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Deng L, Zhou J, Sun Y, Hu Y, Qiao J, Liu Z, Gu L, Lin D, Zhang L, Deng D. CDKN2A somatic copy number amplification in normal tissues surrounding gastric carcinoma reduces cancer metastasis risk in droplet digital PCR analysis. Gastric Cancer 2024:10.1007/s10120-024-01515-4. [PMID: 38822931 DOI: 10.1007/s10120-024-01515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The CDKN2A gene is frequently affected by somatic copy number variations (SCNVs, including deletions and amplifications [SCNdel and SCNamp]) in the cancer genome. Using surgical gastric margin tissue samples (SMs) as the diploid reference in SCNV analysis via CDKN2A/P16-specific real-time PCR (P16-Light), we previously reported that the CDKN2A SCNdel was associated with a high risk of metastasis of gastric carcinoma (GC). However, the status of CDKN2A SCNVs in SMs and their clinical significance have not been reported. METHODS Peripheral white blood cell (WBC) and frozen GC and SM tissue samples were collected from patients (n = 80). Droplet digital PCR (ddPCR) was used to determine the copy number (CN) of the CDKN2A gene in tissue samples using paired WBCs as the diploid reference. RESULTS A novel P16-ddPCR system was initially established with a minimal proportion (or limit, 10%) of the detection of CDKN2A CN alterations. While CDKN2A SCNamp events were detected in both SMs and GCs, fewer CDKN2A SCNdel events were detected in SMs than in GCs (15.0% vs. 41.3%, P = 4.77E-04). Notably, significantly more SCNamp and fewer SCNdel of the CDKN2A gene were detected in SMs from GC patients without metastasis than in those from patients with lymph node metastasis by P16-ddPCR (P = 0.023). The status of CDKN2A SCNVs in SM samples was significantly associated with overall survival (P = 0.032). No cancer deaths were observed among the 11 patients with CDKN2A SCNamp. CONCLUSION CDKN2A SCNVs in SMs identified by P16-ddPCR are prevalent and significantly associated with GC metastasis and overall survival.
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Affiliation(s)
- Lewen Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yu Sun
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Ying Hu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dongmei Lin
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Friedemann M, Jandeck C, Tautz L, Gutewort K, von Rein L, Sukocheva O, Fuessel S, Menschikowski M. Blood-Based DNA Methylation Analysis by Multiplexed OBBPA-ddPCR to Verify Indications for Prostate Biopsies in Suspected Prostate Cancer Patients. Cancers (Basel) 2024; 16:1324. [PMID: 38611002 PMCID: PMC11010987 DOI: 10.3390/cancers16071324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Current prostate carcinoma (PCa) biomarkers, including total prostate-specific antigen (tPSA), have unsatisfactory diagnostic sensitivity and specificity resulting in overdiagnosis and overtreatment. Previously, we described an optimised bias-based preamplification-digital droplet PCR (OBBPA-ddPCR) technique, which detects tumour DNA in blood-derived cell-free DNA (cfDNA) of cancer patients. The current study investigated the performance of newly developed OBBPA-ddPCR-based biomarkers. Blood plasma samples from healthy individuals (n = 90, controls) and PCa (n = 39) and benign prostatic hyperplasia patients (BPH, n = 40) were analysed. PCa and BPH patients had tPSA values within a diagnostic grey area of 2-15 ng/mL, for whom further diagnostic validation is most crucial. Methylation levels of biomarkers RASSF1A, MIR129-2, NRIP3, and SOX8 were found significantly increased in PCa patients compared to controls. By combining classical PCa risk factors (percentage of free PSA compared to tPSA (QfPSA) and patient's age) with cfDNA-based biomarkers, we developed PCa risk scores with improved sensitivity and specificity compared to established tPSA and QfPSA single-marker analyses. The diagnostic specificity was increased to 70% with 100% sensitivity for clinically significant PCa patients. Thus, prostate biopsies could be avoided for 28 out of 40 BPH patients. In conclusion, the newly developed risk scores may help to confirm the clinical decision and prevent unnecessary prostate biopsy.
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Affiliation(s)
- Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany; (C.J.); (K.G.); (L.v.R.)
| | - Carsten Jandeck
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany; (C.J.); (K.G.); (L.v.R.)
| | - Lars Tautz
- Joint Practice of Urology “Am Blauen Wunder”, Schillerplatz 2, 01309 Dresden, Germany
| | - Katharina Gutewort
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany; (C.J.); (K.G.); (L.v.R.)
| | - Lisa von Rein
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany; (C.J.); (K.G.); (L.v.R.)
| | - Olga Sukocheva
- Department of Hepatology, Royal Adelaide Hospital, Port Rd., Adelaide, SA 5000, Australia;
| | - Susanne Fuessel
- Clinic of Urology, Carl Gustav Carus University Hospital, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany;
| | - Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Fetscherstr. 74, 01307 Dresden, Germany; (C.J.); (K.G.); (L.v.R.)
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Wai KM, Swe T, Myar MT, Aisyah CR, Hninn TSS. Telomeres susceptibility to environmental arsenic exposure: Shortening or lengthening? Front Public Health 2023; 10:1059248. [PMID: 36703827 PMCID: PMC9871564 DOI: 10.3389/fpubh.2022.1059248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Maintaining telomere length plays a crucial role in regulating cellular life span. Telomere lengthening or shortening is one of the important biomarkers which could predict the preceding or present diseases. Meanwhile, the impact of environmental arsenic exposure on telomere length has increasingly concerned. Although previous studies demonstrated the effects of arsenic on telomere length, the findings were unclear on whether telomere shortens or lengthens by arsenic exposure. Thus, this manuscript summarized and discussed the telomere length alteration following arsenic exposure and the possible does-response effect of arsenic on telomere length. The present review suggested that different age groups may respond differently to arsenic exposure, and the dose-response effect of arsenic could be a critical factor in its effect on telomere length. Moreover, speciation analysis of arsenic could be more informative in identifying the effect of arsenic on telomere length.
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Affiliation(s)
- Kyi Mar Wai
- Department of Social Medicine, Graduate School of Medicine, Hirosaki University, Hirosaki, Japan,Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Kyi Mar Wai ✉
| | - Thinzar Swe
- Pre-clinical Department, University of Medicine 2, Yangon, Myanmar
| | - Maw Thoe Myar
- Pre-clinical Department, University of Medicine Taunggyi, Taunggyi, Myanmar
| | - Cindy Rahman Aisyah
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Wang W, Li W, Zhang H. An Overview of DNA Methylation Indicators for the Course of Oral Precancer. Appl Bionics Biomech 2022; 2022:6468773. [PMID: 36060560 PMCID: PMC9439927 DOI: 10.1155/2022/6468773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is a physiologically epigenetic alteration that happens when a methyl group is introduced to a CpG dinucleotide in the gene-regulating sequence of DNA. However, the majority of oral cancers have a well-defined precancerous stage; there are few clinical and morphological parameters for detecting and signalling the progression of precancerous to malignant tumours. DNA methylation forms are dynamic and reversible, allowing them to adjust to environmental or therapeutic changes. We did an extensive investigation to compile the data supporting aberrant DNA methylation forms as a possible biomarker for prediction. According to two longitudinal studies, p16 hypermethylation was considerably higher in precancerous lesions that progressed to cancer than in lesions that shrank. Most of the studies examined for this study were tiny cross-sectional research with scant validation and inadequately specified control groups. Existing evidence suggests that DNA methylation sequences can be relevant as a diagnostic biomarker for OPS development; however, sample size and research design restrictions make it difficult to draw definitive conclusions. Strong studies, including extensive epigenome-wide methylation scans of OPS with longitudinal monitoring, are necessary in this study in order to corroborate the recently discovered signals and discover new risk loci and disease progression molecular pathways.
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Affiliation(s)
- Wenjing Wang
- The First Affiliated Hospital of Yangtze University, Department of Stomatology, The First People's Hospital of Jingzhou, Jingzhou 434000, China
| | - Wei Li
- The First Affiliated Hospital of Yangtze University, Department of Stomatology, The First People's Hospital of Jingzhou, Jingzhou 434000, China
| | - Hongyi Zhang
- The First Affiliated Hospital of Yangtze University, Department of Stomatology, The First People's Hospital of Jingzhou, Jingzhou 434000, China
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Tan YL, Chen H, Wu ZK, He J, Jiang JH. Digital Loop-Mediated Isothermal Amplification-Based Absolute Methylation Quantification Revealed Hypermethylated DAPK1 in Cervical Cancer Patients. Anal Chem 2021; 93:8077-8083. [PMID: 34019386 DOI: 10.1021/acs.analchem.1c01510] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aberrant methylation of many genes has been reported to be associated with various carcinomas. Accurate detection of the methylation level could provide critical insights into the diagnostic analysis of diseases. Here, a sensitive HpaII-edited absolute droplet loop-mediated isothermal amplification (HEADLAMP) method based on methylation-sensitive restriction enzyme (MSRE) HpaII was developed for the digital quantification of DNA methylation. Methylation levels of the death-associated protein kinase 1 (DAPK1) gene that is associated with many cancers were studied using β-actin as an internal reference. DAPK1 (2.5 pM) with 0.01% methylation (250 aM) can be detected with the conventional HpaII-edited LAMP assay. Using HEADLAMP, as low as 1% methylation level can be distinguished with an estimated limit of detection of 5 aM (ca. 3 copies/μL). Moreover, HEADLAMP can detect low levels of methylated DAPK1 in normal L-02 cells, while the conventional assay cannot. Finally, HEADLAMP was applied to the detection of DAPK1 methylation in 20 clinical tissue samples, which revealed hypermethylated DAPK1 in cervical cancer patients. We envisage potential applications of this robust, specific, and sensitive HEADLAMP assay in epigenetic studies and early clinical diagnosis.
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Affiliation(s)
- Ya-Ling Tan
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Hongjian Chen
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhen-Kun Wu
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianjun He
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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Saban D, Larisch J, Nickel AC, Pierscianek D, Dammann P, Sure U, Zhu Y. DNA promoter methylation of CCM genes in human cerebral cavernous malformations: Importance of confirming MSP data through sequencing. Eur J Med Genet 2020; 63:104090. [PMID: 33122157 DOI: 10.1016/j.ejmg.2020.104090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/18/2020] [Accepted: 10/18/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cerebral cavernous malformations (CCMs) is the second most common cerebrovascular disease and is classified as familial (20%) and sporadic (80%) forms. Loss of function mutation of three CCM genes results in the familial CCM. Considering the similar clinic presentation of familial and sporadic CCMs, and based on enriched CpG islands in the DNA promoter region of three CCM genes, we hypothesized that DNA methylation of the CpG islands of the CCM genes is involved in human CCM, thereby leading to loss of CCM genes. MATERIAL AND METHODS 69 human CCMs including sporadic (n = 40), multiple (n = 15) and familial (n = 14) cases. DNA was extracted from the surgical specimens of CCMs followed by bisulfite conversion. The methylation status of the promoter regions of three CCM genes was detected by methylation specific PCR (MSP). To confirm the results of MSP, four MSP-positive probes showing CCM3 methylation underwent deep bisulfite sequencing (DBS). RESULTS MSP mostly excluded methylation of CCM1 and CCM2 promotor regions (data not shown). In the case of CCM3, 12 out of 55 sporadic cases showed positivity for MSP (21.8%). Deep bisulfite sequencing revealed that four CCM3 MSP positive cases were all negative for DNA methylation. CONCLUSION The present study suggests that DNA promotor methylation of CCM1-3 genes is not involved in human family CCMs and that it is important to confirm MSP data with DBS. Further study with higher number of sporadic CCM patients is required for better understanding whether this epigenetic mechanism is involved in the pathology of CCM.
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Affiliation(s)
- Dino Saban
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Joel Larisch
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Ann-Christin Nickel
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Daniela Pierscianek
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Philipp Dammann
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Ulrich Sure
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Yuan Zhu
- Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany.
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Kanakis I, Alameddine M, Scalabrin M, van 't Hof RJ, Liloglou T, Ozanne SE, Goljanek-Whysall K, Vasilaki A. Low protein intake during reproduction compromises the recovery of lactation-induced bone loss in female mouse dams without affecting skeletal muscles. FASEB J 2020; 34:11844-11859. [PMID: 32652768 DOI: 10.1096/fj.202001131r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Lactation-induced bone loss occurs due to high calcium requirements for fetal growth but skeletal recovery is normally achieved promptly postweaning. Dietary protein is vital for fetus and mother but the effects of protein undernutrition on the maternal skeleton and skeletal muscles are largely unknown. We used mouse dams fed with normal (N, 20%) or low (L, 8%) protein diet during gestation and lactation and maintained on the same diets (NN, LL) or switched from low to normal (LN) during a 28 d skeletal restoration period post lactation. Skeletal muscle morphology and neuromuscular junction integrity was not different between any of the groups. However, dams fed the low protein diet showed extensive bone loss by the end of lactation, followed by full skeletal recovery in NN dams, partial recovery in LN and poor bone recovery in LL dams. Primary osteoblasts from low protein diet fed mice showed decreased in vitro bone formation and decreased osteogenic marker gene expression; promoter methylation analysis by pyrosequencing showed no differences in Bmpr1a, Ptch1, Sirt1, Osx, and Igf1r osteoregulators, while miR-26a, -34a, and -125b expression was found altered in low protein fed mice. Therefore, normal protein diet is indispensable for maternal musculoskeletal health during the reproductive period.
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Affiliation(s)
- Ioannis Kanakis
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Moussira Alameddine
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Mattia Scalabrin
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Rob J van 't Hof
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Triantafillos Liloglou
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, UK
| | - Susan E Ozanne
- MRC Metabolic Diseases Unit, Metabolic Research Laboratories, University of Cambridge, Cambridge, UK
| | - Katarzyna Goljanek-Whysall
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK.,Department of Physiology, School of Medicine, NUI Galway, Galway, Ireland
| | - Aphrodite Vasilaki
- Institute of Life Course and Medical Sciences, The MRC - Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
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Ashrafizadeh M, Najafi M, Makvandi P, Zarrabi A, Farkhondeh T, Samarghandian S. Versatile role of curcumin and its derivatives in lung cancer therapy. J Cell Physiol 2020; 235:9241-9268. [PMID: 32519340 DOI: 10.1002/jcp.29819] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/24/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is a main cause of death all over the world with a high incidence rate. Metastasis into neighboring and distant tissues as well as resistance of cancer cells to chemotherapy demand novel strategies in lung cancer therapy. Curcumin is a naturally occurring nutraceutical compound derived from Curcuma longa (turmeric) that has great pharmacological effects, such as anti-inflammatory, neuroprotective, and antidiabetic. The excellent antitumor activity of curcumin has led to its extensive application in the treatment of various cancers. In the present review, we describe the antitumor activity of curcumin against lung cancer. Curcumin affects different molecular pathways such as vascular endothelial growth factors, nuclear factor-κB (NF-κB), mammalian target of rapamycin, PI3/Akt, microRNAs, and long noncoding RNAs in treatment of lung cancer. Curcumin also can induce autophagy, apoptosis, and cell cycle arrest to reduce the viability and proliferation of lung cancer cells. Notably, curcumin supplementation sensitizes cancer cells to chemotherapy and enhances chemotherapy-mediated apoptosis. Curcumin can elevate the efficacy of radiotherapy in lung cancer therapy by targeting various signaling pathways, such as epidermal growth factor receptor and NF-κB. Curcumin-loaded nanocarriers enhance the bioavailability, cellular uptake, and antitumor activity of curcumin. The aforementioned effects are comprehensively discussed in the current review to further direct studies for applying curcumin in lung cancer therapy.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pooyan Makvandi
- Institute for Polymers, Composites and Biomaterials (IPCB), National Research Council (CNR), Naples, Italy
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, Turkey
| | - Tahereh Farkhondeh
- Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Saeed Samarghandian
- Healthy Ageing Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
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Woodman C, Vundu G, George A, Wilson CM. Applications and strategies in nanodiagnosis and nanotherapy in lung cancer. Semin Cancer Biol 2020; 69:349-364. [PMID: 32088362 DOI: 10.1016/j.semcancer.2020.02.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is the second most common cancer and the leading cause of death in both men and women in the world. Lung cancer is heterogeneous in nature and diagnosis is often at an advanced stage as it develops silently in the lung and is frequently associated with high mortality rates. Despite the advances made in understanding the biology of lung cancer, progress in early diagnosis, cancer therapy modalities and considering the mechanisms of drug resistance, the prognosis and outcome still remains low for many patients. Nanotechnology is one of the fastest growing areas of research that can solve many biological problems such as cancer. A growing number of therapies based on using nanoparticles (NPs) have successfully entered the clinic to treat pain, cancer, and infectious diseases. Recent progress in nanotechnology has been encouraging and directed to developing novel nanoparticles that can be one step ahead of the cancer reducing the possibility of multi-drug resistance. Nanomedicine using NPs is continuingly impacting cancer diagnosis and treatment. Chemotherapy is often associated with limited targeting to the tumor, side effects and low solubility that leads to insufficient drug reaching the tumor. Overcoming these drawbacks of chemotherapy by equipping NPs with theranostic capability which is leading to the development of novel strategies. This review provides a synopsis of current progress in theranostic applications for lung cancer diagnosis and therapy using NPs including liposome, polymeric NPs, quantum dots, gold NPs, dendrimers, carbon nanotubes and magnetic NPs.
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Affiliation(s)
- Christopher Woodman
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, United Kingdom
| | - Gugulethu Vundu
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, United Kingdom
| | - Alex George
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, United Kingdom; Jubilee Centre for Medical Research, Jubilee Mission Medical College & Research Institute, Thrissur, Kerala, India
| | - Cornelia M Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, United Kingdom; University of Liverpool, Institute of Translation Medicine, Dept of Molecular & Clinical Cancer Medicine, United Kingdom; Novel Global Community Educational Foundation, Australia.
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Bhattacharjee P, Das A, Giri AK, Bhattacharjee P. Epigenetic regulations in alternative telomere lengthening: Understanding the mechanistic insight in arsenic-induced skin cancer patients. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135388. [PMID: 31837846 DOI: 10.1016/j.scitotenv.2019.135388] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Telomere integrity is considered to be one of the primary mechanisms during malignant transformation. Arsenic, a group 1 carcinogenic metalloid, has been reported to cause telomere lengthening in a telomerase-independent manner. Recent studies suggest a significant role for epigenetic modifications in regulating telomeric length and integrity. Here, we have explored the role of epigenetic deregulation in alternative lengthening of telomeres (ALT) in arsenic-exposed skin cancer tissues and corresponding non-tumor tissues. The relative telomere length (RTL) was analyzed by qRT-PCR using 2-ΔΔCt method. The subtelomeric methylation pattern of the four chromosomes (7q, 18p, 21q and XpYp) were analysed by Methylation Specific PCR (MSP) in 40 pairs of arsenic exposed skin cancer tissues and its corresponding control. The role of constitutive heterochromatin histone marks in the regulation of telomere length (TL) was analyzed by targeted ELISA. A 2-fold increase of relative telomere length in 85% of the arsenic-induced skin cancer tissues was observed. Among the four chromosomes, subtelomere of XpYp was found to be hypermethylated (p < 0.001) whereas 18p was hypomethylated (p < 0.01). Additionally, the level of H4K20me3, a heterochromatic mark was found to be significantly down-regulated (p < 0.0003), and inversely correlated with telomere length indicating loss of heterochromatinization of telomeric DNA. These observations highlight the novel role of epigenetic regulation in the maintenance of constitutive heterochromatin structure at telomere. Alteration in subtelomeric DNA methylation patterns and depletion of H4K20me3 might lead to loss of heterochromatinization resulting in arsenic-induced telomeric elongation. We provide novel data indicating possible alternative determinants of telomere elongation through epigenetic modifications during arsenic-induced skin carcinogenesis which could be used as early 'epimarkers' in the near future. The findings provide new insights about the mechanism of arsenic-induced carcinogenesis.
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Affiliation(s)
- Pritha Bhattacharjee
- Department of Zoology, University of Calcutta, Kolkata 700019, India; Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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Panagopoulos I, Gorunova L, Leske H, Niehusmann P, Johannessen LE, Staurseth J, Øino N, Meling TR, Heim S, Micci F, Brandal P. Pyrosequencing Analysis of MGMT Promoter Methylation in Meningioma. Cancer Genomics Proteomics 2018; 15:379-385. [PMID: 30194078 DOI: 10.21873/cgp.20096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 06/28/2018] [Accepted: 07/08/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a well-established predictor of response to the DNA-alkylating agent temozolomide in patients with glioblastoma. MATERIALS AND METHODS Pyrosequencing analysis was used to determine the MGMT promoter methylation status in 61 meningiomas, to clarify whether it might have a predictive role. RESULTS Only two tumors (3%) had a mean methylation frequency higher than the cut-off value of 10% for the four CpG sites examined. CONCLUSION The methylation of the MGMT promoter is uncommon, or occurs at a low frequency in meningiomas. There is no convincing rationale to test such tumors for their MGMT methylation status in a clinical setting.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Henning Leske
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Pitt Niehusmann
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Lene E Johannessen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Julie Staurseth
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Nina Øino
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Torstein R Meling
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Neurosurgery, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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12
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Menschikowski M, Jandeck C, Friedemann M, Nacke B, Hantsche S, Tiebel O, Sukocheva O, Hagelgans A. Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR). Oncotarget 2018; 9:36137-36150. [PMID: 30546833 PMCID: PMC6281424 DOI: 10.18632/oncotarget.26315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/24/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The analysis of aberrant DNA methylations is used for the diagnosis of cancer as significant changes in the gene methylation pattern are often detected during early carcinogenesis. In this study, we evaluated the performance of a two-step method that combines pre-amplification with ddPCR technique. RESULTS By using ddPCR, the dependence of amplification efficiency for methylated and unmethylated DNA fragments on the relevant MgCl2 concentration and the annealing temperature was established in addition to the primer design. We found that the efficiency can be adjusted toward methylated sequences by using primers covering one to four CpG sites under appropriately selected MgCl2 concentration and annealing temperature. Applying a PCR bias between 85% and 95%, five copies of methylated tumor DNA fragments were detected against a background of 700,000 copies of unmethylated DNA fragments with a high signal-to-noise ratio. The analysis of serum samples from patients with prostate cancer showed a significantly improved performance of the new method in comparison with the MS-HRM technique, ddPCR alone, or ddPCR in combination with an unbiased pre-amplification using methylation-independent primers. CONCLUSIONS We define this method as an optimized bias-based pre-amplification-digital droplet PCR (OBBPA-ddPCR) technique. This novel method is recommended for the early detection of cancer-specific DNA methylation biomarkers in the form of a liquid biopsy.
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Affiliation(s)
- Mario Menschikowski
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Carsten Jandeck
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Markus Friedemann
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Brit Nacke
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Saskia Hantsche
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Oliver Tiebel
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Olga Sukocheva
- 2 School of Health Sciences, Flinders University of South Australia, Adelaide, Australia
| | - Albert Hagelgans
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
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13
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Highly sensitive detection of DNA hypermethylation in melanoma cancer cells. Biosens Bioelectron 2018; 124-125:136-142. [PMID: 30366258 DOI: 10.1016/j.bios.2018.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022]
Abstract
Aberrant hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a promising biomarker for early cancer detection. This methylation status is reflected in the methylation pattern of ctDNA shed from the primary tumor; however, to realize the full clinical utility of ctDNA methylation detection via liquid biopsy for early cancer diagnosis, improvements in the sensitivity and multiplexability of existing technologies must be improved. Additionally, the assay must be cheap and easy to perform in a clinical setting. We report the integration of methylation specific PCR (MSP) to melt curve analysis on giant magnetoresistive (GMR) biosensors to greatly enhance the sensitivity of our DNA hybridization assay for methylation detection. Our GMR sensor is functionalized with synthetic DNA probes that target methylated or unmethylated CpG sites in the MSP amplicon, and measures the difference in melting temperature (Tm) between the two probes (ΔTm), giving an analytical limit of detection down to 0.1% methylated DNA in solution. Additionally, linear regression of ΔTm's for serial dilutions of methylated:unmethylated mixtures allows for quantification of methylation percentage, which could have diagnostic and prognostic utility. Lastly, we performed multiplexed MSP on two different genes, and show the ability of our GMR assay to resolve this mixture, despite their amplicons' overlapping Tm's in standard EvaGreen melt analysis. The multiplexing ability of our assay and its enhanced sensitivity, without necessitating deep sequencing, represent important steps toward realizing an assay for the detection of methylated ctDNA in plasma for early cancer detection in a clinical setting.
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14
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Kim SH, Park KH, Shin SJ, Lee KY, Kim TI, Kim NK, Rha SY, Ahn JB. CpG Island Methylator Phenotype and Methylation of Wnt Pathway Genes Together Predict Survival in Patients with Colorectal Cancer. Yonsei Med J 2018; 59:588-594. [PMID: 29869456 PMCID: PMC5990680 DOI: 10.3349/ymj.2018.59.5.588] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/05/2018] [Accepted: 04/30/2018] [Indexed: 01/19/2023] Open
Abstract
PURPOSE Dysregulation of the Wnt pathway is a crucial step in the tumorigenesis of colorectal cancer (CRC). This study aimed to determine whether DNA methylation of Wnt pathway genes helps predict treatment response and survival in patients with metastatic or recurrent CRC. MATERIALS AND METHODS We retrospectively collected primary tumor tissues from 194 patients with metastatic or recurrent CRC. Pyrosequencing was used to examine the methylation of 10 CpG island loci in DNA extracted from formalin-fixed paraffin-embedded specimens. To elucidate the predictive role of DNA methylation markers, Kaplan-Meier survival estimation and Cox regression were performed for progression-free survival and overall survival (OS). RESULTS The methylation frequencies of the 10 genes analyzed (p16, p14, MINT1, MINT2, MINT31, hMLH1, DKK3, WNT5A, AXIN2, and TFAP2E) were 47.9%, 10.8%, 21.1%, 16.0%, 20.6%, 0.5%, 53.1%, 32.0%, 2.6%, and 2.1%, respectively. We divided patients into three groups based on the number of methylated genes (group 1, no methylation n=38; group 2, 1-2 methylations n=92; group 3, 3 or more methylations n=64). Among patients treated with palliative chemotherapy (n=167), median OSs of groups 1, 2, and 3 were 39.1, 39.7, and 29.1 months, respectively (log rank p=0.013). After adjustment, number of methylations was identified as an independent poor prognostic factor (0-2 methylated vs. ≥3 methylated: hazard ratio, 1.72; 95% confidence interval, 1.16-2.56, p=0.007). CONCLUSION This study suggests that methylation of Wnt pathway genes, in addition to known CpG island methylator phenotype markers, may help predict treatment outcome and survival in patients with CRC.
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Affiliation(s)
- Se Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Medicine, Graduate School of Yonsei University, Seoul, Korea
| | - Kyu Hyun Park
- Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Joon Shin
- Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Kang Young Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Il Kim
- Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Nam Kyu Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Sun Young Rha
- Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Joong Bae Ahn
- Department of Medicine, Graduate School of Yonsei University, Seoul, Korea
- Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea.
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15
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Li L, Xu C, Long J, Shen D, Zhou W, Zhou Q, Yang J, Jiang M. E6 and E7 gene silencing results in decreased methylation of tumor suppressor genes and induces phenotype transformation of human cervical carcinoma cell lines. Oncotarget 2016; 6:23930-43. [PMID: 26329329 PMCID: PMC4695162 DOI: 10.18632/oncotarget.4525] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/02/2015] [Indexed: 01/01/2023] Open
Abstract
In SiHa and CaSki cells, E6 and E7-targeting shRNA specifically and effectively knocked down human papillomavirus (HPV) 16 E6 and E7 at the transcriptional level, reduced the E6 and E7 mRNA levels by more than 80% compared with control cells that expressed a scrambled-sequence shRNA. E6 and E7 repression resulted in down-regulation of DNA methyltransferase mRNA and protein expression, decreased DNA methylation and increased mRNA expression levels of tumor suppressor genes, induced a certain apoptosis and inhibited proliferation in E6 and E7 shRNA-infected SiHa and CaSki cells compared with the uninfected cells. Repression of E6 and E7 oncogenes resulted in restoration of DNA methyltransferase suppressor pathways and induced apoptosis in HPV16-positive cervical carcinoma cell lines. Our findings suggest that the potential carcinogenic mechanism of HPV16 through influencing DNA methylation pathway to activate the development of cervical cancer exist, and maybe as a candidate therapeutic strategy for cervical and other HPV-associated cancers.
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Affiliation(s)
- Liming Li
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Cui Xu
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jia Long
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Danbei Shen
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Wuqing Zhou
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qiyan Zhou
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jia Yang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Mingjun Jiang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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16
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Draht MXG, Smits KM, Jooste V, Tournier B, Vervoort M, Ramaekers C, Chapusot C, Weijenberg MP, van Engeland M, Melotte V. Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome. Clin Epigenetics 2016; 8:44. [PMID: 27118999 PMCID: PMC4845472 DOI: 10.1186/s13148-016-0211-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series. Methods In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up. Results Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested-MSP, pyrosequencing, and MS-HRM varied, the prognostic effect seemed similar (HR 1.74, 95 % CI 0.97–3.15; HR 1.85, 95 % CI 0.93–3.86; HR 1.83, 95 % CI 0.92–3.65, respectively). Conclusions Our results show that upon optimizing and aligning four RET methylation assays with regard to primer location and sensitivity, differences in methylation frequencies and clinical sensitivities are observed; however, the effect on the marker’s prognostic outcome is minimal. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0211-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muriel X G Draht
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kim M Smits
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Valérie Jooste
- Registre Bourguignon des cancers digestifs, INSERM U866, Universite de Bourgogne, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Benjamin Tournier
- Service de Pathologie, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Martijn Vervoort
- Zuyd University of Applied Sciences, Heerlen, The Netherlands ; Chemelot Innovation and Learning Labs, Geleen, The Netherlands
| | | | - Caroline Chapusot
- Service de Pathologie, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Matty P Weijenberg
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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17
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Kristensen LS, Michaelsen SR, Dyrbye H, Aslan D, Grunnet K, Christensen IJ, Poulsen HS, Grønbæk K, Broholm H. Assessment of Quantitative and Allelic MGMT Methylation Patterns as a Prognostic Marker in Glioblastoma. J Neuropathol Exp Neurol 2016; 75:246-55. [PMID: 26883115 PMCID: PMC4777218 DOI: 10.1093/jnen/nlv024] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene is a predictive and prognostic marker in newly diagnosed glioblastoma patients treated with temozolomide but how MGMT methylation should be assessed to ensure optimal detection accuracy is debated. We developed a novel quantitative methylation-specific PCR (qMSP) MGMT assay capable of providing allelic methylation data and analyzed 151 glioblastomas from patients receiving standard of care treatment (Stupp protocol). The samples were also analyzed by immunohistochemistry (IHC), standard bisulfite pyrosequencing, and genotyped for the rs1690252 MGMT promoter single nucleotide polymorphism. Monoallelic methylation was observed more frequently than biallelic methylation, and some cases with monoallelic methylation expressed the MGMT protein whereas others did not. The presence of MGMT methylation was associated with better overall survival (p = 0.006; qMSP and p = 0.002; standard pyrosequencing), and the presence of the protein was associated with worse overall survival (p = 0.009). Combined analyses of qMSP and standard pyrosequencing or IHC identified additional patients who benefited from temozolomide treatment. Finally, low methylation levels were also associated with better overall survival (p = 0.061; qMSP and p = 0.02; standard pyrosequencing). These data support the use of both MGMT methylation and MGMT IHC but not allelic methylation data as prognostic markers in patients with temozolomide-treated glioblastoma.
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Affiliation(s)
- Lasse S Kristensen
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB).
| | - Signe R Michaelsen
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Henrik Dyrbye
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Derya Aslan
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Kirsten Grunnet
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Ib J Christensen
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Hans S Poulsen
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Kirsten Grønbæk
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
| | - Helle Broholm
- From the Department of Hematology (LSK, DA, KG); Department of Radiation Biology (SRM, KG, IJC, HSP); and Department of Pathology, Rigshospitalet, Copenhagen Ø, Denmark (HD, HB)
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18
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MGMT testing allows for personalised therapy in the temozolomide era. Tumour Biol 2015; 37:87-96. [PMID: 26518768 DOI: 10.1007/s13277-015-4240-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022] Open
Abstract
Adjuvant temozolomide (TMZ)-based chemoradiation is the standard of care for most glioblastoma patients (GBMs); however, a large proportion of these patients do not respond to TMZ. Silencing of the O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is thought to induce chemosensitivity, and testing for methylation may allow for patient stratification; however, this has yet to become routine clinical practice despite an abundance of literature on the subject. The databases PubMed, Embase, The Cochrane Library, Science Direct and Medline were searched for relevant articles published between 1999 and 2015. Articles utilising MGMT testing in glioblastomas, and treatment of glioblastomas with temozolomide were assessed. Immunohistochemistry, methylation-specific PCR (MSP), reverse transcriptase PCR, pyrosequencing and bisulphite sequencing were the main testing methods identified. Nested-MSP techniques produced poor correlation with survival, whilst bisulphite sequencing showed no evident benefit over MSP. Testing is limited by sample quality and contamination; however, efforts are made to minimise this. Strong evidence for MGMT-based personalised therapy was presented in the elderly but remains controversial in the entire GBM population. MGMT testing presents many obstacles yet to be overcome, and these warrant attention prior to the routine implementation of MGMT testing to aid decision making in GBMs. However, there is evidence to support its use, particularly in the elderly.
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Li YF, Hsiao YH, Lai YH, Chen YC, Chen YJ, Chou JL, Chan MWY, Lin YH, Tsou YA, Tsai MH, Tai CK. DNA methylation profiles and biomarkers of oral squamous cell carcinoma. Epigenetics 2015; 10:229-36. [PMID: 25612142 DOI: 10.1080/15592294.2015.1006506] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) constitutes >90% of oral cancers and is the sixth most common malignancy among males worldwide and the fourth leading cause of death due to cancer among males in Taiwan. However, most patients do not receive a diagnosis of OSCC until the late stages, which have a lower survival rate. The use of molecular marker analysis to identify early-stage OSCC would permit optimal timing for treatments and consequently prolong survival. The aim of this study was to identify biomarkers of OSCC using the Illumina GoldenGate Methylation Cancer Panel, which comprised a total of 1,505 CpG sites covering 807 genes. Samples of buccal mucosa resected from 40 OSCC patients and normal tissue samples obtained from 15 patients (normal mucosa from OSCC patients or from patients undergoing surgery unrelated to OSCC) were analyzed. Fms-related tyrosine kinase 4 (FLT4) methylation exhibited a perfect specificity for detecting OSCC, with an area under the receiver operating characteristic curve of 0.91 for both all-stage and early-stage OSCC. Methylation of 7 genes (ASCL1, FGF3, FLT4, GAS7, KDR, TERT, and TFPI2) constitutes the top-20 panels for detecting OSCC. The top-20 panels for detecting early-stage OSCC contain 8 genes: ADCYAP1, EPHA7, FLT4, GSTM2, KDR, MT1A, NPY, and TFPI2. FLT4 RNA expression and methylation level were validated using RT-PCR and a pyrosequencing methylation assay. The median level of FLT4 expression was 2.14-fold for normal relative to OSCC tissue samples (P < 0.0001). Among the 8 pyrosequenced FLT4 CpG sites, methylation level was much higher in the OSCC samples. In conclusion, methylation statuses of selected genes, and especially FLT4, KDR, and TFPI2, might be of great potential as biomarkers for early detection of buccal OSCC.
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Affiliation(s)
- Yu-Fen Li
- a Institute of Biostatistics; China Medical University ; Taichung , Taiwan
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20
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Choudhury SR, Cui Y, Milton JR, Li J, Irudayaraj J. Selective increase in subtelomeric DNA methylation: an epigenetic biomarker for malignant glioma. Clin Epigenetics 2015; 7:107. [PMID: 26451167 PMCID: PMC4597615 DOI: 10.1186/s13148-015-0140-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/22/2015] [Indexed: 01/12/2023] Open
Abstract
Background Subtelomeric regions dynamically change their epigenetic pattern during development and progression of several malignancies and degenerative disorders. However, DNA methylation of human subtelomeres and their correlation to telomere length (TL) remain undetermined in glioma. Results Herein, we report on the selective changes in subtelomeric DNA methylation at the end of five chromosomes (Chr.) (7q, 8q. 18p, 21q, and XpYp) and ascertain their correlation with TL in patients with glioma. Subtelomeric methylation level was invariably higher in glioma patients compared to the control group, irrespective of their age and tumor grade. In particular, a significant increase in methylation was observed at the subtelomeric CpG sites of Chr. 8q, 21q, and XpYp in tissues, obtained from the brain tumor of glioma patients. In contrast, no significant change in methylation was observed at the subtelomere of Chr. 7q and 18p. Selective changes in the subtelomeric methylation level, however, did not show any significant correlation to the global TL. This observed phenomenon was validated in vitro by inducing demethylation in a glioblastoma cell line (SF-767) using 5-azacytidine (AZA) treatment. AZA treatment caused significant changes in the subtelomeric methylation pattern but did not alter the TL, which supports our hypothesis. Conclusions DNA methylation level dramatically increased at the subtelomere of Chr.8q, 21q, and XpYp in malignant glioma, which could be used as an early epigenetic diagnostic biomarker of the disease. Alterations in subtelomeric methylation, however, have no effects on the TL. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0140-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samrat Roy Choudhury
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
| | - Yi Cui
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
| | - Jacob R Milton
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906 USA
| | - Jian Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Joseph Irudayaraj
- Department of Biological Engineering, Center for Cancer Research, Purdue University, West Lafayette, IN 47906 USA
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Kristensen LS, Asmar F, Dimopoulos K, Nygaard MK, Aslan D, Hansen JW, Ralfkiaer E, Grønbæk K. Hypermethylation of DAPK1 is an independent prognostic factor predicting survival in diffuse large B-cell lymphoma. Oncotarget 2015; 5:9798-810. [PMID: 25229255 PMCID: PMC4259438 DOI: 10.18632/oncotarget.2394] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma. Improvements in overall survival have been observed with the introduction of rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), however, prognostic markers are still needed. Methylation of the death associated protein kinase (DAPK or DAPK1) gene and TP53 mutations are likely to have prognostic value in DLBCL. We have assessed TP53 mutations and allelic DAPK1 methylation patterns in a cohort of 119 DLBCL patients uniformly treated with R-CHOP-like regimens. We found that DAPK1 promoter methylation was associated with shorter overall survival (p=0.017) and disease-specific survival (p=0.023). In multivariate analyses DAPK1 methylation remained as an independent prognostic factor predicting disease-specific survival (p=0.038). When only considering individuals heterozygous for the rs13300553 SNP monoallelic methylation of the A-allele was associated with shorter overall- and disease-specific survival (p<0.001). Patients carrying both DAPK1 methylation and a TP53 mutation had an inferior survival compared to patients carrying only one of these molecular alterations, however, this was borderline statistically significant. Allele-specific DAPK1 methylation patterns were also studied in a cohort of 67 multiple myeloma patients, and all of the methylated multiple myeloma samples heterozygous for the rs13300553 SNP were methylated on both alleles.
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Affiliation(s)
| | - Fazila Asmar
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100-DK, Copenhagen, Denmark
| | | | - Mette Kathrine Nygaard
- Department of Haematology, Aalborg University Hospital, Mølleparkvej 4, 9000-DK, Aalborg, Denmark
| | - Derya Aslan
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100-DK, Copenhagen, Denmark
| | - Jakob Werner Hansen
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100-DK, Copenhagen, Denmark
| | | | - Kirsten Grønbæk
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100-DK, Copenhagen, Denmark
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MGMT promoter methylation and glioblastoma: a comparison of analytical methods and of tumor specimens. Int J Biol Markers 2015; 30:e208-16. [PMID: 25588856 DOI: 10.5301/jbm.5000126] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 11/20/2022]
Abstract
It is already well known that hypermethylation of the O6-methylguanine DNA methyltransferase (MGMT) gene promoter is a predictive biomarker of response to temozolomide treatment and of favorable outcomes in terms of overall survival (OS) and progression-free survival (PFS) in glioblastoma (GBM) patients. Nevertheless, MGMT methylation status has not currently been introduced into routine clinical practice, as the choice of the ideal technique and tissue sample specimen is still controversial. The aim of this study was to compare 2 analytical methods, methylation-specific polymerase chain reaction (MSP) and pyrosequencing (PSQ), and their use on 2 different tissue type samples, snap-frozen and formalin-fixed paraffin-embedded (FFPE), obtained from a single-center and uniformly treated cohort of 46 GBM patients. We obtained methylation data from all frozen tissues, while no results were obtained for 5 FFPE samples. The highest concordance for methylation was found on frozen tissues (88.5%, 23/26 samples), using PSQ (76.7%, 23/30 samples). Moreover, we confirmed that OS and PFS for patients carrying methylation of the MGMT promoter were longer than for patients with an unmethylated promoter. In conclusion, we considered MSP a limited technique for FFPE tissues due to the high risk of false-positive results; in contrast, our data indicated PSQ as the most powerful method to stratify methylated/unmethylated patients as it allows reaching quantitative results with high sensitivity and specificity. Furthermore, frozen tumor tissues were shown to be the best specimens for MGMT methylation analysis, due to the low DNA degradation and homogeneity in methylation throughout the tumor.
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Xie H, Tubbs R, Yang B. Detection of MGMT promoter methylation in glioblastoma using pyrosequencing. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:1790-1796. [PMID: 25973069 PMCID: PMC4396208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
Recent clinical trials on patients with glioblastoma revealed that O6-Methylguanine-DNA methyltransferase (MGMT) methylation status significantly predicts patient's response to alkylating agents. In this study, we sought to develop and validate a quantitative MGMT methylation assay using pyrosequencing on glioblastoma. We quantified promoter methylation of MGMT using pyrosequencing on paraffin-embedded fine needle aspiration biopsy tissues from 43 glioblastoma. Using a 10% cutoff, MGMT methylation was identified in 37% cases of glioblastoma and 0% of the non-neoplastic epileptic tissue. Methylation of any individual CpG island in MGMT promoter ranged between 33% and 95%, with a mean of 65%. By a serial dilution of genomic DNA of a homogenously methylated cancer cell line with an unmethylated cell line, the analytical sensitivity is at 5% for pyrosequencing to detect MGMT methylation. The minimal amount of genomic DNA required is 100 ng (approximately 3,000 cells) in small fine needle biopsy specimens. Compared with methylation-specific PCR, pyrosequencing is comparably sensitive, relatively specific, and also provides quantitative information for each CpG methylation.
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Affiliation(s)
- Hao Xie
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH, USA
| | - Raymond Tubbs
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH, USA
| | - Bin Yang
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH, USA
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Xie H, Tubbs R, Yang B. Detection of MGMT promoter methylation in glioblastoma using pyrosequencing. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:636-642. [PMID: 25755756 PMCID: PMC4348884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
Recent clinical trials on patients with glioblastoma revealed that O(6)-Methylguanine-DNA methyltransferase (MGMT) methylation status significantly predicts patient's response to alkylating agents. In this study, we sought to develop and validate a quantitative MGMT methylation assay using pyrosequencing on glioblastoma. We quantified promoter methylation of MGMT using pyrosequencing on paraffin-embedded fine needle aspiration biopsy tissues from 43 glioblastoma. Using a 10% cutoff, MGMT methylation was identified in 37% cases of glioblastoma and 0% of the non-neoplastic epileptic tissue. Methylation of any individual CpG island in MGMT promoter ranged between 33% and 95%, with a mean of 65%. By a serial dilution of genomic DNA of a homogenously methylated cancer cell line with an unmethylated cell line, the analytical sensitivity is at 5% for pyrosequencing to detect MGMT methylation. The minimal amount of genomic DNA required is 100 ng (approximately 3,000 cells) in small fine needle biopsy specimens. Compared with methylation-specific PCR, pyrosequencing is comparably sensitive, relatively specific, and also provides quantitative information for each CpG methylation.
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Affiliation(s)
- Hao Xie
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH
| | - Raymond Tubbs
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH
| | - Bin Yang
- Robert J. Tomsick Pathology & Laboratory Medicine Institute, Cleveland Clinic Cleveland, OH
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Abstract
Head and neck cancers are characterized by both genetic and epigenetic aberrations. In treating head and neck cancers, ionizing radiation (IR) is an essential modality in either definitive or adjuvant setting. However, radiation-resistant head and neck cancers are not uncommon. The major biological determinator for IR resistance was previously considered at genetic level because DNA is the major target of irradiation damage. However, in head and neck cancers, recent evidence demonstrated epigenetic disturbance after IR, implicating its role in IR resistance. Hence, this chapter intends to establish an in vitro model for investigating DNA methylation changes in IR-resistant head and neck cancer cells. Bisulfite pyrosequencing is the main methodology it introduced.
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Busato F, Tost J. SNP-Based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®. Methods Mol Biol 2015; 1315:291-313. [PMID: 26103907 DOI: 10.1007/978-1-4939-2715-9_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The analysis of allele-specific DNA methylation patterns has recently attracted much interest as loci of allele-specific DNA methylation overlap with known risk loci for complex diseases and the analysis might contribute to the fine-mapping and interpretation of non-coding genetic variants associated with complex diseases and improve the understanding between genotype and phenotype. In the presented protocol, we present a method for the analysis of DNA methylation patterns on both alleles separately using heterozygous Single Nucleotide Polymorphisms (SNPs) as anchor for allele-specific PCR amplification followed by analysis of the allele-specific DNA methylation patterns by Pyrosequencing(®). Pyrosequencing is an easy-to-handle, quantitative real-time sequencing method that is frequently used for genotyping as well as for the analysis of DNA methylation patterns. The protocol consists of three major steps: (1) identification of individuals heterozygous for a SNP in a region of interest using Pyrosequencing; (2) analysis of the DNA methylation patterns surrounding the SNP on bisulfite-treated DNA to identify regions of potential allele-specific DNA methylation; and (3) the analysis of the DNA methylation patterns associated with each of the two alleles, which are individually amplified using allele-specific PCR. The enrichment of the targeted allele is re-enforced by modification of the allele-specific primers at the allele-discriminating base with Locked Nucleic Acids (LNA). For the proof-of-principle of the developed approach, we provide assay details for three imprinted genes (IGF2, IGF2R, and PEG3) within this chapter. The mean of the DNA methylation patterns derived from the individual alleles corresponds well to the overall DNA methylation patterns and the developed approach proved more reliable compared to other protocols for allele-specific DNA methylation analysis.
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Affiliation(s)
- Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
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Optimizing methodologies for PCR-based DNA methylation analysis. Biotechniques 2014; 55:181-97. [PMID: 24107250 DOI: 10.2144/000114087] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 09/10/2013] [Indexed: 02/07/2023] Open
Abstract
Comprehensive analysis of DNA methylation patterns is critical for understanding the molecular basis of many human diseases. While hundreds of PCR-based DNA methylation studies are published every year, the selection and implementation of appropriate methods for these studies can be challenging for molecular genetics researchers not yet familiar with methylation analysis. Here we review the most commonly used PCR-based DNA methylation analysis techniques: bisulfite sequencing PCR (BSP), methylation specific PCR (MSP), MethyLight, and methylation-sensitive high resolution melting (MS-HRM). We provide critical analysis of the strengths and weaknesses of each approach as well as a series of guidelines to assist in selecting and implementing an appropriate method.
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LAN VOTHITHUONG, HA NGOTHI, UYEN NGUYENQUYNH, DUONG NGUYENTHI, HUONG NGUYENTHITHU, THUAN TABICH, DUONG PHAMANHTHUY, VAN TO TA. Standardization of the methylation-specific PCR method for analyzing BRCA1 and ER methylation. Mol Med Rep 2014; 9:1844-50. [DOI: 10.3892/mmr.2014.1990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 02/05/2014] [Indexed: 11/06/2022] Open
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Kristensen LS, Treppendahl MB, Asmar F, Girkov MS, Nielsen HM, Kjeldsen TE, Ralfkiaer E, Hansen LL, Grønbæk K. Investigation of MGMT and DAPK1 methylation patterns in diffuse large B-cell lymphoma using allelic MSP-pyrosequencing. Sci Rep 2013; 3:2789. [PMID: 24071855 PMCID: PMC3784959 DOI: 10.1038/srep02789] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/11/2013] [Indexed: 12/11/2022] Open
Abstract
The tumor suppressor genes MGMT and DAPK1 become methylated in several cancers including diffuse large B-cell lymphoma (DLBCL). However, allelic methylation patterns have not been investigated in DLBCL. We developed a fast and cost-efficient method for the analysis of allelic methylation based on pyrosequencing of methylation specific PCR (MSP) products including a SNP. Allelic methylation patterns were reliably analyzed in standards of known allelic methylation status even when diluted in unmethylated DNA to below 1% methylation. When studying 148 DLBCL patients MGMT and DAPK1 methylation was observed in 19% and 89%, respectively, and among methylated and heterozygous patients 29% and 55%, respectively, were biallelically methylated. An association between the T-allele of the rs16906252 SNP and MGMT methylation was observed (p-value=0.04), and DAPK1 methylation of the A-allele was associated with shorter overall survival (p-value=0.006). In future cancer research allelic MSP-pyrosequencing may be used to study a wide range of other loci.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Alleles
- Antibodies, Monoclonal, Murine-Derived
- Antineoplastic Combined Chemotherapy Protocols
- Cell Line
- Cyclophosphamide
- DNA Methylation
- DNA Modification Methylases/genetics
- DNA Repair Enzymes/genetics
- Death-Associated Protein Kinases/genetics
- Doxorubicin
- Female
- Genotype
- Humans
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Neoplasm Staging
- Polymorphism, Single Nucleotide
- Prednisone
- Rituximab
- Sensitivity and Specificity
- Sequence Analysis, DNA
- Treatment Outcome
- Tumor Suppressor Proteins/genetics
- Vincristine
- Young Adult
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Affiliation(s)
| | | | - Fazila Asmar
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | | | - Helene Myrtue Nielsen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | | | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
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Kristensen LS, Treppendahl MB, Grønbæk K. Analysis of epigenetic modifications of DNA in human cells. ACTA ACUST UNITED AC 2013; Chapter 20:Unit20.2. [PMID: 23595599 DOI: 10.1002/0471142905.hg2002s77] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Epigenetics, the study of somatically heritable changes in gene expression not related to changes in the DNA sequence, is a rapidly expanding research field that plays important roles in healthy as well as in diseased cells. DNA methylation and hydroxymethylation are epigenetic modifications found in human cells, which are deeply implicated in normal cellular processes as well as in several major human diseases. Here, a range of different methods for the analyses of DNA methylation and hydroxymethylation at locus-specific and genome-wide scales is described.
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Hubers AJ, Prinsen CFM, Sozzi G, Witte BI, Thunnissen E. Molecular sputum analysis for the diagnosis of lung cancer. Br J Cancer 2013; 109:530-7. [PMID: 23868001 PMCID: PMC3738145 DOI: 10.1038/bjc.2013.393] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/08/2013] [Accepted: 06/21/2013] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is the leading cause of cancer mortality rate worldwide, mainly because of the presence of metastatic disease at the time of diagnosis. Early detection of lung cancer improves prognosis, and towards this end, large screening trials in high-risk individuals have been conducted since the past century. Despite all efforts, the need for novel (complementary) lung cancer diagnostic and screening methods still exists. In this review, we focus on the assessment of lung cancer-related biomarkers in sputum in the past decennium. Besides cytology, mutation and microRNA analysis, special attention has been paid to DNA promoter hypermethylation, of which all available literature is summarised without time restriction. A model is proposed to aid in the distinction between diagnostic and risk markers. Research on the use of sputum for non-invasive detection of early-stage lung cancer has brought new insights and advanced molecular techniques. The sputum shows a promising potential for routine diagnostic and possibly screening purposes.
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Affiliation(s)
- A J Hubers
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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32
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Gauchotte G, Lacomme S, Brochin L, Tournier B, Cahn V, Monhoven N, Piard F, Klein M, Martinet N, Rochette-Egly C, Vignaud JM. Retinoid acid receptor expression is helpful to distinguish between adenoma and well-differentiated carcinoma in the thyroid. Virchows Arch 2013; 462:619-32. [DOI: 10.1007/s00428-013-1419-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/26/2013] [Accepted: 04/22/2013] [Indexed: 11/24/2022]
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Beggs AD, Jones A, Shepherd N, Arnaout A, Finlayson C, Abulafi AM, Morton DG, Matthews GM, Hodgson SV, Tomlinson IPM. Loss of expression and promoter methylation of SLIT2 are associated with sessile serrated adenoma formation. PLoS Genet 2013; 9:e1003488. [PMID: 23671423 PMCID: PMC3649993 DOI: 10.1371/journal.pgen.1003488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/11/2013] [Indexed: 12/22/2022] Open
Abstract
Serrated adenomas form a distinct subtype of colorectal pre-malignant lesions that may progress to malignancy along a different molecular pathway than the conventional adenoma-carcinoma pathway. Previous studies have hypothesised that BRAF mutation and promoter hypermethylation plays a role, but the evidence for this is not robust. We aimed to carry out a whole-genome loss of heterozygosity analysis, followed by targeted promoter methylation and expression analysis to identify potential pathways in serrated adenomas. An initial panel of 9 sessile serrated adenomas (SSA) and one TSA were analysed using Illumina Goldengate HumanLinkage panel arrays to ascertain regions of loss of heterozygosity. This was verified via molecular inversion probe analysis and microsatellite analysis of a further 32 samples. Methylation analysis of genes of interest was carried out using methylation specific PCR (verified by pyrosequencing) and immunohistochemistry used to correlate loss of expression of genes of interest. All experiments used adenoma samples and normal tissue samples as control. SSA samples were found on whole-genome analysis to have consistent loss of heterozygosity at 4p15.1-4p15.31, which was not found in the sole TSA, adenomas, or normal tissues. Genes of interest in this region were PDCH7 and SLIT2, and combined MSP/IHC analysis of these genes revealed significant loss of SLIT2 expression associated with promoter methylation of SLIT2. Loss of expression of SLIT2 by promoter hypermethylation and loss of heterozygosity events is significantly associated with serrated adenoma development, and SLIT2 may represent a epimutated tumour suppressor gene according to the Knudson "two hit" hypothesis.
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Affiliation(s)
- Andrew D Beggs
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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Abstract
Background: There is relatively little methylation array data available specifically for oral
squamous cell carcinoma (OSCC). This study aims to compare the DNA methylome across a
large cohort of tumour/normal pairs. Methods: DNA was extracted from 44 OSCCs and paired normal mucosa. DNA methylation analysis
employed the Illumina GoldenGate high-throughput array comprising 1505 CpG loci selected
from 807 epigenetically regulated genes. This data was correlated with extracapsular
spread (ECS), human papilloma virus (HPV) status, recurrence and 5-year survival. Results: Differential methylation levels of a number of genes distinguished the tumour tissue
sample from the matched normal. Putative methylation signatures for ECS and recurrence
were identified. The concept of concordant methylation or CpG island methylator
phenotype (CIMP) in OSCC is supported by our data, with an association between
‘CIMP-high' and worse prognosis. Epigenetic deregulation of NOTCH4
signalling in OSCC was also observed, as part of a possible methylation signature for
recurrence, with parallels to recently discovered NOTCH mutations in HNSCC.
Differences in methylation in HPV-driven cases were seen, but are less significant than
that has been recently proposed in other series. Conclusion: Although OSCC seems as much an ‘epigenetic' as a genetic disease, the
translational potential of cancer epigenetics has yet to be fully exploited. This data
points to the application of epigenetic biomarkers and targets available to further the
development of therapy in OSCC.
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Shaw RJ, Hobkirk AJ, Nikolaidis G, Woolgar JA, Triantafyllou A, Brown JS, Liloglou T, Risk JM. Molecular staging of surgical margins in oral squamous cell carcinoma using promoter methylation of p16(INK4A), cytoglobin, E-cadherin, and TMEFF2. Ann Surg Oncol 2012; 20:2796-802. [PMID: 23111707 DOI: 10.1245/s10434-012-2713-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Local recurrence in oral squamous cell carcinoma (OSCC) despite clear surgical margins may indicate the presence of residual, sub-microscopic disease. Molecular assessment of surgical margins may provide a greater prognostic sensitivity compared to histopathology. We aimed to determine whether promoter methylation in deep and mucosal resection margins can predict recurrence in OSCC. METHODS Forty-eight consecutive OSCC cases were recruited and a 5 mm(3) tumor sample plus 5 deep and 5 mucosal margin samples were snap frozen. Clinical, pathological, adjuvant therapy, and outcome data were recorded. Tumors were informative if >5 % promoter methylation was found for ≥1 of 4 genes using qMSP. Margins were declared molecularly positive if >1 % promoter methylation was found in any margin. RESULTS Thirty (63 %) of 48 cases were methylation informative. Mucosal margin samples were largely positive for methylation (26 of 30, 87 %), indicating the presence of field cancerization. Methylation at ≥1 gene promoters in ≥1 deep margin correlated with the presence of close/involved mucosal margins (P = 0.027) and increased pT status (P = 0.027) but not the status of deep margins, recurrence, or survival. CONCLUSIONS The current gene panel did not add prognostic information to histopathological reporting of resection margins. Future efforts should concentrate on improving gene selection, informativity, and assay performance in the patient group with intermediate indications for adjuvant therapy.
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Affiliation(s)
- Richard J Shaw
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
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Saliva collection methods for DNA biomarker analysis in oral cancer patients. Br J Oral Maxillofac Surg 2012; 51:394-8. [PMID: 23068125 DOI: 10.1016/j.bjoms.2012.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/24/2012] [Indexed: 11/22/2022]
Abstract
Patients with head and neck cancers are predisposed to local recurrence and second primaries because of the phenomenon of field cancerisation, and clinical detection of recurrence remains challenging. DNA biomarkers in saliva may prove to be an adjunct to current diagnostic methods, but irradiation of the primary site often leads to xerostomia. We assessed 3 methods of collecting saliva for their ability to generate DNA of sufficient quantity and quality to use in biomarker assays. Paired saliva samples were collected from 2 groups of patients with oral squamous cell carcinoma (SCC). In the first group saliva was collected in Oragene(®) vials and as saline mouthwash from non-irradiated patients (n=21) (4 had had radiotherapy before collection); in the second group it was collected using Oragene(®) sponge kits and as mouthwash from irradiated patients (n=24). Quantitative polymerase chain reaction (qPCR) showed that Oragene(®) vials contained DNA in significantly greater amounts (median 122 μg, range 4-379) than mouthwash (median 17 μg, range 2-194) (p=0.0001) in the non-irradiated patients, while Oragene(®) sponge kits (median 4 μg, range 0.1-61) and mouthwash (median 5.5 μg, range 0.1-75) generated comparable concentrations of DNA from the irradiated group. All 90 samples contained DNA of sufficient quantity and quality for p16 promoter quantitative methylation-specific PCR (qMSP). While Oragene(®) vials contained the most DNA, all 3 methods yielded enough to detect DNA biomarkers using qMSP. The method of collection should depend on the compliance of the patient and oral competency.
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Kristensen LS, Raynor MP, Candiloro I, Dobrovic A. Methylation profiling of normal individuals reveals mosaic promoter methylation of cancer-associated genes. Oncotarget 2012; 3:450-61. [PMID: 22570110 PMCID: PMC3380579 DOI: 10.18632/oncotarget.480] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Epigenetic silencing by promoter methylation of genes associated with cancer initiation and progression is a hallmark of tumour cells. As a consequence, testing for DNA methylation biomarkers in plasma or other body fluids shows great promise for detection of malignancies at early stages and/or for monitoring response to treatment. However, DNA from normal leukocytes may contribute to the DNA in plasma and will affect biomarker specificity if there is any methylation in the leukocytes. DNA from 48 samples of normal peripheral blood mononuclear cells was evaluated for the presence of methylation of a panel of DNA methylation biomarkers that have been implicated in cancer. SMART-MSP, a methylation specific PCR (MSP) methodology based on real time PCR amplification, high-resolution melting and strategic primer design, enabled quantitative detection of low levels of methylated DNA. Methylation was observed in all tested mononuclear cell DNA samples for the CDH1 and HIC1 promoters and in majority of DNA samples for the TWIST1 and DAPK1 promoters. APC and RARB promoter methylation, at a lower average level, was also detected in a substantial proportion of DNA samples. We found no BRCA1, CDKN2A, GSTP1 and RASSF1A promoter methylation in this sample set. Several individuals had higher levels of methylation at several loci suggestive of a methylator phenotype. In conclusion, methylation of many potential DNA methylation biomarkers can be detected in normal peripheral blood mononuclear cells, and is likely to affect their specificity for detecting low level disease. However, we found no evidence of promoter methylation for other genes indicating that panels of analytically sensitive and specific methylation biomarkers in body fluids can be obtained.
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Affiliation(s)
- Lasse Sommer Kristensen
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
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38
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Bijron JG, Bol GM, Verheijen RH, van Diest PJ. Epigenetic biomarkers in the diagnosis of ovarian cancer. ACTA ACUST UNITED AC 2012; 6:421-38. [PMID: 23480807 DOI: 10.1517/17530059.2012.702105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Current diagnostic methods for ovarian cancer have limited performance. Recent advances within the field of epigenetics have shifted the clinical implementation of epigenetic biomarkers as a diagnostic approach from a dream for the future to a present-day consideration. Patients could potentially benefit greatly from this novel diagnostic approach. AREAS COVERED Epigenetic mechanisms in cancer are discussed, with a focus on potential diagnostic epigenetic biomarkers in ovarian cancer in tissue and body fluids. A literature search was undertaken (on 22-09-2011) for these subjects using the search syntax ((((((((((((((("ovarian") OR "ovary") OR "ovarian cancer") OR "ovarian cancers") OR "cancer of the ovary") OR "tumour of the ovary") OR "ovarian tumor") OR "ovarian tumors") OR "ovarian tumour") OR "ovarian tumours") OR "ovarian neoplasm") OR "ovarian neoplasms" OR "ovarian carcinoma") OR "ovarian carcinomas") OR "carcinoma of the ovary")) AND ((((((((("epigenetics") OR "epigenetic") OR "epigenome") OR "methylation") OR "hypermethylation") OR "chromatin modification") OR "histone") OR "histones") OR "acetylation") EXPERT OPINION To date no single epigenetic biomarker is able to accurately detect early ovarian cancer in either tissue or body fluids. A panel of epigenetic biomarkers based on aberrant DNA methylation in body fluids, especially blood, has the best chance of being implemented in clinical practice, as it is semi-invasive. However, progression toward clinical use is hampered by the lack of detection techniques combining high throughput and accuracy with low cost, by difficulties in establishing reliable reference values and by the heterogeneous nature of ovarian cancer. Until addressed, implementation as a diagnostic measure complimenting current techniques in select cases seems a far way to go, and implementation as a primary screening tool is yet even farther away.
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Affiliation(s)
- Jonathan G Bijron
- University Medical Center Utrecht, Department of Pathology , 3508 GA Utrecht , The Netherlands
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Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
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Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
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Christians A, Hartmann C, Benner A, Meyer J, von Deimling A, Weller M, Wick W, Weiler M. Prognostic value of three different methods of MGMT promoter methylation analysis in a prospective trial on newly diagnosed glioblastoma. PLoS One 2012; 7:e33449. [PMID: 22428052 PMCID: PMC3302822 DOI: 10.1371/journal.pone.0033449] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 02/13/2012] [Indexed: 12/02/2022] Open
Abstract
Hypermethylation in the promoter region of the MGMT gene encoding the DNA repair protein O6-methylguanine-DNA methyltransferase is among the most important prognostic factors for patients with glioblastoma and predicts response to treatment with alkylating agents like temozolomide. Hence, the MGMT status is widely determined in most clinical trials and frequently requested in routine diagnostics of glioblastoma. Since various different techniques are available for MGMT promoter methylation analysis, a generally accepted consensus as to the most suitable diagnostic method remains an unmet need. Here, we assessed methylation-specific polymerase chain reaction (MSP) as a qualitative and semi-quantitative method, pyrosequencing (PSQ) as a quantitative method, and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a semi-quantitative method in a series of 35 formalin-fixed, paraffin-embedded glioblastoma tissues derived from patients treated in a prospective clinical phase II trial that tested up-front chemoradiotherapy with dose-intensified temozolomide (UKT-05). Our goal was to determine which of these three diagnostic methods provides the most accurate prediction of progression-free survival (PFS). The MGMT promoter methylation status was assessable by each method in almost all cases (n = 33/35 for MSP; n = 35/35 for PSQ; n = 34/35 for MS-MLPA). We were able to calculate significant cut-points for the continuous methylation signals at each CpG site analysed by PSQ (range, 11.5 to 44.9%) and at one CpG site assessed by MS-MLPA (3.6%) indicating that a dichotomisation of continuous methylation data as a prerequisite for comparative survival analyses is feasible. Our results show that, unlike MS-MLPA, MSP and PSQ provide a significant improvement of predicting PFS compared with established clinical prognostic factors alone (likelihood ratio tests: p<0.001). Conclusively, taking into consideration prognostic value, cost effectiveness and ease of use, we recommend pyrosequencing for analyses of MGMT promoter methylation in high-throughput settings and MSP for clinical routine diagnostics with low sample numbers.
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Affiliation(s)
- Arne Christians
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School (MHH), Hannover, Germany
- * E-mail:
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jochen Meyer
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
- Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurooncology at the National Center for Tumour Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Markus Weiler
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurooncology at the National Center for Tumour Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
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Nanassy L, Carrell DT. Abnormal methylation of the promoter of CREM is broadly associated with male factor infertility and poor sperm quality but is improved in sperm selected by density gradient centrifugation. Fertil Steril 2011; 95:2310-4. [DOI: 10.1016/j.fertnstert.2011.03.096] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/25/2011] [Accepted: 03/26/2011] [Indexed: 11/26/2022]
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Zhou J, Cao J, Lu Z, Liu H, Deng D. A 115-bp MethyLight assay for detection of p16 (CDKN2A) methylation as a diagnostic biomarker in human tissues. BMC MEDICAL GENETICS 2011; 12:67. [PMID: 21569495 PMCID: PMC3120739 DOI: 10.1186/1471-2350-12-67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/13/2011] [Indexed: 12/15/2022]
Abstract
Background p16 Methylation is a potential biomarker for prediction of malignant transformation of epithelial dysplasia. A probe-based, quantitative, methylation-specific PCR (MSP) called MethyLight may become an eligible method for detecting this marker clinically. We studied oral mucosa biopsies with epithelial dysplasia from 78 patients enrolled in a published 4-years' followup cohort, in which cancer risk for patients with p16 methylation-positive dysplasia was significantly higher than those without p16 methylation (by 150-bp MSP and bisulfite sequencing; +133 ~ +283, transcription starting site, +1). The p16 methylation status in samples (N = 102) containing sufficient DNA was analyzed by the 70-bp classic (+238 ~ +307) and 115-bp novel (+157 ~ +272) MethyLight assays, respectively. Results p16 Methylation was detectable in 75 samples using the classic MethyLight assay. The methylated-p16 positive rate and proportion of methylated-p16 by the MethyLight in MSP-positive samples were higher than those in MSP-negative samples (positive rate: 37/44 vs. 38/58, P=0.035, two-sided; proportion [median]: 0.78 vs. 0.02, P <0.007). Using the published results of MSP as a golden standard, we found sensitivity, specificity, and accuracy for this MethyLight assay to be 70.5%, 84.5%, and 55.0%, respectively. Because amplicon of the classic MethyLight procedure only partially overlapped with the MSP amplicon, we further designed a 115-bp novel MethyLight assay in which the amplicon on the sense-strand fully overlapped with the MSP amplicon on the antisense-strand. Using the 115-bp MethyLight assay, we observed methylated-p16 in 26 of 44 MSP-positive samples and 2 of 58 MSP-negative ones (P = 0.000). These results were confirmed with clone sequencing. Sensitivity, specificity, and accuracy using the 115-bp MethyLight assay were 59.1%, 98.3%, and 57.4%, respectively. Significant differences in the oral cancer rate were observed during the followup between patients (≥60 years) with and without methylated-p16 as detected by the 115-bp MethyLight assay (6/8 vs. 6/22, P = 0.034, two-sided). Conclusions The 115-bp MethyLight assay is a useful and practical assay with very high specificity for the detection of p16 methylation clinically.
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Affiliation(s)
- Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Aetiology, Peking University Cancer Hospital & Institute, Beijing, China
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Jha P, Suri V, Jain A, Sharma MC, Pathak P, Jha P, Srivastava A, Suri A, Gupta D, Chosdol K, Chattopadhyay P, Sarkar C. O6-methylguanine DNA methyltransferase gene promoter methylation status in gliomas and its correlation with other molecular alterations: first Indian report with review of challenges for use in customized treatment. Neurosurgery 2011; 67:1681-91. [PMID: 21107199 DOI: 10.1227/neu.0b013e3181f743f5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND O6-methylguanine methyltransferase (MGMT) promoter methylation in adult glioblastomas (glioblastoma multiforme) is considered a promising molecular alteration, predictive of better response to temozolomide therapy and longer overall survival. OBJECTIVE To look at the frequency of MGMT methylation in glial tumors of all grades and types, and correlate this alteration with loss of heterozygosity 1p/19q, TP53 gene mutations, epidermal growth factor receptor (EGFR) amplification, and isocitrate dehydrogenase 1 (IDH1) mutations. METHODS One hundred two gliomas of various grades and subtypes were assessed by methylation-specific polymerase chain reaction for MGMT promoter methylation status. The results were correlated with 1p/19q status, EGFR amplification, TP53, and IDH1 mutations. RESULTS There was an inverse correlation of MGMT promoter methylation frequency with tumor grade, observed in 79.4%, 70.8%, and 56.8% of grade II, grade III, and grade IV gliomas, respectively. The difference was statistically significant in grade II vs IV tumors (P=.036). The majority of cases with 1p/19q loss of heterozygosity also showed MGMT methylation, although the association was not significant. There was no significant correlation of MGMT status with IDH1 mutation. In astrocytic tumors, there was no correlation of MGMT methylation with TP53 mutation or EGFR amplification. CONCLUSION MGMT promoter methylation was observed in a considerable proportion of all grades and subtypes of gliomas, with no significant correlation with other known genetic alterations. On extensive literature review, in both low- and high-grade gliomas, wide variability of data on the frequency of MGMT methylation and its association with other molecular alterations from various centers was noted, mostly owing to technical causes. This raises questions regarding the capacity of this test for use as an objective and reproducible marker for customized treatment in individual cases.
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Affiliation(s)
- Prerana Jha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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Daskalos A, Oleksiewicz U, Filia A, Nikolaidis G, Xinarianos G, Gosney JR, Malliri A, Field JK, Liloglou T. UHRF1-mediated tumor suppressor gene inactivation in nonsmall cell lung cancer. Cancer 2011; 117:1027-37. [PMID: 21351083 DOI: 10.1002/cncr.25531] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/21/2010] [Accepted: 06/14/2010] [Indexed: 12/24/2022]
Abstract
BACKGROUND The UHRF1 gene possesses an essential role in DNA methylation maintenance, but its contribution to tumor suppressor gene hypermethylation in primary human cancers currently remains unclear. METHODS mRNA expression levels of UHRF1, DNMT1, DNMT3A, DNMT3B, and E2F1 were evaluated in 105 primary nonsmall cell lung carcinomas by quantitative polymerase chain reaction. The methylation status of CDKN2A and RASSF1 promoters was examined by pyrosequencing. UHRF1 was knocked down by short hairpin RNA in A549 lung adenocarcinoma cells. RESULTS All 4 genes were overexpressed in a coordinated manner in the lung tumor tissues, and their expression correlated with that of E2F1. Higher UHRF1 expression in tumor tissues correlated with the hypermethylation of CDKN2A (P = .005) and RASSF1 promoters (P = .034), and the relationship with a combined epigenotype was even stronger (P = 2.3 × 10(-4) ). When UHRF1 was knocked down in A549 lung adenocarcinoma cells, lower methylation levels of RASSF1, CYGB, and CDH13 promoters were observed. Also, UHRF1 knockdown clones demonstrated reduced proliferation and decreased cell migration properties. CONCLUSIONS Our data demonstrate that UHRF1 is a key epigenetic switch, which controls cell cycle in nonsmall cell lung carcinoma through its ability to sustain the transcriptional silencing of tumor suppressor genes by maintaining their promoters in a hypermethylated status. Thus, UHRF1 should be considered, along with DNMTs, among the potential targets for cancer treatment and/or therapeutic stratification.
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Affiliation(s)
- Alexandros Daskalos
- Roy Castle Lung Cancer Research Programme, University of Liverpool, Department of Clinical and Molecular Cancer Medicine, Liverpool, United Kingdom
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Global DNA hypomethylation-induced ΔNp73 transcriptional activation in non-small cell lung cancer. Cancer Lett 2011; 300:79-86. [DOI: 10.1016/j.canlet.2010.09.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/02/2010] [Accepted: 09/06/2010] [Indexed: 11/21/2022]
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Quantitative detection of DNA methylation states in minute amounts of DNA from body fluids. Methods 2010; 52:242-7. [DOI: 10.1016/j.ymeth.2010.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 03/20/2010] [Accepted: 03/28/2010] [Indexed: 12/17/2022] Open
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Yalniz Z, Demokan S, Suoglu Y, Ulusan M, Dalay N. Simultaneous methylation profiling of tumor suppressor genes in head and neck cancer. DNA Cell Biol 2010; 30:17-24. [PMID: 20860434 DOI: 10.1089/dna.2010.1090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Head and neck cancer (HNC) is a common cancer, and its prognosis has not changed during the last decades. Detection of the disease at an early stage is crucial for successful treatment, as early diagnosis can significantly increase the survival rate. Methylation of tumor suppressor genes is an early event in cancer responsible for incorrect gene silencing. Since methylation changes are reversible, they also provide a promising target for therapy. So far, only individual genes have been analyzed for aberrant methylation in HNC. In this study, we analyzed the methylation status of 24 tumor suppressor genes simultaneously by methylation-specific multiplex ligation-dependent probe amplification in matched tumor and normal tissue samples from patients with HNC. CHFR, RARβ, DAPK1, and RASFF1 genes were the most frequently methylated genes in tumor tissue. Eight genes were not methylated in any sample. The methylation frequencies for individual genes ranged from 0% to 19%. Our results indicate that methylation of tumor suppressor genes is not high as previously reported by methylation-specific polymerase chain reaction and is confined to a smaller but significant fraction of the tumors. Whether this group represents a unique entity in the disease spectrum warrants further studies.
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Affiliation(s)
- Zubeyde Yalniz
- Department of Basic Oncology, Oncology Institute, Istanbul University, Istanbul, Turkey
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Langevin SM, Stone RA, Bunker CH, Grandis JR, Sobol RW, Taioli E. MicroRNA-137 promoter methylation in oral rinses from patients with squamous cell carcinoma of the head and neck is associated with gender and body mass index. Carcinogenesis 2010; 31:864-70. [PMID: 20197299 DOI: 10.1093/carcin/bgq051] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Head and neck cancer represents 3.3% of all new malignancies and 2.0% of cancer deaths in the USA, the majority of which are squamous in origin. The overall 5 year survival is 60% and worsens with increasing stage at diagnosis. Thus, novel biomarkers for early detection of squamous cell carcinoma of the head and neck (SCCHN) are needed. MicroRNA-137 (miR-137) plays a role in cell cycle control and seems to undergo promoter methylation in oral squamous cell carcinoma tissue. The main objectives of this study were to ascertain whether miR-137 promoter methylation is detectable in oral rinse samples, assess its association with SCCHN and identify potential risk factors for its occurrence. Oral rinse samples were collected from 99 SCCHN patients with no prior history of cancer and 99 cancer-free controls, frequency matched on gender; tumor tissue for 64 patients was also tested. Methylation of the miR-137 promoter, assessed using methylation-specific polymerase chain reaction, was detected in 21.2% oral rinses from SCCHN patients and 3.0% from controls [odds ratio (OR) = 4.80, 95% confidence interval (CI): 1.23-18.82]. Among cases, promoter methylation of miR-137 was associated with female gender (OR = 5.30, 95% CI: 1.20-23.44) and inversely associated with body mass index (BMI) (OR = 0.88, 95% CI: 0.77-0.99). Promoter methylation of miR-137 appears to be a relatively frequently detected event in oral rinse of SCCHN patients and may have future utility as a biomarker in DNA methylation panels. The observed associations with gender and BMI help to shed light on potential risk factors for an altered methylation state in SCCHN.
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Affiliation(s)
- Scott M Langevin
- Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213-1863, USA
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