytokine-Induced Killer Cells/immunology
- Cytokine-Induced Killer Cells/pathology
- Decitabine/therapeutic use
- Digestive System/drug effects
- Digestive System/immunology
- Digestive System/pathology
- Digestive System Neoplasms/drug therapy
- Digestive System Neoplasms/immunology
- Digestive System Neoplasms/pathology
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm
- Female
- Follow-Up Studies
- Humans
- Immunotherapy
- Lymphatic Metastasis
- Male
- Middle Aged
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/immunology
- Neoplasm Recurrence, Local/pathology
- Prognosis
- Salvage Therapy
- Survival Rate
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Affiliation(s)
- Meixia Chen
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Jing Nie
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Yang Liu
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Xiang Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Yan Zhang
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | | | - Kaichao Feng
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Zhiqiang Wu
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Xiaolei Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Lu Shi
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Suxia Li
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Mingzhou Guo
- Department of Gastroenterology and HepatologyChinese PLA General HospitalBeijingPeople's Republic of China
| | - Qian Mei
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Weidong Han
- Department of Molecular Biology and Bio‐therapeuticInstitute of Basic Medicine, Chinese PLA General HospitalBeijingPeople's Republic of China
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Crabb S, Danson SJ, Catto JWF, McDowell C, Lowder JN, Caddy J, Dunkley D, Rajaram J, Ellis D, Hill S, Hathorn D, Whitehead A, Kalevras M, Huddart R, Griffiths G. SPIRE - combining SGI-110 with cisplatin and gemcitabine chemotherapy for solid malignancies including bladder cancer: study protocol for a phase Ib/randomised IIa open label clinical trial. Trials 2018; 19:216. [PMID: 29615077 PMCID: PMC5883402 DOI: 10.1186/s13063-018-2586-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Urothelial bladder cancer (UBC) accounts for 10,000 new diagnoses and 5000 deaths annually in the UK (Cancer Research UK, http://www.cancerresearchuk.org/health-professional/cancer-statistics/statistics-by-cancer-type/bladder-cancer , Cancer Research UK, Accessed 26 Mar 2018). Cisplatin-based chemotherapy is standard of care therapy for UBC for both palliative first-line treatment of advanced/metastatic disease and radical neoadjuvant treatment of localised muscle invasive bladder cancer. However, cisplatin resistance remains a critical cause of treatment failure and a barrier to therapeutic advance in UBC. Based on supportive pre-clinical data, we hypothesised that DNA methyltransferase inhibition would circumvent cisplatin resistance in UBC and potentially other cancers. METHODS The addition of SGI-110 (guadecitabine, a DNA methyltransferase inhibitor) to conventional doublet therapy of gemcitabine and cisplatin (GC) is being tested within the phase Ib/IIa SPIRE clinical trial. SPIRE incorporates an initial, modified rolling six-dose escalation phase Ib design of up to 36 patients with advanced solid tumours followed by a 20-patient open-label randomised controlled dose expansion phase IIa component as neoadjuvant treatment for UBC. Patients are being recruited from UK secondary care sites. The dose escalation phase will determine a recommended phase II dose (RP2D, primary endpoint) of SGI-110, by subcutaneous injection, on days 1-5 for combination with GC at conventional doses (cisplatin 70 mg/m2, IV infusion, day 8; gemcitabine 1000 mg/m2, IV infusion, days 8 and 15) in every 21-day cycle. In the dose expansion phase, patients will be randomised 1:1 to GC with or without SGI-110 at the proposed RP2D. Secondary endpoints will include toxicity profiles, SGI-110 pharmacokinetics and pharmacodynamic biomarkers, and pathological complete response rates in the dose expansion phase. Analyses will not be powered for formal statistical comparisons and descriptive statistics will be used to describe rates of toxicity, efficacy and translational endpoints by treatment arm. DISCUSSION SPIRE will provide evidence for whether SGI-110 in combination with GC chemotherapy is safe and biologically effective prior to future phase II/III trials as a neoadjuvant therapy for UBC and potentially in other cancers treated with GC. TRIAL REGISTRATION EudraCT Number: 2015-004062-29 (entered Dec 7, 2015) ISRCTN registry number: 16332228 (registered on Feb 3, 2016).
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Affiliation(s)
- Simon Crabb
- Southampton Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Sarah J. Danson
- Academic Unit of Clinical Oncology, Weston Park Hospital, University of Sheffield, Sheffield, UK
| | - James W. F. Catto
- Academic Urology Unit, The Medical school, University of Sheffield, Sheffield, UK
| | | | | | - Joshua Caddy
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Denise Dunkley
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Jessica Rajaram
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Deborah Ellis
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Stephanie Hill
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - David Hathorn
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Amy Whitehead
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Mihalis Kalevras
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | | | - Gareth Griffiths
- Southampton Clinical Trials Unit, Centre for Cancer Immunology, University of Southampton, Southampton, UK
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Molokie R, Lavelle D, Gowhari M, Pacini M, Krauz L, Hassan J, Ibanez V, Ruiz MA, Ng KP, Woost P, Radivoyevitch T, Pacelli D, Fada S, Rump M, Hsieh M, Tisdale JF, Jacobberger J, Phelps M, Engel JD, Saraf S, Hsu LL, Gordeuk V, DeSimone J, Saunthararajah Y. Oral tetrahydrouridine and decitabine for non-cytotoxic epigenetic gene regulation in sickle cell disease: A randomized phase 1 study. PLoS Med 2017; 14:e1002382. [PMID: 28880867 PMCID: PMC5589090 DOI: 10.1371/journal.pmed.1002382] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Sickle cell disease (SCD), a congenital hemolytic anemia that exacts terrible global morbidity and mortality, is driven by polymerization of mutated sickle hemoglobin (HbS) in red blood cells (RBCs). Fetal hemoglobin (HbF) interferes with this polymerization, but HbF is epigenetically silenced from infancy onward by DNA methyltransferase 1 (DNMT1). METHODS AND FINDINGS To pharmacologically re-induce HbF by DNMT1 inhibition, this first-in-human clinical trial (NCT01685515) combined 2 small molecules-decitabine to deplete DNMT1 and tetrahydrouridine (THU) to inhibit cytidine deaminase (CDA), the enzyme that otherwise rapidly deaminates/inactivates decitabine, severely limiting its half-life, tissue distribution, and oral bioavailability. Oral decitabine doses, administered after oral THU 10 mg/kg, were escalated from a very low starting level (0.01, 0.02, 0.04, 0.08, or 0.16 mg/kg) to identify minimal doses active in depleting DNMT1 without cytotoxicity. Patients were SCD adults at risk of early death despite standard-of-care, randomized 3:2 to THU-decitabine versus placebo in 5 cohorts of 5 patients treated 2X/week for 8 weeks, with 4 weeks of follow-up. The primary endpoint was ≥ grade 3 non-hematologic toxicity. This endpoint was not triggered, and adverse events (AEs) were not significantly different in THU-decitabine-versus placebo-treated patients. At the decitabine 0.16 mg/kg dose, plasma concentrations peaked at approximately 50 nM (Cmax) and remained elevated for several hours. This dose decreased DNMT1 protein in peripheral blood mononuclear cells by >75% and repetitive element CpG methylation by approximately 10%, and increased HbF by 4%-9% (P < 0.001), doubling fetal hemoglobin-enriched red blood cells (F-cells) up to approximately 80% of total RBCs. Total hemoglobin increased by 1.2-1.9 g/dL (P = 0.01) as reticulocytes simultaneously decreased; that is, better quality and efficiency of HbF-enriched erythropoiesis elevated hemoglobin using fewer reticulocytes. Also indicating better RBC quality, biomarkers of hemolysis, thrombophilia, and inflammation (LDH, bilirubin, D-dimer, C-reactive protein [CRP]) improved. As expected with non-cytotoxic DNMT1-depletion, platelets increased and neutrophils concurrently decreased, but not to an extent requiring treatment holds. As an early phase study, limitations include small patient numbers at each dose level and narrow capacity to evaluate clinical benefits. CONCLUSION Administration of oral THU-decitabine to patients with SCD was safe in this study and, by targeting DNMT1, upregulated HbF in RBCs. Further studies should investigate clinical benefits and potential harms not identified to date. TRIAL REGISTRATION ClinicalTrials.gov, NCT01685515.
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Affiliation(s)
- Robert Molokie
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Donald Lavelle
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Michel Gowhari
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Michael Pacini
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Lani Krauz
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Johara Hassan
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Vinzon Ibanez
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Maria A. Ruiz
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Kwok Peng Ng
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Philip Woost
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Daisy Pacelli
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Sherry Fada
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Matthew Rump
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Matthew Hsieh
- Molecular and Clinical Hematology Section, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John F. Tisdale
- Molecular and Clinical Hematology Section, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James Jacobberger
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mitch Phelps
- College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - James Douglas Engel
- Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Santhosh Saraf
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Lewis L. Hsu
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Victor Gordeuk
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Joseph DeSimone
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
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10
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Ponomaryova AA, Cherdyntseva NV, Bondar AA, Dobrodeev AY, Zavyalov AA, Tuzikov SA, Vlassov VV, Choinzonov EL, Laktionov PP, Rykova EY. Dynamics of LINE-1 retrotransposon methylation levels in circulating DNA from lung cancer patients undergoing antitumor therapy. Mol Biol 2017. [DOI: 10.1134/s0026893317040148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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LINE-1 hypomethylation is not a common event in preneoplastic stages of gastric carcinogenesis. Sci Rep 2017; 7:4828. [PMID: 28684753 PMCID: PMC5500474 DOI: 10.1038/s41598-017-05143-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/16/2017] [Indexed: 02/07/2023] Open
Abstract
LINE-1 hypomethylation is widely accepted as marker for global genomic DNA hypomethylation, which is a frequent event in cancer. The aim of the study was to evaluate LINE-1 methylation status at different stages of gastric carcinogenesis and evaluate its prognostic potential in clinical settings. LINE-1 methylation was analyzed in 267 tissue samples by bisulfite pyrosequencing including primary colorectal cancer tissues (T-CRC) with corresponding adjacent colon mucosa (N-CRC), gastric cancer tissues (T-GC) with corresponding gastric mucosa (N-GC), normal gastric tissues (N), chronic non-atrophic and atrophic gastritis (CG). LINE-1 methylation level was lower in both T-GC and T-CRC when compared to paired adjacent tissues. No difference was observed for LINE-1 methylation status between patients with normal gastric mucosa, CG and N-GC. LINE-1 methylation in T-GC but not N-GC tended to correlate with age. Subgroup stratification analysis did not reveal significant differences in LINE-1 methylation status according to tumor stage, anatomical location, histological subtype, differentiation grade. We observed similar overall survival data between patients with high or low LINE-1 levels. In summary, LINE-1 hypomethylation is a characteristic feature in GC but not very common in early preneoplastic stages of gastric carcinogenesis. Prognostic role of LINE-1 hypomethylation in GC patients could not be confirmed in this cohort.
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12
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Min J, Choi B, Han TS, Lee HJ, Kong SH, Suh YS, Kim TH, Choe HN, Kim WH, Hur K, Yang HK. Methylation Levels of LINE-1 As a Useful Marker for Venous Invasion in Both FFPE and Frozen Tumor Tissues of Gastric Cancer. Mol Cells 2017; 40:346-354. [PMID: 28535662 PMCID: PMC5463043 DOI: 10.14348/molcells.2017.0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) is a retrotransposon that contains a CpG island in its 5'-untranslated region. The CpG island of LINE-1 is often heavily methylated in normal somatic cells, which is associated with poor prognosis in various cancers. DNA methylation can differ between formalin-fixed paraffin-embedded (FFPE) and frozen tissues. Therefore, this study aimed to compare the LINE-1 methylation status between the two tissue-storage conditions in gastric cancer (GC) clinical samples and to evaluate whether LINE-1 can be used as an independent prognostic marker for each tissue-storage type. We analyzed four CpG sites of LINE-1 and examined the methylation levels at these sites in 25 FFPE and 41 frozen GC tissues by quantitative bisulfite pyrosequencing. The LINE-1 methylation status was significantly different between the FFPE and frozen GC tissues (p < 0.001). We further analyzed the clinicopathological features in the two groups separately. In the frozen GC tissues, LINE-1 was significantly hypomethylated in GC tissues compared to their corresponding normal gastric mucosa tissues (p < 0.001), and its methylation status was associated with gender, differentiation state, and lymphatic and venous invasion of GC. In the FFPE GC tissues, the methylation levels of LINE-1 differed according to tumor location and venous invasion of GC. In conclusion, LINE-1 can be used as a useful methylation marker for venous invasion in both FFPE and frozen tumor tissues of GC.
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Affiliation(s)
- Jimin Min
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Boram Choi
- Department of Life Science, Ewha Womans University, Seoul 03760,
Korea
| | - Tae-Su Han
- Biotherapeutics Translational Research Center, Division of Biomedical Science, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141,
Korea
| | - Hyuk-Joon Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Tae-Han Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Hwi-Nyeong Choe
- Department of Nursing, Seoul National University Hospital, Seoul 03080,
Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080,
Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944,
Korea
| | - Han-Kwang Yang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080,
Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080,
Korea
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13
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Abstract
Next-generation sequencing has revealed that more than 50% of human cancers harbour mutations in enzymes that are involved in chromatin organization. Tumour cells not only are activated by genetic and epigenetic alterations, but also routinely use epigenetic processes to ensure their escape from chemotherapy and host immune surveillance. Hence, a growing emphasis of recent drug discovery efforts has been on targeting the epigenome, including DNA methylation and histone modifications, with several new drugs being tested and some already approved by the US Food and Drug Administration (FDA). The future will see the increasing success of combining epigenetic drugs with other therapies. As epigenetic drugs target the epigenome as a whole, these true 'genomic medicines' lessen the need for precision approaches to individualized therapies.
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Affiliation(s)
- Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Stephen Baylin
- Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21287, USA
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14
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Chang HB, Zou JZ, He C, Zeng R, Li YY, Ma FF, Liu Z, Ye H, Wu JX. Association between Long Interspersed Nuclear Element-1 Methylation and Relative Telomere Length in Wilms Tumor. Chin Med J (Engl) 2016; 128:3055-61. [PMID: 26608986 PMCID: PMC4795265 DOI: 10.4103/0366-6999.169071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background: DNA hypomethylation of long interspersed nuclear elements-1 (LINEs-1) occurs during carcinogenesis, whereas information addressing LINE-1 methylation in Wilms tumor (WT) is limited. The main purpose of our study was to quantify LINE-1 methylation levels and evaluate their relationship with relative telomere length (TL) in WT. Methods: We investigated LINE-1 methylation and relative TL using bisulfite-polymerase chain reaction (PCR) pyrosequencing and quantitative PCR, respectively, in 20 WT tissues, 10 normal kidney tissues and a WT cell line. Significant changes were analyzed by t-tests. Results: LINE-1 methylation levels were significantly lower (P < 0.05) and relative TLs were significantly shorter (P < 0.05) in WT compared with normal kidney. There was a significant positive relationship between LINE-1 methylation and relative TL in WT (r = 0.671, P = 0.001). LINE-1 Methylation levels were significantly associated with global DNA methylation (r = 0.332, P < 0.01). In addition, relative TL was shortened and LINE-1 methylation was decreased in a WT cell line treated with the hypomethylating agent 5-aza-2′-deoxycytidine compared with untreated WT cell line. Conclusion: These results suggest that LINE-1 hypomethylation is common and may be linked to telomere shortening in WT.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian-Xin Wu
- Department of Biochemistry, Capital Institute of Pediatrics, Beijing 100020, China
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15
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The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation. Autoimmun Rev 2016; 15:684-9. [DOI: 10.1016/j.autrev.2016.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 02/28/2016] [Indexed: 01/21/2023]
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16
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van den Oord EJCG, Clark SL, Xie LY, Shabalin AA, Dozmorov MG, Kumar G, Vladimirov VI, Magnusson PKE, Aberg KA. A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue. Schizophr Bull 2016; 42:1018-26. [PMID: 26656881 PMCID: PMC4903046 DOI: 10.1093/schbul/sbv182] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Mutated CpG sites (CpG-SNPs) are potential hotspots for human diseases because in addition to the sequence variation they may show individual differences in DNA methylation. We performed methylome-wide association studies (MWAS) to test whether methylation differences at those sites were associated with schizophrenia. We assayed all common CpG-SNPs with methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) using DNA extracted from 1408 blood samples and 66 postmortem brain samples (BA10) of schizophrenia cases and controls. Seven CpG-SNPs passed our FDR threshold of 0.1 in the blood MWAS. Of the CpG-SNPs methylated in brain, 94% were also methylated in blood. This significantly exceeded the 46.2% overlap expected by chance (P-value < 1.0×10(-8)) and justified replicating findings from blood in brain tissue. CpG-SNP rs3796293 in IL1RAP replicated (P-value = .003) with the same direction of effects. This site was further validated through targeted bisulfite pyrosequencing in 736 independent case-control blood samples (P-value < 9.5×10(-4)). Our top result in the brain MWAS (P-value = 8.8×10(-7)) was CpG-SNP rs16872141 located in the potential promoter of ENC1. Overall, our results suggested that CpG-SNP methylation may reflect effects of environmental insults and can provide biomarkers in blood that could potentially improve disease management.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA;
| | - Shaunna L Clark
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA
| | - Lin Ying Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA
| | - Gaurav Kumar
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA
| | - Vladimir I Vladimirov
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA; Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA; Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA
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17
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Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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18
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Desjobert C, El Maï M, Gérard-Hirne T, Guianvarc'h D, Carrier A, Pottier C, Arimondo PB, Riond J. Combined analysis of DNA methylation and cell cycle in cancer cells. Epigenetics 2015; 10:82-91. [PMID: 25531272 DOI: 10.1080/15592294.2014.995542] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
DNA methylation is a chemical modification of DNA involved in the regulation of gene expression by controlling the access to the DNA sequence. It is the most stable epigenetic mark and is widely studied for its role in major biological processes. Aberrant DNA methylation is observed in various pathologies, such as cancer. Therefore, there is a great interest in analyzing subtle changes in DNA methylation induced by biological processes or upon drug treatments. Here, we developed an improved methodology based on flow cytometry to measure variations of DNA methylation level in melanoma and leukemia cells. The accuracy of DNA methylation quantification was validated with LC-ESI mass spectrometry analysis. The new protocol was used to detect small variations of cytosine methylation occurring in individual cells during their cell cycle and those induced by the demethylating agent 5-aza-2'-deoxycytidine (5AzadC). Kinetic experiments confirmed that inheritance of DNA methylation occurs efficiently in S phase and revealed a short delay between DNA replication and completion of cytosine methylation. In addition, this study suggests that the uncoupling of 5AzadC effects on DNA demethylation and cell proliferation might be related to the duration of the DNA replication phase.
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Affiliation(s)
- Cécile Desjobert
- a CNRS - Pierre Fabre USR 3388 ETaC; CRDPF BP12562 ; Toulouse , France
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19
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Byun HM, Barrow TM. Analysis of pollutant-induced changes in mitochondrial DNA methylation. Methods Mol Biol 2015; 1265:271-83. [PMID: 25634281 DOI: 10.1007/978-1-4939-2288-8_19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
There is increasing evidence that exposure to air pollutants is associated with human disease and may act through epigenetic modification of the nuclear genome, but there have been few publications describing their impact upon the mitochondrial genome. Mitochondrial DNA may be more susceptible to pollutant-induced changes via increased oxidative stress in the cell, and therefore this field of research is of growing interest. Many techniques employed to study DNA methylation of the nuclear genome are also applicable to mitochondrial epigenetic studies. In this chapter, we describe a protocol for the isolation of mitochondrial DNA from peripheral blood samples and the analysis of 5-methylcytosine content by bisulfite pyrosequencing.
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Affiliation(s)
- Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA,
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20
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Odunsi K, Matsuzaki J, James SR, Mhawech-Fauceglia P, Tsuji T, Miller A, Zhang W, Akers SN, Griffiths EA, Miliotto A, Beck A, Batt CA, Ritter G, Lele S, Gnjatic S, Karpf AR. Epigenetic potentiation of NY-ESO-1 vaccine therapy in human ovarian cancer. Cancer Immunol Res 2014; 2:37-49. [PMID: 24535937 DOI: 10.1158/2326-6066.cir-13-0126] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The cancer-testis/cancer-germline antigen NY-ESO-1 is a vaccine target in epithelial ovarian cancer (EOC), but its limited expression is a barrier to vaccine efficacy. As NY-ESO-1 is regulated by DNA methylation, we hypothesized that DNA methyltransferase (DNMT) inhibitors may augment NY-ESO-1 vaccine therapy. In agreement, global DNA hypomethylation in EOC was associated with the presence of circulating antibodies to NY-ESO-1. Pre-clinical studies using EOC cell lines showed that decitabine treatment enhanced both NY-ESO-1 expression and NY-ESO-1-specific CTL-mediated responses. Based on these observations, we performed a phase I dose-escalation trial of decitabine, as an addition to NY-ESO-1 vaccine and doxorubicin liposome (doxorubicin) chemotherapy, in 12 patients with relapsed EOC. The regimen was safe, with limited and clinically manageable toxicities. Both global and promoter-specific DNA hypomethylation occurred in blood and circulating DNAs, the latter of which may reflect tumor cell responses. Increased NY-ESO-1 serum antibodies and T cell responses were observed in the majority of patients, and antibody spreading to additional tumor antigens was also observed. Finally, disease stabilization or partial clinical response occurred in 6/10 evaluable patients. Based on these encouraging results, evaluation of similar combinatorial chemo-immunotherapy regimens in EOC and other tumor types is warranted.
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Affiliation(s)
- Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Junko Matsuzaki
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Smitha R James
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | | | - Takemasa Tsuji
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Austin Miller
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Wa Zhang
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68198
| | - Stacey N Akers
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | | | - Anthony Miliotto
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Amy Beck
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Carl A Batt
- Department of Food Science, Cornell University, Ithaca, NY, 14853
| | - Gerd Ritter
- Ludwig Institute for Cancer Research, NY Branch at Memorial Sloan Kettering, New York, NY, 10021
| | - Shashikant Lele
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263
| | - Sacha Gnjatic
- Tisch Cancer Institute, Mount Sinai School of Medicine, Omaha, NE, 68198
| | - Adam R Karpf
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263 ; Eppley Institute, University of Nebraska Medical Center, Omaha, NE, 68198
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21
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Aberg KA, McClay JL, Nerella S, Clark S, Kumar G, Chen W, Khachane AN, Xie L, Hudson A, Gao G, Harada A, Hultman CM, Sullivan PF, Magnusson PKE, van den Oord EJCG. Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry 2014; 71:255-64. [PMID: 24402055 PMCID: PMC4331014 DOI: 10.1001/jamapsychiatry.2013.3730] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
IMPORTANCE Epigenetic studies present unique opportunities to advance schizophrenia research because they can potentially account for many of its clinical features and suggest novel strategies to improve disease management. OBJECTIVE To identify schizophrenia DNA methylation biomarkers in blood. DESIGN, SETTING, AND PARTICIPANTS The sample consisted of 759 schizophrenia cases and 738 controls (N = 1497) collected in Sweden. We used methyl-CpG-binding domain protein-enriched genome sequencing of the methylated genomic fraction, followed by next-generation DNA sequencing. We obtained a mean (SD) number of 68 (26.8) million reads per sample. This massive data set was processed using a specifically designed data analysis pipeline. Critical top findings from our methylome-wide association study (MWAS) were replicated in independent case-control participants using targeted pyrosequencing of bisulfite-converted DNA. MAIN OUTCOMES AND MEASURES Status of schizophrenia cases and controls. RESULTS Our MWAS suggested a considerable number of effects, with 25 sites passing the highly conservative Bonferroni correction and 139 sites significant at a false discovery rate of 0.01. Our top MWAS finding, which was located in FAM63B, replicated with P = 2.3 × 10-10. It was part of the networks regulated by microRNA that can be linked to neuronal differentiation and dopaminergic gene expression. Many other top MWAS results could be linked to hypoxia and, to a lesser extent, infection, suggesting that a record of pathogenic events may be preserved in the methylome. Our findings also implicated a site in RELN, one of the most frequently studied candidates in methylation studies of schizophrenia. CONCLUSIONS AND RELEVANCE To our knowledge, the present study is one of the first MWASs of disease with a large sample size using a technology that provides good coverage of methylation sites across the genome. Our results demonstrated one of the unique features of methylation studies that can capture signatures of environmental insults in peripheral tissues. Our MWAS suggested testable hypotheses about disease mechanisms and yielded biomarkers that can potentially be used to improve disease management.
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Affiliation(s)
- Karolina A. Aberg
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Joseph L. McClay
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Srilaxmi Nerella
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Shaunna Clark
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Gaurav Kumar
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Wenan Chen
- Department of Biostatistics, Virginia Commonwealth University, Richmond
| | - Amit N. Khachane
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Linying Xie
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Alexandra Hudson
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Guimin Gao
- Department of Biostatistics, Virginia Commonwealth University, Richmond
| | - Aki Harada
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden4Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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22
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Clinical implications of the LINE-1 methylation levels in patients with gastrointestinal cancer. Surg Today 2013; 44:1807-16. [DOI: 10.1007/s00595-013-0763-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/30/2013] [Indexed: 12/17/2022]
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23
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Grövdal M, Karimi M, Tobiasson M, Reinius L, Jansson M, Ekwall K, Ungerstedt J, Kere J, Greco D, Hellström-Lindberg E. Azacitidine induces profound genome-wide hypomethylation in primary myelodysplastic bone marrow cultures but may also reduce histone acetylation. Leukemia 2013; 28:411-3. [DOI: 10.1038/leu.2013.265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Poloni A, Goteri G, Zizzi A, Serrani F, Trappolini S, Costantini B, Mariani M, Olivieri A, Catarini M, Centurioni R, Alesiani F, Giantomassi F, Stramazzotti D, Biagetti S, Alfonsi S, Berardinelli E, Leoni P. Prognostic role of immunohistochemical analysis of 5 mc in myelodysplastic syndromes. Eur J Haematol 2013; 91:219-227. [DOI: 10.1111/ejh.12145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Antonella Poloni
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Gaia Goteri
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Antonio Zizzi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Federica Serrani
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Silvia Trappolini
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Benedetta Costantini
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Marianna Mariani
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Attilio Olivieri
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | | | | | | | - Federica Giantomassi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Daniela Stramazzotti
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Simona Biagetti
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Simona Alfonsi
- Anatomia Patologica; Dipartimento di Neuroscienze; Università Politecnica Marche; Ancona; Italy
| | - Eleonora Berardinelli
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
| | - Pietro Leoni
- Clinica di Ematologia; Dipartimento di Scienze Cliniche e Molecolari; Università Politecnica Marche; Ancona; Italy
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Johnen G, Rozynek P, von der Gathen Y, Bryk O, Zdrenka R, Johannes C, Weber DG, Igwilo-Okuefuna OB, Raiko I, Hippler J, Brüning T, Dopp E. Cross-contamination of a UROtsa stock with T24 cells--molecular comparison of different cell lines and stocks. PLoS One 2013; 8:e64139. [PMID: 23691160 PMCID: PMC3656924 DOI: 10.1371/journal.pone.0064139] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/08/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND UROtsa is an authentic, immortalized human urothelial cell line that is used to study the effects of metals and other toxic substances, mostly in the context of bladder cancer carcinogenesis. Unusual properties on the molecular level of a provided UROtsa cell line stock prompted us to verify its identity. METHODS UROtsa cell line stocks from different sources were tested on several molecular levels and compared with other cell lines. MicroRNA and mRNA expression was determined by Real-Time PCR. Chromosome numbers were checked and PCR of different regions of the large T-antigen was performed. DNA methylation of RARB, PGR, RASSF1, CDH1, FHIT, ESR1, C1QTNF6, PTGS2, SOCS3, MGMT, and LINE1 was analyzed by pyrosequencing and compared with results from the cell lines RT4, T24, HeLa, BEAS-2B, and HepG2. Finally, short tandem repeat (STR) profiling was applied. RESULTS All tested UROtsa cell line stocks lacked large T-antigen. STR analysis unequivocally identified our main UROtsa stock as the bladder cancer cell line T24, which was different from two authentic UROtsa stocks that served as controls. Analysis of DNA methylation patterns and RNA expression confirmed their differences. Methylation pattern and mRNA expression of the contaminating T24 cell line showed moderate changes even after long-term culture of up to 56 weeks, whereas miRNAs and chromosome numbers varied markedly. CONCLUSIONS It is important to check the identity of cell lines, especially those that are not distributed by major cell banks. However, for some cell lines STR profiles are not available. Therefore, new cell lines should either be submitted to cell banks or at least their STR profile determined and published as part of their initial characterization. Our results should help to improve the identification of UROtsa and other cells on different molecular levels and provide information on the use of urothelial cells for long-term experiments.
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Affiliation(s)
- Georg Johnen
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, IPA, Bochum, Germany.
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Absence of global hypomethylation in promoter hypermethylated Mixed Lineage Leukaemia-rearranged infant acute lymphoblastic leukaemia. Eur J Cancer 2013; 49:175-84. [DOI: 10.1016/j.ejca.2012.07.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 06/25/2012] [Accepted: 07/11/2012] [Indexed: 02/08/2023]
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Abstract
After completion of the human genome, genome-wide association studies were conducted to identify single nucleotide polymorphisms (SNPs) associated with cancer initiation and progression. Most of the studies identified SNPs that were located outside the coding region, and the odds ratios were too low to implement in clinical practice. Although the genome gives information about genome sequence and structure, the human epigenome provides functional aspects of the genome. Epigenome-wide association studies (EWAS) provide an opportunity to identify genome-wide epigenetic variants that are associated with cancer. However, there are problems and issues in implementing EWAS to establish an association between epigenetic profiles and cancer. Few challenges include selection and handling of samples, choice of population and sample size, accurate measurement of exposure, integrating data, and insufficient information about the role of repeat sequences. The current status of EWAS, challenges in the field, and their potential solutions are discussed in this article.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, Division of Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), 6130 Executive Boulevard, Suite 5100, Bethesda, MD 20892-7324, USA
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Epigenomic diversity of colorectal cancer. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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29
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Determination of Global DNA Methylation in Biological Samples by Liquid Chromatography-Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60566-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Baccarelli A, Rusconi F, Bollati V, Catelan D, Accetta G, Hou L, Barbone F, Bertazzi PA, Biggeri A. Nasal cell DNA methylation, inflammation, lung function and wheezing in children with asthma. Epigenomics 2012; 4:91-100. [PMID: 22332661 DOI: 10.2217/epi.11.106] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIMS DNA methylation is increasingly proposed as a mechanism for underlying asthma-related inflammation. However, epigenetic studies are constrained by uncertainties on whether samples that can be easily collected in human individuals can provide informative results. METHODS Two nasal cell DNA samples were collected on different days by nasal brushings from 35 asthmatic children aged between 8 and 11 years old. We correlated DNA methylation of IL-6, iNOS, Alu and LINE-1 with fractional exhaled nitric oxide, forced expiratory volume in 1 s and wheezing. RESULTS Fractional exhaled nitric oxide increased in association with lower promoter methylation of both IL-6 (+29.0%; p = 0.004) and iNOS (+41.0%; p = 0.002). Lower IL-6 methylation was nonsignificantly associated with wheezing during the week of the study (odds ratio = 2.3; p = 0.063). CONCLUSION Our findings support the use of nasal cell DNA for human epigenetic studies of asthma.
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Affiliation(s)
- Andrea Baccarelli
- Exposure Epidemiology & Risk Program, Harvard School of Public Health, Boston, MA 02215, USA.
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31
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Cowan LA, Talwar S, Yang AS. Will DNA methylation inhibitors work in solid tumors? A review of the clinical experience with azacitidine and decitabine in solid tumors. Epigenomics 2012; 2:71-86. [PMID: 22122748 DOI: 10.2217/epi.09.44] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The recent approval of azacitidine (Vidaza®), decitabine (Dacogen®) and vorinostat (Zolinza™) for myelodysplastic syndrome and cutaneous T-cell lymphoma has led to a wave of interest in epigenetic therapy. These DNA methylation inhibitors and the histone deacetylase inhibitor clearly have demonstrated activity in hematologic malignancies, but the future role of epigenetic therapy in solid tumors is still unknown. What is not commonly known is that azacitidine and decitabine were originally developed as cytotoxic nucleoside analogs and clinical trials were previously conducted in a variety of cancer types prior to the knowledge of their ability to inhibit DNA methylation. We review the experience of azacitidine and decitabine in early clinical trials and demonstrate the activity of epigenetic therapy in solid tumors.
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Abstract
Biochemical, epigenetic, genetic, and imaging biomarkers are used to identify people at high risk for developing cancer. In cancer epidemiology, epigenetic biomarkers offer advantages over other types of biomarkers because they are expressed against a person's genetic background and environmental exposure, and because epigenetic events occur early in cancer development. This chapter describes epigenetic biomarkers that are being used to study the epidemiology of different types of cancer. Because epigenetic alterations can be reversed by chemicals and activate gene expression, epigenetic biomarkers potentially have numerous clinical applications in cancer intervention and treatment and significant implications in public health. This review discusses cancer biomarkers, the characteristics of an ideal biomarker for cancer, and technologies for biomarker detection.
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Iwagami S, Baba Y, Watanabe M, Shigaki H, Miyake K, Ida S, Nagai Y, Ishimoto T, Iwatsuki M, Sakamoto Y, Miyamoto Y, Baba H. Pyrosequencing assay to measure LINE-1 methylation level in esophageal squamous cell carcinoma. Ann Surg Oncol 2011; 19:2726-32. [PMID: 22187122 DOI: 10.1245/s10434-011-2176-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Indexed: 12/28/2022]
Abstract
BACKGROUND Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. DNA methylation in the long interspersed nucleotide element 1 L1 (LINE-1) repetitive element is a good indicator of global DNA methylation level. LINE-1 methylation is a useful marker for predicting cancer prognosis and monitoring efficacy of adjuvant therapy. Nonetheless, no study has examined LINE-1 methylation in esophageal squamous cell carcinoma (ESCC). The aim of this study is to assess the precision of sodium bisulfite conversion and polymerase chain reaction (PCR) pyrosequencing assay for evaluating LINE-1 methylation in ESCC. METHODS To measure assay precision, we performed bisulfite conversion on 5 different DNA specimen aliquots (bisulfite-to-bisulfite) and repeated PCR pyrosequencing five times (run to run). Second, to assess heterogeneity of LINE-1 methylation levels within tumor, we made 5 different tissue sections from one tumor and examined LINE-1 methylation level of each section (section to section). Third, to evaluate LINE-1 methylation status in ESCC, we applied this assay to 30 ESCCs and 30 matched normal esophageal mucosa. RESULTS Bisulfite-to-bisulfite standard deviation (SD) ranged from 1.44 to 2.90 (median 2.32) in ESCCs; and 0.57 to 4.02 (median 1.23) in normal esophagus. Run-to-run SD ranged from 0.63 to 3.25 (median 1.54) in ESCCs. Section-to-section SD ranged from 1.37 to 3.31 (median 1.94). ESCC tissues showed significantly lower levels of LINE-1 methylation than matched normal mucosa (P < .0001; n = 30). There was no significant relationship between LINE-1 methylation level and tumor stage (P = 0.14). CONCLUSIONS Bisulfite conversion and PCR pyrosequencing assay can measure LINE-1 methylation in ESCC, and may be useful in clinical and research settings.
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Affiliation(s)
- Shiro Iwagami
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
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Piyathilake CJ, Macaluso M, Alvarez RD, Chen M, Badiga S, Siddiqui NR, Edberg JC, Partridge EE, Johanning GL. A higher degree of LINE-1 methylation in peripheral blood mononuclear cells, a one-carbon nutrient related epigenetic alteration, is associated with a lower risk of developing cervical intraepithelial neoplasia. Nutrition 2011; 27:513-9. [PMID: 21463750 DOI: 10.1016/j.nut.2010.08.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 08/17/2010] [Accepted: 08/22/2010] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The objective of the study was to evaluate LINE-1 methylation as an intermediate biomarker for the effect of folate and vitamin B12 on the occurrence of higher grades of cervical intraepithelial neoplasia (CIN ≥ 2). METHODS This study included 376 women who tested positive for high-risk human papillomaviruses and were diagnosed with CIN ≥ 2 (cases) or CIN ≤ 1 (non-cases). CIN ≥ 2 (yes/no) was the dependent variable in logistic regression models that specified the degree of LINE-1 methylation of peripheral blood mononuclear cells (PBMCs) and of exfoliated cervical cells (CCs) as the independent predictors of primary interest. In analyses restricted to non-cases, PBMC LINE-1 methylation (≥ 70% versus <70%) and CC LINE-1 methylation (≥ 54% versus <54%) were the dependent variables in logistic regression models that specified the circulating concentrations of folate and vitamin B12 as the primary independent predictors. RESULTS Women in the highest tertile of PBMC LINE-1 methylation had 56% lower odds of being diagnosed with CIN ≥ 2 (odds ratio 0.44, 95% confidence interval 0.24-0.83, P = 0.011), whereas there was no significant association between degree of CC LINE-1 methylation and CIN ≥ 2 (odds ratio 0.86, 95% confidence interval 0.51-1.46, P = 0.578). Among non-cases, women with supraphysiologic concentrations of folate (>19.8 ng/mL) and sufficient concentrations of plasma vitamin B12 (≥ 200.6 ng/mL) were significantly more likely to have highly methylated PBMCs compared with women with lower folate and lower vitamin B12 (odds ratio 3.92, 95% confidence interval 1.06-14.52, P = 0.041). None of the variables including folate and vitamin B12 were significantly associated with CC LINE-1 methylation. CONCLUSION These results suggest that a higher degree of LINE-1 methylation in PBMCs, a one-carbon nutrient-related epigenetic alteration, is associated with a lower risk of developing CIN.
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Affiliation(s)
- Chandrika J Piyathilake
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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Alva AS, Hahn NM, Aparicio AM, Singal R, Yellapragada S, Sonpavde G. Hypomethylating agents for urologic cancers. Future Oncol 2011; 7:447-63. [PMID: 21417907 DOI: 10.2217/fon.11.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter-region methylation as an epigenetic mechanism of gene regulation is increasingly recognized as beneficial in cancer. Initially developed as cytotoxic high-dose therapies, azacitidine and decitabine are now being reinvestigated in lower-dose cancer treatment regimens with a different paradigm - hypomethylation. Recent evidence for benefit in myelodysplastic syndromes and acute myeloid leukemias has renewed interest in hypomethylation as a therapeutic option in epithelial cancers. In this article, we describe the mechanistic aspects of DNA methylation, which alters gene expression, and review the evidence for hypomethylation as a therapeutic option in urologic cancers. Potential correlative studies that may assist in developing tailored therapy with hypomethylating agents are reviewed. Given that the population with urologic cancers is typically elderly with multiple comorbidities, the excellent tolerability of lower-dose hypomethylating agents provides a high therapeutic index and rational development is warranted, bearing in mind that the cytostatic and delayed activity present challenges in the choice of appropriate trial end points.
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Affiliation(s)
- Ajjai S Alva
- Baylor College of Medicine & Michael E DeBakey VA Medical Center, Houston, TX 77030, USA
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36
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Sigalotti L, Fratta E, Bidoli E, Covre A, Parisi G, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M. Methylation levels of the "long interspersed nucleotide element-1" repetitive sequences predict survival of melanoma patients. J Transl Med 2011; 9:78. [PMID: 21615918 PMCID: PMC3123580 DOI: 10.1186/1479-5876-9-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Background The prognosis of cutaneous melanoma (CM) differs for patients with identical clinico-pathological stage, and no molecular markers discriminating the prognosis of stage III individuals have been established. Genome-wide alterations in DNA methylation are a common event in cancer. This study aimed to define the prognostic value of genomic DNA methylation levels in stage III CM patients. Methods Overall level of genomic DNA methylation was measured using bisulfite pyrosequencing at three CpG sites (CpG1, CpG2, CpG3) of the Long Interspersed Nucleotide Element-1 (LINE-1) sequences in short-term CM cultures from 42 stage IIIC patients. The impact of LINE-1 methylation on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analysis. Results Hypomethylation (i.e., methylation below median) at CpG2 and CpG3 sites significantly associated with improved prognosis of CM, CpG3 showing the strongest association. Patients with hypomethylated CpG3 had increased OS (P = 0.01, log-rank = 6.39) by Kaplan-Meyer analysis. Median OS of patients with hypomethylated or hypermethylated CpG3 were 31.9 and 11.5 months, respectively. The 5 year OS for patients with hypomethylated CpG3 was 48% compared to 7% for patients with hypermethylated sequences. Among the variables examined by Cox regression analysis, LINE-1 methylation at CpG2 and CpG3 was the only predictor of OS (Hazard Ratio = 2.63, for hypermethylated CpG3; 95% Confidence Interval: 1.21-5.69; P = 0.01). Conclusion LINE-1 methylation is identified as a molecular marker of prognosis for CM patients in stage IIIC. Evaluation of LINE-1 promises to represent a key tool for driving the most appropriate clinical management of stage III CM patients.
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Affiliation(s)
- Luca Sigalotti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
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Kitkumthorn N, Mutirangura A. Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. Clin Epigenetics 2011; 2:315-30. [PMID: 22704344 PMCID: PMC3365388 DOI: 10.1007/s13148-011-0032-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/20/2011] [Indexed: 12/31/2022] Open
Abstract
Epigenetic changes in long interspersed nuclear element-1s (LINE-1s or L1s) occur early during the process of carcinogenesis. A lower methylation level (hypomethylation) of LINE-1 is common in most cancers, and the methylation level is further decreased in more advanced cancers. Consequently, several previous studies have suggested the use of LINE-1 hypomethylation levels in cancer screening, risk assessment, tumor staging, and prognostic prediction. Epigenomic changes are complex, and global hypomethylation influences LINE-1s in a generalized fashion. However, the methylation levels of some loci are dependent on their locations. The consequences of LINE-1 hypomethylation are genomic instability and alteration of gene expression. There are several mechanisms that promote both of these consequences in cis. Therefore, the methylation levels of different sets of LINE-1s may represent certain phenotypes. Furthermore, the methylation levels of specific sets of LINE-1s may indicate carcinogenesis-dependent hypomethylation. LINE-1 methylation pattern analysis can classify LINE-1s into one of three classes based on the number of methylated CpG dinucleotides. These classes include hypermethylation, partial methylation, and hypomethylation. The number of partial and hypermethylated loci, but not hypomethylated LINE-1s, is different among normal cell types. Consequently, the number of hypomethylated loci is a more promising marker than methylation level in the detection of cancer DNA. Further genome-wide studies to measure the methylation level of each LINE-1 locus may improve PCR-based methylation analysis to allow for a more specific and sensitive detection of cancer DNA or for an analysis of certain cancer phenotypes.
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Fabris S, Bollati V, Agnelli L, Morabito F, Motta V, Cutrona G, Matis S, Grazia Recchia A, Gigliotti V, Gentile M, Deliliers GL, Bertazzi PA, Ferrarini M, Neri A, Baccarelli A. Biological and clinical relevance of quantitative global methylation of repetitive DNA sequences in chronic lymphocytic leukemia. Epigenetics 2011; 6:188-94. [PMID: 20930513 DOI: 10.4161/epi.6.2.13528] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Global DNA hypomethylation affecting repeat sequences has been reported in different cancer types. Herein, we investigated the methylation levels of repetitive DNA elements in chronic lymphocytic leukemia (CLL), their correlation with the major cytogenetic and molecular features, and clinical relevance in predicting therapy-free survival (TFS). A quantitative bisulfite-PCR Pyrosequencing method was used to evaluate methylation of Alu, long interspersed nuclear elements-1 (LINE-1) and satellite-α (SAT-α) sequences in 77 untreated early-stage (Binet A) CLL patients. Peripheral B-cells from 7 healthy donors were used as controls. Methylation levels (median %5mC) were lower in B-CLLs compared with controls (21.4 vs. 25.9; 66.8 vs. 85.7; 84.0, vs. 88.2 for Alu, LINE-1 and SAT-α, respectively) (p < 0.001). Among CLL patients, a significant association was observed with 17p13.1 deletion (16.8 vs. 22.4; 51.2 vs. 68.5; 52.6 vs. 85.0, for Alu, LINE-1 and SAT-α) but not with other major genetic lesions, IgVH mutation status, CD38 or ZAP-70 expression. Follow-up analyses showed that lower SAT-α methylation levels appeared to be an independent prognostic marker significantly associated with shorter TFS. Our study extended previous limited evidences in methylation of repetitive sequences in CLL suggesting an important biological and clinical relevance in the disease.
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Affiliation(s)
- Sonia Fabris
- Medical Sciences Department, University of Milan and Hematology 1, Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Milan, Italy
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Chowdhury S, Cleves MA, MacLeod SL, James SJ, Zhao W, Hobbs CA. Maternal DNA hypomethylation and congenital heart defects. ACTA ACUST UNITED AC 2011; 91:69-76. [PMID: 21254366 DOI: 10.1002/bdra.20761] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/01/2010] [Accepted: 10/12/2010] [Indexed: 01/08/2023]
Abstract
BACKGROUND Congenital heart defects (CHDs) are among the most prevalent and serious of birth defects. Multiple maternal factors are thought to contribute to CHD development, including folate intake. Maternal DNA methylation, which is dependent on folate metabolism, may impact the risk of CHDs. Our study was designed to determine whether maternal long interspersed nucleotide elements-1 (LINE-1) DNA hypomethylation is associated with increased occurrence of non-syndromic CHDs and whether maternal folate-dependent metabolites are correlated with DNA methylation status. METHODS Using a case-control study design, we measured global DNA methylation status among mothers whose pregnancies were affected by non-syndromic CHDs (n = 180) and mothers of unaffected pregnancies (n = 187). Methylation of LINE-1 was used as a surrogate marker of global DNA methylation status. The association between DNA methylation and CHD risk was determined while adjusting for selected lifestyle factors. RESULTS LINE-1 DNA methylation was significantly lower in cases compared to controls (p = 0.049). After covariate adjustments, a significant difference between cases and controls remained (p = 0.010). Among women with LINE-1 methylation in the lowest decile of DNA methylation, the estimated risk of having a CHD-affected pregnancy was almost twice that of women in all other deciles (odds ratio [OR], 1.91; 95% confidence interval [CI], 1.03-3.58). CONCLUSIONS Our findings indicate that maternal LINE-1 DNA hypomethylation is associated with an increased risk of CHDs. Future studies investigating the association between maternal DNA methylation patterns and CHDs should be pursued.
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Affiliation(s)
- Shimul Chowdhury
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Hospital Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
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Corrie SR, Sova P, Feng Q, Blair T, Kiviat NB, Trau M. Bisulfite-free analysis of 5MeC-binding proteins and locus-specific methylation density using a microparticle-based flow cytometry assay. Analyst 2011; 136:688-91. [DOI: 10.1039/c0an00790k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Mikeska T, Felsberg J, Hewitt CA, Dobrovic A. Analysing DNA methylation using bisulphite pyrosequencing. Methods Mol Biol 2011; 791:33-53. [PMID: 21913070 DOI: 10.1007/978-1-61779-316-5_4] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bisulphite pyrosequencing is a quantitative methodology for the investigation of DNA methylation of sequences up to 100-bp in length. Biotin-labelled, single-stranded PCR products generated from bisulphite-treated DNA are used as a template with an internal primer to perform the pyrosequencing reaction. Nucleotides are added in a predetermined order in each pyrosequencing cycle and the amount of incorporated nucleotide results in a proportional emission of light. DNA methylation ratios are calculated from the levels of light emitted from each nucleotide incorporated at individual CpG positions in a strand-dependent manner. The methylation detection limit at individual CpG sites is approximately 5% and the results are displayed as an average methylation level for each CpG position assayed across all amplification products generated during a PCR reaction. As a consequence, bisulphite pyrosequencing allows the identification of heterogeneous DNA methylation patterns but does not provide information at a single allele resolution. This methodology is suited to analyse short DNA sequences such as those typically extracted from formalin-fixed paraffin-embedded specimens. Nevertheless, longer PCR products can be sequenced by serial bisulphite pyrosequencing, which utilises tandem assays along the amplicon. The general information provided is applicable for all formats of current pyrosequencing instruments, however, a specific protocol for the PyroMark Q24 instrument is provided.
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Affiliation(s)
- Thomas Mikeska
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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Si J, Boumber YA, Shu J, Qin T, Ahmed S, He R, Jelinek J, Issa JPJ. Chromatin remodeling is required for gene reactivation after decitabine-mediated DNA hypomethylation. Cancer Res 2010; 70:6968-77. [PMID: 20713525 DOI: 10.1158/0008-5472.can-09-4474] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The DNA hypomethylating drug decitabine (DAC) reactivates silenced gene expression in cancer and is approved for the treatment of the myelodysplastic syndrome. Gene reactivation after DAC is variable and incompletely understood. Here, we established a cell line system (YB5) derived from the SW48 colon cancer cell line to study DAC-induced reactivation. YB5 contains a hypermethylated cytomegalovirus promoter driving green fluorescent protein (GFP), and the locus is transcriptionally silent. GFP reexpression can be achieved by DAC treatment, but the expression level of individual cells is heterogeneous. DAC-treated YB5 cells were separated into GFP-positive and GFP-negative subpopulations. By comparing DAC-treated sorted GFP-positive and GFP-negative cells, we found that their methylation levels were similarly decreased but that histone modifications and histone H3 densities were remarkably different. Despite a similar degree of (incomplete) DNA hypomethylation, GFP-positive cells reverted to an active chromatin structure marked by higher H3K9 acetylation, lower H3K27 trimethylation, and lower promoter nucleosome density. GFP-negative cells had histone modifications and promoter nucleosome density, similar to parental cells. On DAC withdrawal, gradual resilencing and remethylation occurred in both GFP-positive and GFP-negative cells, and the resilencing correlated with a gradual increase in nucleosome occupancy in GFP-positive cells. These data show that hypomethylation alone after DAC is insufficient for gene expression induction, and that chromatin resetting to an active state including nucleosome eviction is required for activation of protein expression. Our findings suggest that gene expression is the key in optimizing DAC treatment strategies in the clinic.
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Affiliation(s)
- Jiali Si
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, TX, USA
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Demethylating Agents in the Treatment of Cancer. Pharmaceuticals (Basel) 2010; 3:2022-2044. [PMID: 27713340 PMCID: PMC4036667 DOI: 10.3390/ph3072022] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/22/2010] [Accepted: 06/29/2010] [Indexed: 02/06/2023] Open
Abstract
Gene silencing resulting from aberrant DNA methylation can lead to tumorigenesis. Therefore, drugs that inhibit or interfere with DNA methylation have been used to reactivate and induce silenced gene re-expression in malignancies. Two demethylating agents, azacitidine and decitabine, are approved for the treatment of myelodysplastic syndromes (MDS) by the U.S. Food and Drug Administration (FDA), and are now considered the standard of care in MDS. In this review, we discuss clinical data, including clinical benefits and toxicities, which led to the approval of azacitidine and decitabine. We also summarize findings from clinical trials that used these two demethylating agents in the treatment of solid tumors. Lastly, we discuss some limitations in the use of azacitidine and decitabine in cancer therapy.
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Pathiraja TN, Stearns V, Oesterreich S. Epigenetic regulation in estrogen receptor positive breast cancer--role in treatment response. J Mammary Gland Biol Neoplasia 2010; 15:35-47. [PMID: 20101445 PMCID: PMC2874203 DOI: 10.1007/s10911-010-9166-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 01/07/2010] [Indexed: 02/07/2023] Open
Abstract
Recent advances in breast cancer treatment have allowed increasing numbers of patients with estrogen receptor (ER) positive (+) breast cancer to receive various forms of endocrine therapy. Unfortunately, de novo and acquired resistance to endocrine therapy remains a major challenge in the clinic. A number of possible mechanisms for drug resistance have been described, which include activation of growth factor receptor pathways, overexpression of ER coactivators, and metabolic resistance due to polymorphisms in metabolizing enzymes. While many of these changes are caused by genetic alterations, there is also increasing evidence to implicate epigenetic gene regulatory mechanisms in the development of endocrine resistance. Since epigenetic modifications are easier to reverse than genetic mutations, they are appealing therapeutic targets, and thus future improvements in medical care for breast cancer patients will depend upon a better understanding of the roles epigenetic modifications play in endocrine resistance. In this review we will focus on recent advances made in the understanding of epigenetic gene regulation in estrogen response and endocrine resistance in breast cancer. We will also summarize current clinical-translational advances in epigenetic therapy, and discuss potential future clinical use of epigenetic changes as therapeutic targets, especially with respect to endocrine treatment.
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Affiliation(s)
- Thushangi N. Pathiraja
- Translational Biology and Molecular Medicine Graduate Program, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Vered Stearns
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steffi Oesterreich
- Lester and Sue Smith Breast Center, Department of Medicine, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA,
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Irahara N, Nosho K, Baba Y, Shima K, Lindeman NI, Hazra A, Schernhammer ES, Hunter DJ, Fuchs CS, Ogino S. Precision of pyrosequencing assay to measure LINE-1 methylation in colon cancer, normal colonic mucosa, and peripheral blood cells. J Mol Diagn 2010; 12:177-83. [PMID: 20093385 DOI: 10.2353/jmoldx.2010.090106] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genome-wide DNA hypomethylation plays an important role in epigenomic and genomic instability and colorectal carcinogenesis. DNA methylation in the long interspersed nucleotide element-1, L1 (LINE-1) repetitive element is a good indicator of global DNA methylation level. In addition, LINE-1 hypomethylation in blood cells has been associated with colorectal adenoma risk, and LINE-1 hypomethylation in colorectal cancer is related with prognosis and linearly predicts shorter patient survival. However, no study has comprehensively evaluated the precision of sodium bisulfite conversion and PCR-pyrosequencing to measure LINE-1 methylation. Using 10 paraffin-embedded colon cancers, 5 matched normal colon mucosa, and 5 unrelated peripheral blood buffy coat leukocyte specimens, we enriched tumor DNA by macrodissection and laser capture microdissection. LINE-1 methylation was calculated as an average of 100 * C/(C + T) at 4 CpG sites after bisulfite-PCR-pyrosequencing. The LINE-1 methylation value in colon cancers varied, ranging approximately from 30 to 80. To measure assay precision, we performed bisulfite conversion on seven different DNA specimen aliquots and repeated PCR-pyrosequencing seven times. Run-to-run (between-run) SD ranged from 1.3 to 4.4 (median, 3.0) in macrodissected colon cancers; 1.1 to 10.5 (median, 3.8) in laser capture microdissection specimens; 1.3 to 2.5 (median, 1.9) in normal colon; and 1.5 to 3.4 (median, 1.9) in leukocyte DNA. In conclusion, bisulfite conversion and PCR-pyrosequencing assay can measure LINE-1 methylation in macrodissected colon cancer, normal colon, and blood DNA, and may be useful in clinical and research settings.
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Affiliation(s)
- Natsumi Irahara
- Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 44 Binney St., Room JF-215C, Boston, MA 02115, USA
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Sonpavde G, Aparicio AM, Zhan F, North B, Delaune R, Garbo LE, Rousey SR, Weinstein RE, Xiao L, Boehm KA, Asmar L, Fleming MT, Galsky MD, Berry WR, Von Hoff DD. Azacitidine favorably modulates PSA kinetics correlating with plasma DNA LINE-1 hypomethylation in men with chemonaïve castration-resistant prostate cancer. Urol Oncol 2009; 29:682-9. [PMID: 19959380 DOI: 10.1016/j.urolonc.2009.09.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 09/24/2009] [Indexed: 01/10/2023]
Abstract
BACKGROUND Azacitidine is a hypomethylating agent that activates genes repressed by promoter methylation. Preclinically, demethylating agents reverse resistance of prostate cancer to androgen ablation. A phase II trial evaluated azacitidine for men with castration-resistant prostate cancer (CRPC) progressing on combined androgen blockade (CAB). METHODS Chemonaïve patients with CRPC on CAB and PSA-doubling time (DT) < 3 months were eligible. The primary endpoint was prolongation of PSA-DT to ≥ 3 months. Correlation of biologic activity (fetal hemoglobin, plasma DNA LINE-1 methylation) with prolongation of PSA-DT was tested. CAB was continued and azacitidine 75 mg/m(2) was administered subcutaneously on days 1-5 of each 28-day cycle up to 12 cycles or until clinical progression/intolerable toxicities. RESULTS Thirty-six patients were enrolled, 80.6% had metastatic disease, and 34 were evaluable. A PSA-DT ≥ 3 months was attained in 19 patients (55.8%). Overall median PSA-DT was significantly prolonged compared to baseline (2.8 vs. 1.5 months, P < 0.01). Fourteen patients had some PSA decline during therapy and 1 patient had a ≥ 30% decline compared with baseline. The median clinical progression-free survival was 12.4 weeks. Grade 3 toxicities included fatigue (12%), and neutropenia (6%), with 4 patients discontinuing due to toxicities. A trend in decreasing plasma DNA LINE-1 methylation was seen with longer treatment duration (P = 0.06), which significantly correlated with prolongation of PSA-DT (P = 0.02). CONCLUSIONS Azacitidine favorably modulates PSA kinetics in chemonaïve CRPC that correlates with decreasing plasma DNA LINE-1 methylation. Given the excellent tolerability, further development of azacitidine for CRPC may be warranted, with exploration of combination regimens.
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Affiliation(s)
- Guru Sonpavde
- US Oncology Research, Inc., The Woodlands, TX 77380, USA.
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