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Santourlidis S, Araúzo-Bravo MJ, Brodell RT, Hassan M, Bendhack ML. hTERT Epigenetics Provides New Perspectives for Diagnosis and Evidence-Based Guidance of Chemotherapy in Cancer. Int J Mol Sci 2024; 25:7331. [PMID: 39000438 PMCID: PMC11242863 DOI: 10.3390/ijms25137331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Strong epigenetic pan-cancer biomarkers are required to meet several current, urgent clinical needs and to further improve the present chemotherapeutic standard. We have concentrated on the investigation of epigenetic alteration of the hTERT gene, which is frequently epigenetically dysregulated in a number of cancers in specific developmental stages. Distinct DNA methylation profiles were identified in our data on early urothelial cancer. An efficient EpihTERT assay could be developed utilizing suitable combinations with sequence-dependent thermodynamic parameters to distinguish between differentially methylated states. We infer from this data set, the epigenetic context, and the related literature that a CpG-rich, 2800 bp region, a prominent CpG island, surrounding the transcription start of the hTERT gene is the crucial epigenetic zone for the development of a potent biomarker. In order to accurately describe this region, we have named it "Acheron" (Ἀχέρων). In Greek mythology, this is the river of woe and misery and the path to the underworld. Exploitation of the DNA methylation profiles focused on this region, e.g., idiolocal normalized Methylation Specific PCR (IDLN-MSP), opens up a wide range of new possibilities for diagnosis, determination of prognosis, follow-up, and detection of residual disease. It may also have broad implications for the choice of chemotherapy.
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Affiliation(s)
- Simeon Santourlidis
- Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany
| | - Marcos J. Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Robert T. Brodell
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS 39216, USA;
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, 67000 Strasbourg, France;
- Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Marcelo L. Bendhack
- Department of Urology, Red Cross University Hospital, Positivo University, Rua Mauá 1111, Curitiba 80030-200, Brazil;
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Li Y, Liu B, Zhou X, Yang H, Han T, Hong Y, Wang C, Huang M, Yan S, Li S, Li J, Liu Y, Zhang E, Ni Y, Shen N, Chen W, Huang YS, Wu N. Genome-Scale Multimodal Analysis of Cell-Free DNA Whole-Methylome Sequencing for Noninvasive Esophageal Cancer Detection. JCO Precis Oncol 2024; 8:e2400111. [PMID: 38976830 DOI: 10.1200/po.24.00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 07/10/2024] Open
Abstract
PURPOSE Simultaneous profiling of cell-free DNA (cfDNA) methylation and fragmentation features to improve the performance of cfDNA-based cancer detection is technically challenging. We developed a method to comprehensively analyze multimodal cfDNA genomic features for more sensitive esophageal squamous cell carcinoma (ESCC) detection. MATERIALS AND METHODS Enzymatic conversion-mediated whole-methylome sequencing was applied to plasma cfDNA samples extracted from 168 patients with ESCC and 251 noncancer controls. ESCC characteristic cfDNA methylation, fragmentation, and copy number signatures were analyzed both across the genome and at accessible cis-regulatory DNA elements. To distinguish ESCC from noncancer samples, a first-layer classifier was developed for each feature type, the prediction results of which were incorporated to construct the second-layer ensemble model. RESULTS ESCC plasma genome displayed global hypomethylation, altered fragmentation size, and chromosomal copy number alteration. Methylation and fragmentation changes at cancer tissue-specific accessible cis-regulatory DNA elements were also observed in ESCC plasma. By integrating multimodal genomic features for ESCC detection, the ensemble model showed improved performance over individual modalities. In the training cohort with a specificity of 99.2%, the detection sensitivity was 81.0% for all stages and 70.0% for stage 0-II. Consistent performance was observed in the test cohort with a specificity of 98.4%, an all-stage sensitivity of 79.8%, and a stage 0-II sensitivity of 69.0%. The performance of the classifier was associated with the disease stage, irrespective of clinical covariates. CONCLUSION This study comprehensively profiles the epigenomic landscape of ESCC plasma and provides a novel noninvasive and sensitive ESCC detection approach with genome-scale multimodal analysis.
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Affiliation(s)
- Yulong Li
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuantong Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hechuan Yang
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Tiancheng Han
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Yuanyuan Hong
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Ciran Wang
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Miao Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shaolei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jingjing Li
- The Precision Medicine Centre, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yanfang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Enli Zhang
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Yang Ni
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Ning Shen
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Weizhi Chen
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Yu S Huang
- Genecast Biotechnology Co, Ltd, Wuxi, Jiangsu, China
| | - Nan Wu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
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Santourlidis S, Araúzo-Bravo MJ, Erichsen L, Bendhack ML. Epigenetics Meets CAR-T-Cell Therapy to Fight Cancer. Cancers (Basel) 2024; 16:1941. [PMID: 38792020 PMCID: PMC11119853 DOI: 10.3390/cancers16101941] [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: 04/04/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Based on the impressive success of Car-T-cell therapy in the treatment of hematological malignancies, a broad application for solid tumors also appears promising. However, some important hurdles need to be overcome. One of these is certainly the identification of specific target antigens on cancer cells. Hypomethylation is a characteristic epigenetic aberration in many tumor entities. Genome-wide screenings for consistent DNA hypomethylations in tumors enable the identification of aberrantly upregulated transcripts, which might result in cell surface proteins. Thus, this approach provides a new perspective for the discovery of potential new Car-T-cell target antigens for almost every tumor entity. First, we focus on this approach as a possible treatment for prostate cancer.
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Affiliation(s)
- Simeon Santourlidis
- Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany;
| | - Marcos J. Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Lars Erichsen
- Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany;
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Marcelo L. Bendhack
- Department of Urology, Red Cross University Hospital, Positivo University, Rua Mauá 1111, Curitiba 80030-200, Brazil;
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Adampourezare M, Nikzad B, Amini M, Sheibani N. Fluorimetric detection of DNA methylation by cerium oxide nanoparticles for early cancer diagnosis. Heliyon 2024; 10:e28695. [PMID: 38586346 PMCID: PMC10998132 DOI: 10.1016/j.heliyon.2024.e28695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
In this study, a very sensitive fluorescence nano-biosensor was developed using CeO2 nanoparticles for the rapid detection of DNA methylation. The characteristics of CeO2 nanoparticles were determined by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) spectroscopy, UV-visible spectroscopy, and fluorescence spectroscopy. The CeO2 nanoparticles were reacted with a single-stranded DNA (ssDNA) probe, and then methylated and unmethylated target DNAs hybridized with an ssDNA probe, and the fluorescence emission was measured. Upon adding the target unmethylated and methylated ssDNA, the fluorescence intensity increased in the linear range of concentration from 2 × 10-13 - 10-18 M. The limit of detection (LOD) was 1.597 × 10-6 M for methylated DNA and 1.043 × 10-6 M for unmethylated DNA. The fluorescence emission intensity of methylated sequences was higher than of that unmethylated sequences. The fabricated DNA nanobiosensor showed a fluorescence emission at 420 nm with an excitation wavelength of 280 nm. The impact of CeO2 binding on methylated and unmethylated DNA was further demonstrated by agarose gel electrophoresis. Finally, the actual sample analysis suggested that the nanobiosensor could have practical applications for detecting methylation in the human plasma samples.
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Affiliation(s)
- Mina Adampourezare
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Behzad Nikzad
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Mojtaba Amini
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison WI 53705, USA
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Yokoyama S, Matsuo K, Tanimoto A. Methylation-Specific Electrophoresis. Methods Mol Biol 2024; 2763:259-268. [PMID: 38347417 DOI: 10.1007/978-1-0716-3670-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Methylation of CpG sites in the promoter region of genomic DNA is an important epigenetic modification that plays a critical role in gene regulation, particularly in gene silencing. Epigenetic abnormalities, along with genetic alterations, are implicated in carcinogenesis and cancer progression. Numerous studies have investigated the role of epigenetics in cancer using various tools to assess DNA methylation. However, conventional analysis methods for DNA methylation require a large amount of DNA but lack higher sensitivity, making them unsuitable for analysis of samples with high heterogeneity, such as tumor tissues. In this study, we introduce a novel electrophoresis method named "methylation-specific electrophoresis (MSE)," which utilizes a denaturing gradient acrylamide gel. We demonstrate the applicability of the MSE method for DNA methylation analysis of the mucin gene as an example.
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Affiliation(s)
- Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan.
| | - Kei Matsuo
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima, Japan
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6
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Baba Y, Hara Y, Toihata T, Kosumi K, Iwatsuki M, Iwagami S, Miyamoto Y, Yoshida N, Komohara Y, Baba H. Relationship between gut microbiome Fusobacterium nucleatum and LINE-1 methylation level in esophageal cancer. Esophagus 2023; 20:704-712. [PMID: 37173453 DOI: 10.1007/s10388-023-01009-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND We previously demonstrated the relationship of human microbiome Fusobacterium nucleatum with unfavorable clinical outcomes and inferior chemotherapeutic responses in esophageal cancer. Global DNA methylation is associated with the occurrence and development of various cancers. In our previous study, LINE-1 hypomethylation (i.e., global DNA hypomethylation) was associated with a poor prognosis in esophageal cancer. As the gut microbiota may play crucial roles in the DNA methylation of host cells, we hypothesized that F. nucleatum might influence LINE-1 methylation levels in esophageal cancer. METHODS We qualified the F. nucleatum DNA using a quantitative PCR assay and LINE-1 methylation via a pyrosequencing assay using formalin-fixed paraffin-embedded specimens from 306 esophageal cancer patients. RESULTS Intratumoral F. nucleatum DNA was detected in 65 cases (21.2%). The LINE-1 methylation scores ranged from 26.9 to 91.8 (median = 64.8) in tumors. F. nucleatum DNA was related to the LINE-1 hypomethylation of tumor lesions in esophageal cancer (P < 0.0001). The receiver operating characteristic curve analysis showed that the area under the curve was 0.71 for F. nucleatum positivity. Finally, we found that the impact of F. nucleatum on clinical outcomes was not modified by LINE-1 hypomethylation (P for interaction = 0.34). CONCLUSIONS F. nucleatum alters genome-wide methylation levels in cancer cells, which may be one of the mechanisms by which F. nucleatum affects the malignant behavior of esophageal cancer.
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Affiliation(s)
- Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.
- Department of Next-Generation Surgical Therapy Development, Kumamoto University Hospital, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.
| | - Yoshihiro Hara
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Tasuku Toihata
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Keisuke Kosumi
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
- Department of Next-Generation Surgical Therapy Development, Kumamoto University Hospital, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Shiro Iwagami
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Yoshihiro Komohara
- Department of Cell Pathology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
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Xu H, Huang K, Lin Y, Gong H, Ma X, Zhang D. Glycosyltransferase GLT8D1 and GLT8D2 serve as potential prognostic biomarkers correlated with Tumor Immunity in Gastric Cancer. BMC Med Genomics 2023; 16:123. [PMID: 37277853 PMCID: PMC10242987 DOI: 10.1186/s12920-023-01559-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/27/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Glycosylation involved in various biological function, aberrant glycosylation plays an important role in cancer development and progression. Glycosyltransferase 8 domain containing 1 (GLT8D1) and GLT8D2, as members of the glycosyltransferase family proteins, are associated with transferase activity. However, the association between GLT8D1/2 and gastric cancer (GC) remains unclear. We aimed to investigate the potential prognostic value and oncogenic role of GLT8D1/2 in GC. METHODS The relationship between GLT8D1/2 and GC was evaluated through comprehensive bioinformatics approaches. A series of factors like gene expression patterns, Kaplan-Meier survival analyses, Cox regression analyses, prognostic nomogram, calibration curves, ROC curves, function enrichment analyses, tumor immunity association, genetic alterations, and DNA methylation were included. Data and statistical analyses were performed using R software (v3.6.3). RESULTS Both GLT8D1 and GLT8D2 expression were significantly upregulated in GC tissues(n = 414) compared with normal tissues(n = 210), and high expression of GLT8D1/2 was remarkably correlated with poor prognosis for GC patients. Cox regression analyses implied that GLT8D1/2 could act as independent prognostic factors in GC. Furthermore, gene function analyses indicated that multiple signaling pathways involving tumor oncogenesis and development enriched, such as mTOR, cell cycle, MAPK, Notch, Hedgehog, FGF, and PI3K-Akt signaling pathways. Moreover, GLT8D1/2 was significantly associated with immune cell infiltration, immune checkpoint genes, and immune regulators TMB/MSI. CONCLUSION GLT8D1/2 may serve as potential prognostic markers of poor prognosis in GC correlated with tumor immunity. The study provided an insight into identifying potential biomarkers and targets for prognosis, immunotherapy response, and therapy in GC.
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Affiliation(s)
- Huimei Xu
- Department of Gastroenterology, The Second Clinical Medical College of Lanzhou University, Lanzhou, 730030, P.R. China
- Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China
| | - Ke Huang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730030, P.R. China
| | - Yimin Lin
- Department of Gastroenterology, The Second Clinical Medical College of Lanzhou University, Lanzhou, 730030, P.R. China
- Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China
| | - Hang Gong
- Department of Gastroenterology, The Second Clinical Medical College of Lanzhou University, Lanzhou, 730030, P.R. China
- Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China
| | - Xueni Ma
- Department of Gastroenterology, The Second Clinical Medical College of Lanzhou University, Lanzhou, 730030, P.R. China
- Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China
| | - Dekui Zhang
- Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China.
- Key Laboratory of Digestive Diseases of Lanzhou University Second Hospital, Lanzhou, 730030, P.R. China.
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Juan YC, Su YF, Bai CH, Fan YC, Kuo TT, Ko HH, Peng HH, Chiang CP, Fwu CW, Cheng SJ. ZNF582 hypermethylation as a prognostic biomarker for malignant transformation of oral lesions. Oral Dis 2023; 29:505-514. [PMID: 34145953 DOI: 10.1111/odi.13946] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/12/2021] [Accepted: 06/05/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES This hospital-based cohort study evaluated whether ZNF582 and PAX1 methylation levels at baseline can be used as biomarkers to identify lesions with a high potential for malignant transformation in patients with normal mucosa and oral potentially malignant disorders. PATIENTS AND METHODS We recruited 171 adult patients with normal mucosa and oral potentially malignant disorders in 2012-2014. They were followed until 2017. Outcomes, including advanced histopathological findings and oral cancer occurrence, were obtained from medical charts, the Taiwan Cancer Registry, and cause-of-death data. Kaplan-Meier analysis and Cox proportional hazards regression models were used to examine the association of ZNF582 and PAX1 methylation levels at baseline with subsequent outcome occurrences. RESULTS After 260,192 days of follow-up, 11 cases of oral cancer and 4 cases of advanced histopathological progression occurred. Patients with higher ZNF582 and PAX1 methylation levels at baseline had a higher incidence of disease progression. After adjustment for all studied factors using Cox proportional hazards regression models, ZNF582m level (adjusted hazard ratio, 11.41; 95% CI, 2.05-63.36; p = 0.005) was the only significant and independent predictor of disease progression. CONCLUSIONS ZNF582 hypermethylation can be an effective and noninvasive biomarker for identifying oral lesions with a high potential for malignant transformation.
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Affiliation(s)
- Yi-Chen Juan
- iStat Biomedical Co., Ltd., New Taipei City, Taiwan
| | - Yee-Fun Su
- iStat Biomedical Co., Ltd., New Taipei City, Taiwan
| | - Chyi-Huey Bai
- Department of Public Health, College of Medicine, Taipei Medical University, Taipei, Taiwan.,School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Yen-Chun Fan
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Tung Kuo
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Hui-Hsin Ko
- School of Dentistry, Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Hsin-Hui Peng
- School of Dentistry, Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Chun-Pin Chiang
- School of Dentistry, Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Dentistry, Far Eastern Memorial Hospital, New Taipei City, Taiwan.,Department of Dentistry, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | | | - Shih-Jung Cheng
- School of Dentistry, Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan.,Department of Dentistry, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan.,School of Dentistry, National Taiwan University, Taipei, Taiwan
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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Abstract
DNA methylation of promoter CpG islands silences their downstream genes, and enhancer methylation can be associated with decreased or increased gene expression. DNA methylation alterations in normal and diseased cells provide rich information, such as tissue origin, disease risk, patient response, and prognosis. DNA methylation status is detected by bisulfite conversion, which converts unmethylated cytosines into uracils but methylated cytosines very inefficiently. A genome-wide DNA methylation analysis is conducted by a BeadChip microarray or next-generation sequencing (NGS) of bisulfite-treated DNA. A region-specific DNA methylation analysis can be conducted by various methods, such as methylation-specific PCR (MSP), quantitative MSP, and bisulfite sequencing. This chapter provides protocols for bisulfite-mediated conversion, a BeadChip array-based method (Infinium), quantitative MSP, and bisulfite sequencing.
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Affiliation(s)
- Naoko Hattori
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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11
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Inference of epigenetic subnetworks by Bayesian regression with the incorporation of prior information. Sci Rep 2022; 12:20224. [PMID: 36418365 PMCID: PMC9684215 DOI: 10.1038/s41598-022-19879-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Changes in gene expression have been thought to play a crucial role in various types of cancer. With the advance of high-throughput experimental techniques, many genome-wide studies are underway to analyze underlying mechanisms that may drive the changes in gene expression. It has been observed that the change could arise from altered DNA methylation. However, the knowledge about the degree to which epigenetic changes might cause differences in gene expression in cancer is currently lacking. By considering the change of gene expression as the response of altered DNA methylation, we introduce a novel analytical framework to identify epigenetic subnetworks in which the methylation status of a set of highly correlated genes is predictive of a set of gene expression. By detecting highly correlated modules as representatives of the regulatory scenario underling the gene expression and DNA methylation, the dependency between DNA methylation and gene expression is explored by a Bayesian regression model with the incorporation of g-prior followed by a strategy of an optimal predictor subset selection. The subsequent network analysis indicates that the detected epigenetic subnetworks are highly biologically relevant and contain many verified epigenetic causal mechanisms. Moreover, a survival analysis indicates that they might be effective prognostic factors associated with patient survival time.
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Mathebela P, Damane BP, Mulaudzi TV, Mkhize-Khwitshana ZL, Gaudji GR, Dlamini Z. Influence of the Microbiome Metagenomics and Epigenomics on Gastric Cancer. Int J Mol Sci 2022; 23:13750. [PMID: 36430229 PMCID: PMC9693604 DOI: 10.3390/ijms232213750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Gastric cancer (GC) is one of the major causes of cancer deaths worldwide. The disease is seldomly detected early and this limits treatment options. Because of its heterogeneous and complex nature, the disease remains poorly understood. The literature supports the contribution of the gut microbiome in the carcinogenesis and chemoresistance of GC. Drug resistance is the major challenge in GC therapy, occurring as a result of rewired metabolism. Metabolic rewiring stems from recurring genetic and epigenetic factors affecting cell development. The gut microbiome consists of pathogens such as H. pylori, which can foster both epigenetic alterations and mutagenesis on the host genome. Most of the bacteria implicated in GC development are Gram-negative, which makes it challenging to eradicate the disease. Gram-negative bacterium co-infections with viruses such as EBV are known as risk factors for GC. In this review, we discuss the role of microbiome-induced GC carcinogenesis. The disease risk factors associated with the presence of microorganisms and microbial dysbiosis are also discussed. In doing so, we aim to emphasize the critical role of the microbiome on cancer pathological phenotypes, and how microbiomics could serve as a potential breakthrough in determining effective GC therapeutic targets. Additionally, consideration of microbial dysbiosis in the GC classification system might aid in diagnosis and treatment decision-making, taking the specific pathogen/s involved into account.
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Affiliation(s)
- Precious Mathebela
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield 0028, South Africa
| | - Botle Precious Damane
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield 0028, South Africa
| | - Thanyani Victor Mulaudzi
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield 0028, South Africa
| | - Zilungile Lynette Mkhize-Khwitshana
- School of Medicine, University of Kwa-Zulu Natal, Durban, KwaZulu-Natal 4013, South Africa
- SAMRC Research Capacity Development Division, South African Medical Research Council, Tygerberg, Cape Town 7501, South Africa
| | - Guy Roger Gaudji
- Department of Urology, Level 7, Bridge C, Steve Biko Academic Hospital, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia 0007, South Africa
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa
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13
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The Central Nervous Mechanism of Stress-Promoting Cancer Progression. Int J Mol Sci 2022; 23:ijms232012653. [PMID: 36293510 PMCID: PMC9604265 DOI: 10.3390/ijms232012653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Evidence shows that stress can promote the occurrence and development of tumors. In recent years, many studies have shown that stress-related hormones or peripheral neurotransmitters can promote the proliferation, survival, and angiogenesis of tumor cells and impair the body’s immune response, causing tumor cells to escape the “surveillance” of the immune system. However, the perception of stress occurs in the central nervous system (CNS) and the role of the central nervous system in tumor progression is still unclear, as are the underlying mechanisms. This review summarizes what is known of stress-related CNS-network activation during the stress response and the influence of the CNS on tumors and discusses available adjuvant treatment methods for cancer patients with negative emotional states, such as anxiety and depression.
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14
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Bücker L, Lehmann U. CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story. Cancers (Basel) 2022; 14:cancers14184377. [PMID: 36139537 PMCID: PMC9497067 DOI: 10.3390/cancers14184377] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used. Abstract Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.
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Affiliation(s)
| | - Ulrich Lehmann
- Correspondence: ; Tel.: +49-(0)511-532-4501; Fax: +49-(0)511-532-5799
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15
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Liu W, Fan Z, Li L, Li M. DNA-Based Nanoprobes for Simultaneous Detection of Telomerase and Correlated Biomolecules. Chembiochem 2022; 23:e202200307. [PMID: 35927933 DOI: 10.1002/cbic.202200307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/02/2022] [Indexed: 11/12/2022]
Abstract
Telomerase (TE), a ribonucleoprotein reverse transcriptase, is enzymatically activated in most tumor cells and is responsible for promoting tumor progression and malignancy by enabling replicative immortality of cancer cells. TE has become an important hallmark for cancer diagnosis and a potential therapy target. Therefore, accurate and in site detection of TE activity, especially the simultaneous imaging of TE activity and its correlated biomolecules, is highly essential to medical diagnostics and therapeutics. DNA-based nanoprobes, with their effective cell penetration capability and programmability, are the most advantageous for detection of intracellular TE activity. This concept article introduces the recent strategies for in situ sensing and imaging of TE activity, with a focus on simultaneous detection of TE and related biomolecules, and provides challenges and perspectives for the development of new strategies for such correlated imaging.
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Affiliation(s)
- Wenjing Liu
- Capital Medical University, Beijing Chest Hospital, CHINA
| | - Zetan Fan
- National Center for Nanoscience and Technology, cas key lab, CHINA
| | - Lele Li
- National Center for Nanoscience and Technology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, 11 ZhongGuanCun BeiYiTiao, Haidian District, 100190, Beijing, CHINA
| | - Mengyuan Li
- University of Science and Technology Beijing, Chemistry, CHINA
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16
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Padin-Iruegas E, Chamorro-Petronacci CM, Sines-Cajade I, Lorenzo-Pouso AI, Blanco-Carrión A, Pérez-Jardón A, Gándara-Vila P, Pérez-Sayans M. DNA Methylation by Bisulfite Next-Generation Sequencing for MLH1 and MGMT in Oral Squamous Cell Carcinomas and Potentially Malignant Disorders: An Integrative Analysis towards Field Cancerization. Medicina (B Aires) 2022; 58:medicina58070878. [PMID: 35888599 PMCID: PMC9322644 DOI: 10.3390/medicina58070878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/07/2023] Open
Abstract
Background and Objectives: MGMT methylation is a well-described biomarker in several solid tumors and MLH1 seems to occur in the initial stages of oral carcinogenesis. The aims of this study were to evaluate MHL1 and MGMT methylation levels in oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMDs), and to integrate this information with The Cancer Genome Atlas (TCGA) database. Materials and Methods: To determine the percentage of gene methylation in MLH1 and MGMT, pyrosequencing analysis was conducted. Samples were divided as follows: (1) patients diagnosed with OSCC (N = 16); (2) patients with OPDM who developed OSCC in the same location (N = 47); and (3) patients with OPDM who developed OSCC in a different location (N = 22). As a validation cohort in this study, data from The Cancer Genomic Atlas (TCGA) database, particularly regarding Head and Neck Squamous Cell Carcinoma, was used. Results: Overall MLH1 methylation levels of 8.6 ± 11.5% and 8.1 ± 9.2% for MGMT were obtained. With regard to MHL1, the OSCC presented the highest degree of methylation with 9.3 ± 7.3% (95%CI 5.1–13.6), and with regards to MGMT, the simultaneous malignancy group presented the highest degree of methylation with 10 ± 13.5% (95%CI 6–10), although no significant differences were found between the groups (p = 0.934 and p = 0.515, respectively). The estimated survival was higher for MGMT methylated cases (19.1 months, 95%CI 19.1–19.1) than for unmethylated cases (9.4 months, 95%CI 6–12.8), but not statistically significant. Conclusions: Our results did not show a correlation between MGMT and MLH1 methylation and any clinicopathological feature or survival in our institutional cohort. MLH1 methylation was present mainly in OSCC, whilst MGMT in OPMD represented a modest contribution to field cancerization, with an overall consistency with the TCGA database.
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Affiliation(s)
- Elena Padin-Iruegas
- Human Anatomy and Embryology Area, Department of Functional Biology and Health Sciences, Faculty of Physiotherapy, University of Vigo, 36001 Pontevedra, Spain;
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
| | - Cintia M. Chamorro-Petronacci
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
| | - Iria Sines-Cajade
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
| | - Alejandro I. Lorenzo-Pouso
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
- Correspondence: ; Tel.: +34-636-67-67-84
| | - Andrés Blanco-Carrión
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
| | - Alba Pérez-Jardón
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
| | - Pilar Gándara-Vila
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
| | - Mario Pérez-Sayans
- Health Research Institute of Santiago de Compostela (IDIS), Department of Oral Medicine, University of Santiago de Compostela (ORALRES Group), 15782 Santiago de Compostela, Spain; (C.M.C.-P.); (A.B.-C.); (A.P.-J.); (P.G.-V.); (M.P.-S.)
- Department of Oral Medicine, University of Santiago de Compostela (MedOralRes Group), 15782 Santiago de Compostela, Spain;
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17
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Yang CC, Su YF, Cheng HC, Juan YC, Chiu YW, Wu CH, Chen PY, Lee YH, Chen YL, Chen YT, Peng CY, Lu MY, Yu CH, Huang YF, Kao SY, Fwu CW, Liu CJ. Improving the Diagnostic Performance by Adding Methylation Marker to Conventional Visual Examination in Identifying Oral Cancer. Diagnostics (Basel) 2022; 12:diagnostics12071544. [PMID: 35885450 PMCID: PMC9320763 DOI: 10.3390/diagnostics12071544] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022] Open
Abstract
Background: Visual oral examination (VOE) is a conventional oral cancer screening method. This study aimed to evaluate the value of methylation marker to assist VOE in identifying oral epithelial dysplasia and oral squamous cell carcinoma (OED/OSCC) from non-cancerous lesions in a real-world situation. Methods: 201 patients with high-risk personal habits who self-perceived oral anomaly were VOE examined, ZNF582 methylation (ZNF582m) tested, and histologically diagnosed. Results: Among them, 132 patients (65.7%) were histologically diagnosed OED/OSCC. Using VOE, 56.1% OED/OSCC patients had possible oral cancer, whereas 37.7% non-OED/OSCC patients had leukoplakia. ZNF582m-positive was detected in 90.2% OED/OSCC patients and 44.9% non-OED/OSCC patients. Various logistic regression models were postulated to evaluate the diagnostic performance of conventional VOE and new strategies using ZNF582m. ROC analysis and its corresponding C-index demonstrated that either triage or co-testing models of VOE and ZNF582m could improve diagnostic performance and discriminative abilities compared with the VOE only approach. Conclusions: In conclusion, methylation marker test shows equivalent performance to an experienced judgment by oral maxillofacial surgeons and plays a significantly supplementary role in increasing the efficacy in identifying oral malignant lesions. ZNF582m may be an especially important tool for family physicians or general dentists to properly diagnose suspicious oral lesions.
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Affiliation(s)
- Cheng-Chieh Yang
- Department of Stomatology, Oral and Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.Y.); (H.-C.C.); (C.-H.W.); (S.-Y.K.)
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Yee-Fun Su
- iStat Biomedical Co., Ltd., New Taipei City 22102, Taiwan; (Y.-F.S.); (Y.-C.J.)
| | - Han-Chieh Cheng
- Department of Stomatology, Oral and Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.Y.); (H.-C.C.); (C.-H.W.); (S.-Y.K.)
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Yi-Chen Juan
- iStat Biomedical Co., Ltd., New Taipei City 22102, Taiwan; (Y.-F.S.); (Y.-C.J.)
| | - Yu-Wei Chiu
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Cheng-Hsien Wu
- Department of Stomatology, Oral and Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.Y.); (H.-C.C.); (C.-H.W.); (S.-Y.K.)
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Pei-Yin Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Yu-Hsien Lee
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Yen-Lin Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Yi-Tzu Chen
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chih-Yu Peng
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Ming-Yi Lu
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chuan-Hang Yu
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Yu-Feng Huang
- Department of Stomatology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan; (P.-Y.C.); (Y.-H.L.); (Y.-L.C.); (Y.-T.C.); (C.-Y.P.); (M.-Y.L.); (C.-H.Y.); (Y.-F.H.)
- College of Oral Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Shou-Yen Kao
- Department of Stomatology, Oral and Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.Y.); (H.-C.C.); (C.-H.W.); (S.-Y.K.)
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan;
| | - Chyng-Wen Fwu
- iStat Biomedical Co., Ltd., New Taipei City 22102, Taiwan; (Y.-F.S.); (Y.-C.J.)
- Correspondence: (C.-W.F.); (C.-J.L.); Tel.: +886-(2)2696-3518 (C.-W.F.); +886-(2)5433535 (C.-J.L.)
| | - Chung-Ji Liu
- Department of Oral and Maxillofacial Surgery, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Correspondence: (C.-W.F.); (C.-J.L.); Tel.: +886-(2)2696-3518 (C.-W.F.); +886-(2)5433535 (C.-J.L.)
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18
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Choy LYL, Peng W, Jiang P, Cheng SH, Yu SCY, Shang H, Tse OYO, Wong J, Wong VWS, Wong GLH, Lam WKJ, Chan SL, Chiu RWK, Chan KCA, Lo YMD. Single-molecule Sequencing Enables Long Cell-free DNA Detection and Direct Methylation Analysis for Cancer Patients. Clin Chem 2022; 68:1151-1163. [PMID: 35587130 DOI: 10.1093/clinchem/hvac086] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Analysis of circulating tumor DNA has become increasingly important as a tool for cancer care. However, the focus of previous studies has been on short fragments of DNA. Also, bisulfite sequencing, a conventional approach for methylation analysis, causes DNA degradation, which is not ideal for the assessment of long DNA properties and methylation patterns. This study attempted to overcome such obstacles by single-molecule sequencing. METHODS Single-molecule real-time (SMRT) sequencing was used to sequence plasma DNA. We performed fragment size and direct methylation analysis for each molecule. A methylation score concerning single-molecule methylation patterns was used for cancer detection. RESULTS A substantial proportion of plasma DNA was longer than 1 kb with a median of 16% in hepatocellular carcinoma (HCC) patients, hepatitis B virus carriers and healthy individuals. The longest plasma DNA molecule in the HCC patients was 39.8 kb. Tumoral cell-free DNA (cfDNA) was generally shorter than nontumoral cfDNA. The longest tumoral cfDNA was 13.6 kb. Tumoral cfDNA had lower methylation levels compared with nontumoral cfDNA (median: 59.3% versus 76.9%). We developed and analyzed a metric reflecting single-molecule methylation patterns associated with cancer, named the HCC methylation score. HCC patients displayed significantly higher HCC methylation scores than those without HCC. Interestingly, compared to using short cfDNA (Area-Under-the-Curve, AUC: 0.75), the use of long cfDNA molecules greatly enhanced the discriminatory power (AUC: 0.91). CONCLUSIONS A previously unidentified long cfDNA population was revealed in cancer patients. The presence and direct methylation analysis of these molecules open new possibilities for cancer liquid biopsy.
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Affiliation(s)
- L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Wenlei Peng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Suk Hang Cheng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Huimin Shang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - O Y Olivia Tse
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Grace L H Wong
- Medical Data Analytics Centre (MDAC), Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - W K Jacky Lam
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Stephen L Chan
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Department of Clinical Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
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Ferreira WAS, Vitiello GAF, da Silva Medina T, de Oliveira EHC. Comprehensive analysis of epigenetics regulation, prognostic and the correlation with immune infiltrates of GPX7 in adult gliomas. Sci Rep 2022; 12:6442. [PMID: 35440701 PMCID: PMC9018725 DOI: 10.1038/s41598-022-10114-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most commonly occurring malignant brain tumor characterized by an immunosuppressive microenvironment accompanied by profound epigenetic changes, thus influencing the prognosis. Glutathione peroxidase 7 (GPX7) is essential for regulating reactive oxygen species homeostasis under oxidative stress. However, little is known about the function of GPX7 in gliomas. In this study, we hypothesized that GPX7 methylation status could influence biological functions and local immune responses that ultimately impact prognosis in adult gliomas. We conducted an integrated bioinformatics analysis mining GPX7 DNA methylation status, transcriptional and survival data of glioma patients. We discovered that GPX7 was remarkably increased in glioma tissues and cell lines, and was associated with poor prognosis. This upregulation was significantly linked to clinicopathological and molecular features, besides being expressed in a cell cycle-dependent manner. Our results consistently demonstrated that upregulation of GPX7 is tightly modulated by epigenetic processes, which also impacted the overall survival of patients with low-grade gliomas (LGG). Based on the analysis of biological functions, we found that GPX7 might be involved in immune mechanisms involving both innate and adaptive immunity, type I interferon production and regulation of synaptic transmission in LGG, whereas in GBM, it is mainly related to metabolic regulation of mitochondrial dynamics. We also found that GPX7 strongly correlates with immune cell infiltration and diverse immune cell markers, suggesting its role in tumor-specific immune response and in regulating the migration of immune cell types to the tumor microenvironment. Combining these multiple data, we provided the first evidence regarding the epigenetic-mediated regulatory mechanisms underlying GPX7 activation in gliomas. Furthermore, our study brings key insights into the significant effect of GPX7 in modulating both immune molecules and in immune cell infiltration in the microenvironment of gliomas, which might impact the patient outcome, opening up future opportunities to regulate the local immune response.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil.
| | | | - Tiago da Silva Medina
- Translational Immuno-Oncology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil
- Institute of Exact and Natural Sciences, Faculty of Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
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20
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Shi D, Xi XX. Regulation of MUC6 Methylation Correlates with Progression of Gastric Cancer. Yonsei Med J 2021; 62:1005-1015. [PMID: 34672134 PMCID: PMC8542475 DOI: 10.3349/ymj.2021.62.11.1005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/04/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE This study aimed to investigate the mechanistic downregulation of mucin 6 (MUC6) and its influence on the progression of gastric cancer (GC). MATERIALS AND METHODS The expression of MUC6 was examined in 40 GC patients. The methylation status of the MUC6 promoter region was investigated using GC cell lines and GC tissue specimens by immunohistochemistry and/or quantitative polymerase chain reaction (qPCR). MUC6 was knocked down in the gastric epithelial cells (GES-1) cell and overexpressed in the SGC7901 cell. The effects of MUC6 knockdown and overexpression on cell migration and invasion were examined using Transwell assays. The effects of demethylation and methylation on MUC6 expression were examined by western blot, qPCR, or double luciferase reporter assays. RESULTS The expression of MUC6 in GC with lymph node metastasis and poor pathological stage was significantly lower than that in GC without lymph node metastasis and good pathological stage, respectively. While cell migration and invasion were significantly decreased after overexpression of MUC6, these abilities significantly increased after the knockdown of MUC6. The methylation levels of MUC6 in GC tissues and GC cell lines were significantly higher than those in para-cancerous tissues and normal GES. Promoter methylation could significantly reduce the binding of related transcription factors to the MUC6 promoter. The expression of MUC6 increased with the concentration and time of action of demethylation drugs. CONCLUSION Expression of MUC6 was regulated by promotor methylation. This methylation of the MUC6 promoter may lead to significant downregulation of MUC6 in GC and promote the progression of GC.
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Affiliation(s)
- Ding Shi
- Department of Gastroenterology, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Xiao-Xia Xi
- Department of Gastroenterology, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China.
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21
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Teng JJ, Zhao WJ, Zhang XL, Zhao DK, Qiu XY, Chen XD, Yang L. Downregulation of promoter methylation gene PRDM5 contributes to the development of tumor proliferation and predicts poor prognosis in gastric cancer. J Cancer 2021; 12:6921-6930. [PMID: 34659579 PMCID: PMC8518008 DOI: 10.7150/jca.59998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Epigenetic aberrations of tumor suppressor genes (TSGs), particularly DNA methylation, are frequently involved in the pathogenesis of gastric cancer (GC). Previous studies have shown that PRDM5 is methylated and silenced in GC. However, the role of PRDM5 in GC progression has not been explored. Methods: The expression and epigenetic alterations of PRDM5 in GC were analyzed in public datasets. The mRNA and protein expression of PRDM5 in fresh tissues were detected by semi-quantitative PCR and Western blot. And expression of PRDM5 in gastric paracarcinoma and carcinoma tissues from 162 patients was detected by immunohistochemistry (IHC) and assessed the association with different clinicopathological features. The prognostic value of PRDM5 in GC patients was evaluated using Kaplan-Meier plotter. We also studied promoter region methylation of PRDM5 in GC by methylation-specific PCR (MSP). The effects of PRDM5 on cell proliferation and migration were conducted by functional experiments in vitro. Results: The expression of PRDM5 was downregulated in GC, and that was associated with poor survival and tumor progression. And PRDM5 expression was found to be an independent prognostic factor for GC. We also found that the methylation of PRDM5 promoter was closely related to the histopathological types and the progression of tumors through the public relations database. In vitro, ectopical expression of PRDM5 inhibited the growth of tumor cells, while knockdown of PRDM5 increased the proliferation and migration of tumor cells. Conclusion: These results suggest that PRDM5 may be a novel TSG methylated in GC that plays important roles in GC development. And we found PRDM5 as a potential survival biomarker for GC, especially in well differentiated GC. PRDM5 expression was significantly correlated with tumor stage and histological type.
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Affiliation(s)
- Jing-Jing Teng
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, No.30 Tongyang North Road, Nantong 226361, China
| | - Wen-Jing Zhao
- Cancer Research Center Nantong, Tumor Hospital Affiliated to Nantong University, Nantong
| | - Xun-Lei Zhang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, No.30 Tongyang North Road, Nantong 226361, China
| | - Da-Kun Zhao
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, No.30 Tongyang North Road, Nantong 226361, China
| | - Xin-Yue Qiu
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, No.30 Tongyang North Road, Nantong 226361, China
| | - Xu-Dong Chen
- Department of Pathology, Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Lei Yang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, No.30 Tongyang North Road, Nantong 226361, China
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22
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Kim CW, Kim H, Kim HR, Kye BH, Kim HJ, Min BS, Oh TJ, An S, Lee SH. Colorectal cancer screening using a stool DNA-based SDC2 methylation test: a multicenter, prospective trial. BMC Gastroenterol 2021; 21:173. [PMID: 33858326 PMCID: PMC8050895 DOI: 10.1186/s12876-021-01759-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prevention and early detection of colorectal cancer (CRC) is a global priority, with many countries conducting population-based CRC screening programs. Although colonoscopy is the most accurate diagnostic method for early CRC detection, adherence remains low because of its invasiveness and the need for extensive bowel preparation. Non-invasive fecal occult blood tests or fecal immunochemical tests are available; however, their sensitivity is relatively low. Syndecan-2 (SDC2) is a stool-based DNA methylation marker used for early detection of CRC. Using the EarlyTect™-Colon Cancer test, the sensitivity and specificity of SDC2 methylation in stool DNA for detecting CRC were previously demonstrated to be greater than 90%. Therefore, a larger trial to validate its use for CRC screening in asymptomatic populations is now required. METHODS All participants will collect their stool (at least 20 g) before undergoing screening colonoscopy. The samples will be sent to a central laboratory for analysis. Stool DNA will be isolated using a GT Stool DNA Extraction kit, according to the manufacturer's protocol. Before performing the methylation test, stool DNA (2 µg per reaction) will be treated with bisulfite, according to manufacturer's instructions. SDC2 and COL2A1 control reactions will be performed in a single tube. The SDC2 methylation test will be performed using an AB 7500 Fast Real-time PCR system. CT values will be calculated using the 7500 software accompanying the instrument. Results from the EarlyTect™-Colon Cancer test will be compared against those obtained from colonoscopy and any corresponding diagnostic histopathology from clinically significant biopsied or subsequently excised lesions. Based on these results, participants will be divided into three groups: CRC, polyp, and negative. The following clinical data will be recorded for the participants: sex, age, colonoscopy results, and clinical stage (for CRC cases). DISCUSSION This trial investigates the clinical performance of a device that allows quantitative detection of a single DNA marker, SDC2 methylation, in human stool DNA in asymptomatic populations. The results of this trial are expected to be beneficial for CRC screening and may help make colonoscopy a selective procedure used only in populations with a high risk of CRC. TRIAL REGISTRATION This trial (NCT04304131) was registered at ClinicalTrials.gov on March 11, 2020 and is available at https://clinicaltrials.gov/ct2/show/NCT04304131?cond=NCT04304131&draw=2&rank=1 .
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Affiliation(s)
- Chang Woo Kim
- Department of Surgery, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, 892 Dongnam-ro, Seoul, Gangdong-gu, 05278, Korea
| | - Hyunjin Kim
- Department of Surgery, Koo Hospital, 141 Gamsambuk-gil, Daegu, Korea
| | - Hyoung Rae Kim
- Department of Surgery, Busan Hangun Hospital, 348 Chungnyeol-daero, Dongnae-gu, Busan, Korea
| | - Bong-Hyeon Kye
- Department of Surgery, St. Vincent's Hospital, The Catholic University of Korea, 93 Jungbu-daero, Suwon, Korea
| | - Hyung Jin Kim
- Department of Surgery, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Tongil-ro, Seoul, 1021, Korea
| | - Byung Soh Min
- Department of Surgery, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Korea
| | - Tae Jeong Oh
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, Korea
| | - Sungwhan An
- Genomictree, Inc, 44-6 Techno 10-ro Yuseong-gu, Daejeon, Korea
| | - Suk-Hwan Lee
- Department of Surgery, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, 892 Dongnam-ro, Seoul, Gangdong-gu, 05278, Korea.
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Evaluation of Methylation Profiles of An Epidermal Growth Factor Receptor Gene in a Head and Neck Squamous Cell Carcinoma Patient Group. Balkan J Med Genet 2021; 23:65-72. [PMID: 33816074 PMCID: PMC8009575 DOI: 10.2478/bjmg-2020-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey, and 48 unrelated healthy volunteers from different geographic regions of Turkey, were included in this study. Methylation status of the promoter region of the EGFR gene was detected by methylation-specific-polymerase chain reaction (MS-PCR). The correlation between EGFR gene promoter methylation profiles and clinical characteristics were examined using the χ2 test. Methylation was observed in 79.0% of HNSCC patients, whereas this ratio was 90.0% in healthy individuals. The results show that promoter region methylation of the EGFR gene was not associated with HNSCC development in the studied Turkish patient group. In addition, the methylation status of the EGFR gene promoter was not found to be related to age, gender or tumor stage.
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24
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Papatheodoridi A, Chatzigeorgiou A, Chrysavgis L, Lembessis P, Loglio A, Facchetti F, Cholongitas E, Koutsilieris M, Lampertico P, Papatheodoridis G. Circulating cell-free DNA species affect the risk of hepatocellular carcinoma in treated chronic hepatitis B patients. J Viral Hepat 2021; 28:464-474. [PMID: 33260272 DOI: 10.1111/jvh.13446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 01/08/2023]
Abstract
Hepatocellular carcinoma (HCC) may still develop in chronic hepatitis B (CHB) patients even under effective long-term oral antiviral therapy, but its pathogenesis in the setting of long-standing inhibition of viral replication has not been completely elucidated. We investigated whether species of circulating cell-free DNA (cfDNA) may be involved in the process of hepatocarcinogenesis in treated CHB patients. Serum samples were obtained from HBeAg-negative CHB patients with (HCC cases, n = 37) or without HCC development during the first 5 years of oral antiviral therapy (controls, n = 74). HCC cases and controls were matched 1:2 for age, sex and platelets. Determination of different circulating cfDNA species (before HCC diagnosis in HCC cases) including total cfDNA quantity, levels of Alu repeat DNA and RNase P coding DNA, copies of mitochondrial DNA and levels of 5-methyl-2'-deoxycytidine as an indicator of DNA methylation was performed. HCC cases compared with controls had higher median levels of Alu247 (123 vs 69 genomic equivalent, p = .042) and RNase P coding DNA (68 vs 15 genomic equivalent, p < .001). In contrast, median cfDNA concentration, Alu115 levels, Alu247/Alu115 ratio as an index of DNA integrity and mitochondrial DNA copies did not differ significantly between HCC cases and controls. Receiver operating characteristic curve analysis showed that levels RNase P coding DNA offered good prediction of subsequent HCC development (c-statistic: 0.80, p < .001). In conclusion, serum levels of RNase P coding DNA are increased years before HCC diagnosis and could be potentially helpful in the prediction of the HCC risk in treated HBeAg-negative CHB patients.
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Affiliation(s)
- Alkistis Papatheodoridi
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece.,Department of Clinical Therapeutics, 'Alexandra' General Hospital of Athens, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Lampros Chrysavgis
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Lembessis
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Alessandro Loglio
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, CRC 'A. M. and A. Migliavacca' Center for Liver Disease, Milan, Italy
| | - Floriana Facchetti
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, CRC 'A. M. and A. Migliavacca' Center for Liver Disease, Milan, Italy
| | - Evangelos Cholongitas
- 1st Department of Internal Medicine, General Hospital of Athens 'Laiko', Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Koutsilieris
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Pietro Lampertico
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, CRC 'A. M. and A. Migliavacca' Center for Liver Disease, Milan, Italy
| | - George Papatheodoridis
- Department of Gastroenterology, General Hospital of Athens 'Laiko', Medical School of National and Kapodistrian University of Athens, Athens, Greece
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25
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Kondo M, Aboshi H, Yoshikawa M, Ogata A, Murayama R, Takei M, Aizawa S. A newly developed age estimation method based on CpG methylation of teeth-derived DNA using real-time methylation-specific PCR. J Oral Sci 2020; 63:54-58. [PMID: 33281149 DOI: 10.2334/josnusd.20-0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Age estimation of unidentified bodies is important in forensic medicine and crime scenes. There is accumulating evidence that DNA methylation in the human genome isolated from body fluids changes with age. Most of the data have been obtained by pyrosequencing. In the forensic field, a simple, quick, and economical method is required to evaluate the age of various types of samples. In this study, an age estimation method based on methylation levels of DNA extracted from teeth using real-time methylation-specific PCR (MSP) was developed. The CpG island in the upstream region of ELOVL2, which is known as a validated biomarker in blood samples, was selected as a target site. The CpG methylation levels highly correlated with age (r = 0.843, n = 29). Age-related increase in DNA methylation levels was not affected by sex differences. In addition, the simple regression model based on methylation status of the CpG island exhibited moderate accuracy with a mean absolute deviation between chronological age and predicted age of 8.94 years. The results imply that real-time MSP can be a new tool to perform age prediction of unidentified bodies in forensic scenes.
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Affiliation(s)
- Masahiro Kondo
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Hirofumi Aboshi
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Masaaki Yoshikawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine
| | - Ayano Ogata
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Ryosuke Murayama
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine
| | - Shin Aizawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine
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26
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Chen D, Yan Y, Xie J, Pan J, Chen Y, Li Q, Yuan Y, Zeng W, Xing W. Amide-type local anesthetics may suppress tumor cell proliferation and sensitize Human Hepatocellular Carcinoma Cells to Cisplatin via upregulation of RASSF1A expression and demethylation. J Cancer 2020; 11:7312-7319. [PMID: 33193895 PMCID: PMC7646167 DOI: 10.7150/jca.46630] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/10/2020] [Indexed: 12/18/2022] Open
Abstract
Background: It has been reported that local anesthetics are toxic to various types of cells. Furthermore, several local anesthetics have been confirmed to exert demethylation effects and regulate the proliferation of human cancer cells. Our previous findings suggest that lidocaine may exert potential antitumor activity and enhance the sensitivity of cisplatin to hepatocellular carcinoma in vitro and in vivo. A recent study proved that lidocaine sensitizes breast cancer cells to cisplatin via upregulation of RASSF1A, a promotor of tumor suppressive gene (TSG) demethylation. We sought to determine whether amide-type local anesthetics (lidocaine, ropivacaine and bupivacaine) exert growth-inhibitory effects on human hepatoma cells and to determine whether amide-type local anesthetics sensitize human hepatoma cells to cisplatin-mediated cytotoxicity via upregulation of RASSF1A expression. Methods: Human hepatoma cell lines HepG2 and BEL-7402 were incubated with lidocaine, ropivacaine and bupivacaine. The viability of local anesthetic-treated cells with or without cisplatin was investigated. Further, we evaluated RASSF1A expression after treatment of HepG2 and BEL-7402 cells with three local anesthetics and determined the influence of RASSF1A expression on the toxicity of cisplatin to these cells. Results: The viability of HepG2 and BEL-7402 cells was significantly decreased by treatment with amide-type local anesthetics (lidocaine, ropivacaine and bupivacaine). In these cells, the combination treatment with cisplatin and local anesthetics exhibited a stronger reduction in viability. Lidocaine, ropivacaine and bupivacaine promoted a significant increase in RASSF1A expression and a decrease in RASSF1A methylation. The combined treatment with both local anesthetics and cisplatin resulted in a significantly lower level of HepG2 and BEL-7402 cell viability than that with singular local anesthetics or cisplatin treatment. Moreover, local anesthetics enhanced the cytotoxicity of cisplatin against HepG2 and BEL-7402 cells, accompanied by an increase in RASSF1A expression. Conclusions: These data indicated that amide-type local anesthetics (lidocaine, ropivacaine and bupivacaine) have growth-inhibitory and demethylation effects in human hepatoma cells. We also found that these amide local anesthetics may enhance the cytotoxicity of cisplatin in human hepatocellular carcinoma cells possibly via upregulation of RASSF1A expression and demethylation.
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Affiliation(s)
- Dongtai Chen
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yan Yan
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Anesthesiology, Huizhou Municipal Central Hospital, Huizhou 516001, China
| | - Jingdun Xie
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiahao Pan
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yonghua Chen
- Department of Anesthesiology, Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Qiang Li
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yunfei Yuan
- Department of Hepatobiliary Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Weian Zeng
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wei Xing
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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27
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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28
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Raut JR, Guan Z, Schrotz-King P, Brenner H. Fecal DNA methylation markers for detecting stages of colorectal cancer and its precursors: a systematic review. Clin Epigenetics 2020; 12:122. [PMID: 32778176 PMCID: PMC7418412 DOI: 10.1186/s13148-020-00904-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation biomarkers in stool may have applications in early colorectal cancer (CRC) detection; however, their association with stages of CRC carcinogenesis or their performance in detecting various stages is unclear. We aimed to systematically review the evidence for DNA methylation markers in stool for risk stratification or detection of specific CRC stages, as well as precursors of CRC. Methods We conducted a systematic search in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 14th January 2020. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, odds ratios (ORs), overall and stage-specific sensitivities, specificities, areas under the receiver operating characteristics curve, and p-values for statistical significance for OR and for association of methylation levels with stage. Results Twenty-seven studies that reported stage-specific associations or performances of fecal DNA methylation markers for detecting colorectal neoplasms were identified. All studies used methylation-specific polymerase chain reaction for assessing methylation levels in the promoter or exon 1 regions of targeted genes. However, most studies were underpowered and limited by their case-control design. Furthermore, the stage-specific associations or sensitivities were validated for two markers (hypermethylation of GATA4 and VIM) only. Conclusion Methylation markers in stool may be useful for detection of CRC precursors or CRC staging, but promising candidate markers need to be validated in longitudinal studies on large screening populations, performing epigenome-wide analyses. Identification of stage-specific DNA methylation biomarkers in stool could boost current strategies towards early detection and enable different approaches to precision medicine for CRC.
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Affiliation(s)
- Janhavi R Raut
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Zhong Guan
- Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Zhang Y, Li CC, Zhang X, Xu Q, Zhang CY. Development of Oxidation Damage Base-Based Fluorescent Probe for Direct Detection of DNA Methylation. Anal Chem 2020; 92:10223-10227. [PMID: 32664718 DOI: 10.1021/acs.analchem.0c01880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation has become a promising epigenetic biomarker for cancer diagnosis, prognosis, and therapy monitoring. Herein, we demonstrate for the first time the development of a new oxidation damage base (8-oxo-7,8-dihydroguanine (8-oxoG))-modified fluorescent probe for direct detection of DNA methylation. This fluorescent probe is labeled with carboxy-X-rhodamine (ROX) and black hole quencher 2 (BHQ2) at the 5' and 3' termini, respectively, with one 8-oxoG base modification in the middle position, and it can discriminate the methylated cytosine from the unmethylated cytosine. The presence of target methylated DNA may induce the recycle cleavage of fluorescent probes with the assistance of human 8-oxoG DNA glycosylase 1 (hOGG1) enzyme, resulting in an enhanced fluorescence signal. In comparison with the reported bisulfite treatment-based indirect approaches, this fluorescent probe can be used for direct detection of DNA methylation under isothermal conditions without the requirement of a stringent primer/template design, any thermal cycling, and ligation procedures, greatly simplifying the experimental processes. Moreover, this fluorescent probe exhibits good specificity and high sensitivity, and it can distinguish a 0.01% methylation level even in the presence of excess unmethylated DNA. Furthermore, this fluorescent probe can be used to detect DNA methylation in genomic DNA extracted from human colon cancer cells, holding great potential in epigenetic study and early clinical diagnosis.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xuechong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
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İNANDIKLIOGLU N, DEMİRHAN O, BAYRAM İ, TANYELİ A. Çukurova Bölgesinde akut lenfoblastik lösemili çocuklarda vasküler endotelyal büyüme faktörü (VEGF-C) ve temel fibroblast büyüme faktörü (bFGF) plazma ekspresyonu ve metilasyon seviyeleri. CUKUROVA MEDICAL JOURNAL 2020. [DOI: 10.17826/cumj.676515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Ma J, Xia LL, Yao XQ, Zheng SM, Li S, Xu LS, Sha WH, Li ZS. BARX2 expression is downregulated by CpG island hypermethylation and is associated with suppressed cell proliferation and invasion of gastric cancer cells. Oncol Rep 2020; 43:1805-1818. [PMID: 32236603 PMCID: PMC7160541 DOI: 10.3892/or.2020.7558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/21/2020] [Indexed: 12/18/2022] Open
Abstract
BarH-like homeobox 2 (BARX2), a homeobox gene, is associated with several types of cancers. The present study aimed to determine whether DNA methylation downregulates BARX2 expression and whether BARX2 is associated with suppression of gastric carcinogenesis. BARX2 protein expression in normal and cancerous gastric tissues and various gastric cancer (GC) cell lines was detected using immunohistochemical and western blot assays. BARX2 mRNA levels were detected using both reverse transcription-polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR). Promoter hypermethylation in GC cells was detected using methylation-specific PCR or bisulfite DNA sequencing PCR. Effects of BARX2 expression on GC cell proliferation, clonal formation, and migration were evaluated after lentivirus-BARX2 transfection. The effect of stable BARX2 transfection on tumor formation was assessed in a nude xenograft mouse model. BARX2 was strongly expressed in the normal gastric mucosa, but weakly or not expressed in GC tissues and most GC cell lines. BARX2 expression was negatively correlated with DNMT (a marker for DNA methylation) expression in the gastric tissues. The BARX2 promoter fragment was hypermethylated in the GC cell lines. Overexpression of BARX2 significantly inhibited GC cell proliferation, clonal formation, and migration. Stable BARX2 transfection inhibited tumor formation in xenograft mice, which was correlated with decreased expression of E-cadherin, proliferation markers, and matrix metalloproteinases. In conclusion, BARX2 expression is aberrantly reduced in GC, which is associated with increased DNA methylation of its promoter. BARX2 inhibits GC cell proliferation, migration, and tumor formation, suggesting that BARX2 acts as a tumor suppressor in gastric carcinogenesis.
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Affiliation(s)
- Juan Ma
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Ling-Ling Xia
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Xue-Qing Yao
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Shi-Min Zheng
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Shi Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Li-Shu Xu
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Wei-Hong Sha
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Ze-Song Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
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Xu X, Chang X, Xu Y, Deng P, Wang J, Zhang C, Zhu X, Chen S, Dai D. SAMD14 promoter methylation is strongly associated with gene expression and poor prognosis in gastric cancer. Int J Clin Oncol 2020; 25:1105-1114. [PMID: 32206938 DOI: 10.1007/s10147-020-01647-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/20/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Gastric cancer (GC) is the fifth most common malignancy worldwide and the third leading cause of cancer-related mortality. In recent years, SAMD14 has been studied in various malignant cancers; however, little is known about the exact mechanisms of SAMD14 involvement in carcinogenesis and malignant progression. METHODS 60 paired GC-normal gastric tissues were evaluated for their SAMD14 mRNA expression in relation to SAMD14 gene promoter methylation. GC patient survival was assessed by Kaplan-Meier analyses and a Cox's proportional hazard model was employed for multivariate analyses. RESULTS SAMD14 expression was significantly inversely correlated with the Borrmann type (P = 0.017), lymph node metastasis (P = 0.006) and tumor-node-metastasis (TNM) stage (P = 0.033). Methylation-specific PCR (MSP) revealed hyper-methylation of the SAMD14 promoter in 56.7% (34/60) of the primary GC tissues tested and in 10% (6/60) of matched non-malignant tissues. The SAMD14 promoter methylation status was also related to pathological differentiation, Borrmann type, TNM stage and lymph node metastasis. The results showed SAMD14 expression was significantly downregulated in Borrmann type, lymph node metastasis and TNM stage, which showed significantly higher methylation. SAMD14 promoter hyper-methylation was significantly associated with a poor prognosis and could serve as an independent marker for survival using multivariate Cox regression analysis. CONCLUSIONS Our results indicated that promoter methylation was a key mechanism contributing to the downregulation of SAMD14 in GC. SAMD14 may be an epigenetically silenced tumor suppressor gene, and hyper-methylation of the SAMD14 promoter may serve as a biomarker to predict the clinical outcome of GC.
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Affiliation(s)
- Xiaoyang Xu
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
- Department of Surgery, Fushun Mining Bureau General Hospital of Liaoning Health Industry Group (the Seventh Affiliated Hospital of China Medical University), Fushun, China
| | - Xiaojing Chang
- Department of Radiotherapy, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yan Xu
- The First Department of Radiotherapy, Fushun Fourth Hospital, Fushun, China
| | - Peng Deng
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Jiang Wang
- Department of Surgery, Fushun Mining Bureau General Hospital of Liaoning Health Industry Group (the Seventh Affiliated Hospital of China Medical University), Fushun, China
| | - Chundong Zhang
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Xinjiang Zhu
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Shuchen Chen
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Dongqiu Dai
- Department of Gastrointestinal Surgery and Cancer Center, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China.
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Perillo B, Di Donato M, Pezone A, Di Zazzo E, Giovannelli P, Galasso G, Castoria G, Migliaccio A. ROS in cancer therapy: the bright side of the moon. Exp Mol Med 2020; 52:192-203. [PMID: 32060354 PMCID: PMC7062874 DOI: 10.1038/s12276-020-0384-2] [Citation(s) in RCA: 1118] [Impact Index Per Article: 279.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species (ROS) constitute a group of highly reactive molecules that have evolved as regulators of important signaling pathways. It is now well accepted that moderate levels of ROS are required for several cellular functions, including gene expression. The production of ROS is elevated in tumor cells as a consequence of increased metabolic rate, gene mutation and relative hypoxia, and excess ROS are quenched by increased antioxidant enzymatic and nonenzymatic pathways in the same cells. Moderate increases of ROS contribute to several pathologic conditions, among which are tumor promotion and progression, as they are involved in different signaling pathways and induce DNA mutation. However, ROS are also able to trigger programmed cell death (PCD). Our review will emphasize the molecular mechanisms useful for the development of therapeutic strategies that are based on modulating ROS levels to treat cancer. Specifically, we will report on the growing data that highlight the role of ROS generated by different metabolic pathways as Trojan horses to eliminate cancer cells. Highly reactive molecules called reactive oxygen species (ROS), which at low levels are natural regulators of important signaling pathways in cells, might be recruited to act as “Trojan horses” to kill cancer cells. Researchers in Italy led by Bruno Perillo of the Institute of Food Sciences in Avelllino review the growing evidence suggesting that stimulating production of natural ROS species could become useful in treating cancer. Although ROS production is elevated in cancer cells it can also promote a natural process called programmed cell death. This normally regulates cell turnover, but could be selectively activated to target diseased cells. The authors discuss molecular mechanisms underlying the potential anti-cancer activity of various ROS-producing strategies, including drugs and light-stimulated therapies. They expect modifying the production of ROS to have potential for developing new treatments.
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Affiliation(s)
- Bruno Perillo
- Istituto di Scienze dell'Alimentazione, C.N.R., 83100, Avellino, Italy. .,Istituto per l'Endocrinologia e l'Oncologia Sperimentale, C.N.R., 80131, Naples, Italy.
| | - Marzia Di Donato
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131, Naples, Italy
| | - Erika Di Zazzo
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Pia Giovannelli
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Giovanni Galasso
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Gabriella Castoria
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Antimo Migliaccio
- Dipartimento di Medicina di Precisione, Università della Campania "L. Vanvitelli", 80138, Naples, Italy
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Yin Z, Zhang X, Li J, Jiao Y, Kong Q, Mu Y. Identification of Imprinted Genes and Their Differentially Methylated Regions in Porcine. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gaya-Bover A, Hernández-López R, Alorda-Clara M, Ibarra de la Rosa JM, Falcó E, Fernández T, Company MM, Torrens-Mas M, Roca P, Oliver J, Sastre-Serra J, Pons DG. Antioxidant enzymes change in different non-metastatic stages in tumoral and peritumoral tissues of colorectal cancer. Int J Biochem Cell Biol 2020; 120:105698. [PMID: 31981728 DOI: 10.1016/j.biocel.2020.105698] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/20/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022]
Abstract
Antioxidant defences and oxidative stress are related to development, progression and malignancy of colorectal cancer. However, their role in early stages of cancer remains unknown. More and more recent studies have revealed that non-tumour adjacent tissue is not a normal tissue. Thus, our aim was to analyse protein levels of MnSOD (Manganese Superoxide Dismutase), acMnSOD (Acetylated Manganese superoxide Dismutase), SIRT3 (Sirtuin 3), CuZnSOD (Cupper Zinc Superoxide Dismutase), CAT (Catalase), GPx (Glutathione Peroxidase), and GRd (Glutathione Reductase) both in tumour and non-tumour adjacent tissue from colorectal cancer patients by western blot. Non-tumour adjacent tissue seemed to have higher levels of antioxidant enzymes that detoxify hydrogen peroxide compared to tumour tissue. In contrast, tumour tissue had higher levels of MnSOD and acMnSOD. Furthermore, most of the proteins analysed showed significant differences between stage I and II in both non-tumour adjacent and tumour tissue. This could indicate that antioxidant enzymes, especially MnSOD, play a crucial role in early stages of colorectal cancer in both tissues, so they could be analysed as novel biomarkers to improve colorectal cancer diagnosis.
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Affiliation(s)
- Auba Gaya-Bover
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain
| | - Reyniel Hernández-López
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain
| | - Marina Alorda-Clara
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain
| | - Javier M Ibarra de la Rosa
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Hospital Son Llàtzer, Palma de Mallorca, 07198, Illes Balears, Spain
| | - Esther Falcó
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Hospital Son Llàtzer, Palma de Mallorca, 07198, Illes Balears, Spain
| | - Teresa Fernández
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Hospital Son Llàtzer, Palma de Mallorca, 07198, Illes Balears, Spain
| | - Maria Margarita Company
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Clinica Rotger, Palma de Mallorca, 07012, Islas Baleares, Spain
| | - Margalida Torrens-Mas
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain
| | - Pilar Roca
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, Madrid, Spain
| | - Jordi Oliver
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, Madrid, Spain
| | - Jorge Sastre-Serra
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain; Ciber Fisiopatología Obesidad y Nutrición (CB06/03), Instituto Salud Carlos III, Madrid, Spain.
| | - Daniel Gabriel Pons
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d´Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, E-07122 Illes Balears, Spain; Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, edificio S, Palma de Mallorca, E-07120, Illes Balears, Spain
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Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing. Theranostics 2020; 10:4737-4748. [PMID: 32308746 PMCID: PMC7163439 DOI: 10.7150/thno.42565] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.
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Affiliation(s)
- Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
- ✉ Corresponding author: Rui Zhang, Ph.D, Mailing address: National Center for Clinical Laboratories, Beijing Hospital, No.1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China. Tel: 86-10-58115053; Fax: 86-10-65212064; E-mail:
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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Feng Q, Qin L, Wang M, Wang P. Signal-on electrochemical detection of DNA methylation based on the target-induced conformational change of a DNA probe and exonuclease III-assisted target recycling. Biosens Bioelectron 2019; 149:111847. [PMID: 31733487 DOI: 10.1016/j.bios.2019.111847] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 11/16/2022]
Abstract
A promising electrochemical system was explored for DNA methylation detection according to the construction of a signal-on biosensor. Based on the ingenious design of probe DNA and auxiliary DNA, methylated target DNA triggered the exonuclease III (Exo III) digestion of auxiliary DNA from 3'-terminus, resulting in the conformational change of probe DNA with an electroactive methylene blue (MB) tag at 5'-terminus. Consequently, the MB tag in the probe DNA was close to the electrode surface for electron transfer, generating an increased current signal. Because of the target recycling of methylated DNA, significant signal amplification was obtained. Moreover, bisulfite conversion conferred an efficient approach for the universal analysis of any CpG sites without the restriction of specific DNA sequence. As a result, the target DNA with different methylation statuses were clearly recognized, and the fully methylated DNA was quantified in a wide range from 10 fM to 100 pM, with a detection limit of 4 fM. The present work realized the assay of methylated target DNA in serum samples with satisfactory results, illustrating the application performance of the system in complex sample matrix.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Li Qin
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mengying Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China.
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Xia L, Zhu Y, Zhang C, Deng S, Deng Y, Yang Z, Mei J, Liu L. Decreased expression of EFCC1 and its prognostic value in lung adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:672. [PMID: 31930073 DOI: 10.21037/atm.2019.10.41] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background So far, there is a lack of reliable prognostic biomarkers for lung adenocarcinoma (ADC). Initially, we found that EF-hand and coiled-coil domain containing 1 (EFCC1) was a novel gene which was downregulated consistently with the progression of lung ADC in The Cancer Genome Atlas (TCGA) data through bioinformatics analysis. In this study, we aimed to evaluate the prognostic significance of EFCC1 in lung ADC in both TCGA data and clinical samples. Methods Firstly, the expression level and prognostic significance of EFCC1 in lung ADC were investigated in TCGA data. Then, the expression level of EFCC1 was validated by qPCR, Western blot, and immunohistochemistry (IHC) in five clinical lung ADC and matched adjacent non-tumor tissues. Finally, the association of EFCC1 expression with clinicopathological characteristics and overall survival (OS) in lung ADC patients was further evaluated in 130 clinical lung ADC samples with tissue microarray (TMA). Results In TCGA data, we found that decreased mRNA expression (P<0.001), elevated DNA methylation (P<0.001) of EFCC1 in lung ADC samples compared with normal lung samples, and low EFCC1 mRNA expression was associated with poor OS in lung ADC patients (HR =0.856, 95% CI: 0.754-0.970, P=0.015). In five clinical lung ADC and matched adjacent non-tumor tissues, both mRNA and protein levels of EFCC1 were lower in all lung ADC tissues than in their adjacent non-tumor counterparts. In 130 clinical lung ADC samples with TMA, EFCC1 expression was correlated with tumor-node-metastasis (TNM) stages (P=0.040) and lymph node metastasis status (P=0.001). The Kaplan-Meier survival curve revealed that low EFCC1 expression was significantly associated with poor OS in lung ADC patients (P=0.001) and multivariate Cox regression hazard model demonstrated that EFCC1 expression level was an independent prognostic factor for lung ADC patients (HR =0.557, 95% CI: 0.351-0.883, P=0.013). Conclusions Our findings suggested that decreased expression of EFCC1 was significantly associated with progression of lung ADC and could serve as a novel prognostic biomarker for lung ADC patients.
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Affiliation(s)
- Liang Xia
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yunke Zhu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Chuanfen Zhang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Senyi Deng
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Yulan Deng
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Zhenyu Yang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Jiandong Mei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu 610041, China
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Fukuchi H, Hayashida Y, Inoue K, Sadamura Y. Forkhead box B2 inhibits the malignant characteristics of the pancreatic cancer cell line Panc-1 in vitro. Genes Cells 2019; 24:674-681. [PMID: 31433897 DOI: 10.1111/gtc.12717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
Forkhead box (FOX) proteins constitute a family of transcription factors that are evolutionarily conserved in various species ranging from yeast to humans. These proteins have functions during development as well as in adulthood. To date, many reports have described the functions of FOX family genes in cancer cells, but the role of FOXB2 is not well understood. In one of the pancreas ductal adenocarcinoma cell lines, Panc-1 cells, we showed here that FOXB2 expression is barely detectable and that CpG islands in the 5' regions of the FOXB2 are highly methylated. These findings led us to hypothesize that FOXB2 acts as a tumor suppressor. To clarify our hypotheses, we investigated the effects of FOXB2 over-expression in Panc-1 cells. We obtained FOXB2 stable transfectants, and these clones exhibited reduced spheroid formation ability. Expression of β-catenin, which is reported to be over-expressed in various cancer cells, was highly suppressed in FOXB2 stable transfectants. Moreover, side population (SP) cell fractions, which have a high tumorigenesis and metastatic potential, as well as anchorage-independent growth ability, were reduced. These results suggest that FOXB2 has the ability to inhibit the malignant characteristics of Panc-1 in vitro.
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Affiliation(s)
- Hiroki Fukuchi
- Life Science Research Laboratories, FUJIFILM Wako Pure Chemical Corporation, Amagasaki, Japan
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Yukinobu Hayashida
- Life Science Research Laboratories, FUJIFILM Wako Pure Chemical Corporation, Amagasaki, Japan
| | - Kunio Inoue
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Yoshifusa Sadamura
- Life Science Research Laboratories, FUJIFILM Wako Pure Chemical Corporation, Amagasaki, Japan
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41
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Singi P, Rocha RP, de Carli ML, Hanemann JAC, Pereira AAC, Coelho LFL, Malaquias LCC. Different
DNA
methylation profile is demonstrated in paracoccidioidomycosis patients without oral lesions. Mycoses 2019; 62:1133-1139. [DOI: 10.1111/myc.13000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Paola Singi
- Department of Clinic and Surgery School of Dentistry Federal University of Alfenas Alfenas MG Brazil
| | - Raissa P. Rocha
- Graduate Program in Microbiology Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Marina L. de Carli
- Department of Clinic and Surgery School of Dentistry Federal University of Alfenas Alfenas MG Brazil
| | - João Adolfo C. Hanemann
- Department of Clinic and Surgery School of Dentistry Federal University of Alfenas Alfenas MG Brazil
| | - Alessandro A. C. Pereira
- Department of Pathology and Parasitology Institute of Biomedical Sciences Federal University of Alfenas Alfenas MG Brazil
| | - Luiz Felipe L. Coelho
- Department of Microbiology and Immunology Institute of Biomedical Sciences Federal University of Alfenas Alfenas MG Brazil
| | - Luiz Cosme C. Malaquias
- Department of Microbiology and Immunology Institute of Biomedical Sciences Federal University of Alfenas Alfenas MG Brazil
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42
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Pero R, Angrisano T, Brancaccio M, Falanga A, Lombardi L, Natale F, Laneri S, Lombardo B, Galdiero S, Scudiero O. Beta-defensins and analogs in Helicobacter pylori infections: mRNA expression levels, DNA methylation, and antibacterial activity. PLoS One 2019; 14:e0222295. [PMID: 31537016 PMCID: PMC6752957 DOI: 10.1371/journal.pone.0222295] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/26/2019] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial peptides can protect the gastric mucosa from bacteria, but Helicobacter pylori (H. pylori) can equally colonize the gastric apparatus. To understand beta-defensin function in H. pylori-associated chronic gastritis, we investigated susceptibility, human beta-defensin mRNA expression, and DNA methylation changes to promoters in the gastric mucosa with or without H. pylori infection. We studied the expression of HBD2 (gene name DEFB4A), HBD3 (DEFB103A), and HBD4 (DEFB104) using real-time PCR in 15 control and 10 H. pylori infection patient gastric specimens. This study demonstrates that H. pylori infection is related to gastric enhancement of inducible HBD2, but inducible HBD3 and HBD4 expression levels remained unchanged. HBD2 gene methylation levels were overall higher in H. pylori-negative samples than in H. pylori-positive samples. We also assessed antimicrobial susceptibility using growth on blood agar. The H. pylori strain Tox+ was susceptible to all defensins tested and their analogs (3N, 3NI). These results show that HBD2 is involved in gastritis development driven by H. pylori, which facilitates the creation of an epigenetic field during H. pylori-associated gastric tumorigenesis.
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Affiliation(s)
- Raffaela Pero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Task Force sugli Studi del Microbioma, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- * E-mail: (RP); (OS)
| | - Tiziana Angrisano
- Dipartimento di Biologia, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Mariarita Brancaccio
- Dipartimento di Biologia ed Evoluzione degli Organismi Marini, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Annarita Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Lucia Lombardi
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Francesco Natale
- Dipartimento di Biologia, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Sonia Laneri
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Barbara Lombardo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- CEINGE-Biotecnologie Avanzate Scarl, Napoli, Italy
| | - Stefania Galdiero
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Olga Scudiero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Task Force sugli Studi del Microbioma, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- CEINGE-Biotecnologie Avanzate Scarl, Napoli, Italy
- * E-mail: (RP); (OS)
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FGF5 methylation is a sensitivity marker of esophageal squamous cell carcinoma to definitive chemoradiotherapy. Sci Rep 2019; 9:13347. [PMID: 31527639 PMCID: PMC6746740 DOI: 10.1038/s41598-019-50005-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
Definitive chemoradiotherapy (dCRT) is the major treatment for esophageal squamous cell carcinoma (ESCC), and prediction of the response to dCRT is important so as not to miss an opportunity to cure an ESCC. Nevertheless, few validated markers are available. Here, we aimed to identify a highly reproducible marker using multi-layer omics analysis. 117 ESCC samples from 67 responders and 50 non-responders were divided into screening, validation, and re-validation sets. In the screening cohort (n = 41), somatic mutations in 114 genes showed no association with dCRT response. Genome-wide DNA methylation analysis using Infinium HumanMethylation450 BeadChip array identified four genic regions significantly associated with dCRT response. Among them, FGF5 methylation was validated to be associated with dCRT response (n = 34; P = 0.001), and further re-validated (n = 42; P = 0.020) by bisulfite-pyrosequencing. The sensitivity and specificity in the combined validation and re-validation sets (n = 76) were 45% and 90%, respectively, by using the cut-off value established in the screening set, and FGF5 methylation had predictive power independent from clinicopathological parameters. In ESCC cell lines, FGF5 promoter methylation repressed its expression. FGF5 expression was induced by cisplatin (CDDP) treatment in three unmethylated cell lines, but not in two methylated cell lines. Exogenous FGF5 overexpression in a cell line with its methylation conferred resistance to CDDP. In non-cancerous esophageal tissues, FGF5 was not expressed, and its methylation was present in a small fraction of cells. These results showed that FGF5 methylation is a validated marker for ESCC sensitivity to dCRT.
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Whole-blood DNA Methylation Markers for Risk Stratification in Colorectal Cancer Screening: A Systematic Review. Cancers (Basel) 2019; 11:cancers11070912. [PMID: 31261771 PMCID: PMC6678372 DOI: 10.3390/cancers11070912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/24/2022] Open
Abstract
DNA methylation profiles within whole-blood samples have been reported to be associated with colorectal cancer (CRC) occurrence and might enable risk stratification for CRC. We systematically reviewed and summarized studies addressing the association of whole-blood DNA methylation markers and risk of developing CRC or its precursors. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 12th November 2018. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, methylation levels of patients in comparison to healthy controls, p-values, and odds ratios of the markers. Overall, 19 studies reporting 102 methylation markers for risk assessment of colorectal neoplasms met our inclusion criteria. The studies mostly used Methylation Specific Polymerase Chain Reaction (MS-PCR) for assessing the methylation status of a defined set of genes. Only two studies applied array-based genome-wide assays to assess the methylation levels. Five studies incorporated panels consisting of 2–10 individual methylation markers to assess their potential for stratifying the risk of developing colorectal neoplasms. However, none of these associations was confirmed in an independent cohort. In conclusion, whole-blood DNA methylation markers may be useful as biomarkers for risk stratification in CRC screening, but reproducible risk prediction algorithms are yet to be established by large scale epigenome-wide studies with thorough validation of results in prospective study cohorts including large screening populations. The possibilities of enhancing predictive power by combining methylation data with polygenetic risk scores and environmental risk factors need to be explored.
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45
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Li W, Xu L. Epigenetic Function of TET Family, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Hematologic Malignancies. Oncol Res Treat 2019; 42:309-318. [PMID: 31055566 DOI: 10.1159/000498947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
Abstract
DNA methylation plays significant roles in a variety of biological and pathological processes including mammalian development, genomic imprinting, retrotransposon silencing, and X-chromosome inactivation. Recent discoveries indicated that ten-eleven translocation (TET) family of dioxygenases can convert 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC). The TET family includes three members: TET1, TET2, and TET3. With increasing evidence, more and more biological and pathological processes in which 5-hmC and TET family serve unparalleled biological roles are noticed, for example, DNA demethylation and transcriptional regulation of different target genes, which are involved in many human diseases, especially hematologic malignancies, resembling chronic myelomonocytic leukemia, myelodysplastic syndromes, and so on. In this review, we focus on the diverse functions of TET family and the novel epigenetic marks, 5-mC and 5-hmC, in hematologic malignancies. This review will provide valuable insights into the potential targets of hematologic malignancies. Further understanding of the normal and pathological functions of TET family may provide new methods to develop novel epigenetic therapies for treating hematologic malignancies.
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Affiliation(s)
- Wei Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Linping Xu
- Department of Research and Foreign Affairs, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China,
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46
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LINC00162 confers sensitivity to 5-Aza-2'-deoxycytidine via modulation of an RNA splicing protein, HNRNPH1. Oncogene 2019; 38:5281-5293. [PMID: 30914798 DOI: 10.1038/s41388-019-0792-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022]
Abstract
DNA demethylation therapy is now expanding from hematological tumors to solid tumors. To exploit its maximum efficacy, long-term treatment is needed, and stratification of sensitive patients is critically important. Here, we identified a long non-coding RNA, LINC00162, as highly and frequently expressed in gastric cancer cell lines sensitive to 5-aza-2'-deoxycytidine (5-aza-dC). Knockdown of LINC00162 decreased the sensitivity while its overexpression increased the sensitivity. In vivo experiments also showed that LINC00162 overexpression increased the sensitivity. LINC00162 enhanced cell cycle arrest and apoptosis induced by 5-aza-dC, but did not affect its DNA demethylation effect. Mechanistically, LINC00162 interacted with an RNA splicing protein, HNRNPH1, and decreased splicing of an anti-apoptotic splicing variant, BCL-XL. LINC00162 may have translational value to predict patients who will respond to 5-aza-dC.
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Khalaj-Kondori M, Hosseinnejad M, Hosseinzadeh A, Behroz Sharif S, Hashemzadeh S. Aberrant hypermethylation of OGDHL gene promoter in sporadic colorectal cancer. Curr Probl Cancer 2019; 44:100471. [PMID: 30904169 DOI: 10.1016/j.currproblcancer.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 03/05/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Aberrant methylation patterns of certain genes including tumor suppressors, a major epigenetic event, contribute mainly to tumorigenesis. Promoter CpG island methylation in Oxoglutarate dehydrogenase like (OGDHL) gene has been reported to reduce gene expression and hence apoptosis induction. This gene has been shown to be involved in colorectal cancer progression. In the present study, we investigated methylation status of OGDHL gene promoter in patients with colorectal cancer and evaluated its potential as a diagnostic biomarker. METHODS AND MATERIAL After collecting clinicopathologic data of patients, tumor and matched tumor free margin samples were obtained from 40 individuals; total genomic DNA was extracted and subjected to bisulfite modification. Methylation status of the gene promoter was studied using quantitative methylation-specific PCR method. Finally, its potential as a diagnostic biomarker was evaluated by receiver operating characteristic curve analysis. RESULTS There was not any significant correlation for clinicopathologic features including tumor stage, grade, size, and location with methylation status of OGDHL promoter. However, a significant high methylation level was observed in tumoral tissues compared with nontumoral marginal samples (P < 0.0001). Moreover, receiver operating characteristic curve analysis revealed 97.5% sensitivity and 95%, specificity for OGDHL promoter methylation in a cut off of 27.37% methylation as a biomarker for colorectal cancer. CONCLUSION The promoter of OGDHL gene is hypermethylated in colorectal cancer and might be considered as a biomarker for its development.
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Affiliation(s)
- Mohammad Khalaj-Kondori
- Dept. of Genetics, Animal Biology Group, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Mina Hosseinnejad
- Department of Biology, Tabriz Branch of Islamic Azad University, Tabriz, Iran
| | - Asghar Hosseinzadeh
- Department of Biology, Tabriz Branch of Islamic Azad University, Tabriz, Iran
| | - Shahin Behroz Sharif
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Shahriar Hashemzadeh
- Department of General & Vascular Surgery, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Kako K, Kim JD, Fukamizu A. Emerging impacts of biological methylation on genetic information. J Biochem 2019; 165:9-18. [PMID: 30219914 DOI: 10.1093/jb/mvy075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The central dogma of molecular biology explains the fundamental flow of genetic information for life. Although genome sequence (DNA) itself is a static chemical signature, it includes multiple layers of information composed of mRNA, tRNA, rRNA and small RNAs, all of which are involved in protein synthesis and is passing from parents to offspring via DNA. Methylation is a biologically important modification, because DNA, RNAs and proteins, components of the central dogma, are methylated by a set of methyltransferases. Recent works focused on understanding a variety of biological methylation have shed light on new regulation of cellular functions. In this review, we briefly discuss some of those recent findings of methylation, including DNA, RNAs and proteins.
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Affiliation(s)
- Koichiro Kako
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
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The Emerging Role of Estrogens in Thyroid Redox Homeostasis and Carcinogenesis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2514312. [PMID: 30728883 PMCID: PMC6343143 DOI: 10.1155/2019/2514312] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS) are the most critical class of free radicals or reactive metabolites produced by all living organisms. ROS regulate several cellular functions through redox-dependent mechanisms, including proliferation, differentiation, hormone synthesis, and stress defense response. However, ROS overproduction or lack of appropriate detoxification is harmful to cells and can be linked to the development of several diseases, such as cancer. Oxidative damage in cellular components, especially in DNA, can promote the malignant transformation that has already been described in thyroid tissue. In thyrocyte physiology, NADPH oxidase enzymes produce large amounts of ROS that are necessary for hormone biosynthesis and might contribute to the high spontaneous mutation rate found in this tissue. Thyroid cancer is the most common endocrine malignancy, and its incidence is significantly higher in women than in men. Several lines of evidence suggest the sex hormone estrogen as a risk factor for thyroid cancer development. Estrogen in turn, besides being a potent growth factor for both normal and tumor thyroid cells, regulates different mechanisms of ROS generation. Our group demonstrated that the thyroid gland of adult female rats exhibits higher hydrogen peroxide (H2O2) production and lower enzymatic antioxidant defense in comparison with male glands. In this review, we discuss the possible involvement of thyroid redox homeostasis and estrogen in the development of thyroid carcinogenesis.
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50
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Kerachian MA, Kerachian M. Long interspersed nucleotide element-1 (LINE-1) methylation in colorectal cancer. Clin Chim Acta 2018; 488:209-214. [PMID: 30445031 DOI: 10.1016/j.cca.2018.11.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) represents a group of molecularly heterogeneous diseases characterized by genetic and epigenetic alterations. Long interspersed nuclear elements (LINEs) are a form of retrotransposable element found in many eukaryotic genomes. These LINEs, when active, can mobilize in the cell and steadily cause genomic rearrangement. Active LINE reorganization is a source of endogenous mutagenesis and polymorphism in the cell that brings about individual genomic variation. In normal somatic cells, these elements are heavily methylated and thus mostly suppressed, in turn, preventing their potential for bringing about genomic instability. When LINEs are inadequately controlled, they can play a role in the pathogenesis of several genetic diseases, such as cancer. In tumor cells, LINE hypomethylation can reactivate the mobilization of these elements and is associated with both an advanced stage and a poor prognosis. In this article, we summarize the current knowledge surrounding LINE methylation, its correlation to CRC and its application as a diagnostic, prognostic and predictive biomarker in colon cancer.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Matin Kerachian
- Faculty of Medicine, McGill University, Montreal, Canada; Research Institute at McGill University Health Center, Montreal, Canada
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