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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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2
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Wang Z, Liu Z, Wang PS, Lin HP, Rea M, Kondo K, Yang C. Epigenetic downregulation of O 6-methylguanine-DNA methyltransferase contributes to chronic hexavalent chromium exposure-caused genotoxic effect and cell transformation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122978. [PMID: 37995958 PMCID: PMC11372728 DOI: 10.1016/j.envpol.2023.122978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a common environmental pollutant and chronic exposure to Cr(VI) causes lung cancer and other types of cancer in humans, although the mechanism of Cr(VI) carcinogenesis remains elusive. Cr(VI) has been considered as a genotoxic carcinogen, but accumulating evidence indicates that Cr(VI) also causes various epigenetic toxic effects that play important roles in Cr(VI) carcinogenesis. However, it is not clear how Cr(VI)-caused epigenetic dysregulations contributes to Cr(VI) carcinogenesis. This study investigates whether Cr(VI) epigenetic toxic effect has an impact on its genotoxic effect. It was found that chronic low dose of Cr(VI) exposure time-dependently down-regulates the expression of a critical DNA damage repair protein O6-methylguanine-DNA methyltransferase (MGMT), leading to the increases of the levels of the highly mutagenic and carcinogenic DNA lesion O6-methylguanine (O6-MeG) in human bronchial epithelial BEAS-2B cells. Moreover, the levels of MGMT and O6-MeG in chronic Cr(VI) exposure-caused human lung cancer tissues are also significantly lower and higher than that in the adjacent normal lung tissues, respectively. It was further determined that chronic low dose of Cr(VI) exposure-transformed BEAS-2B cells display impaired DNA damage repair capacity and a high sensitivity to the toxicity of the alkylating chemotherapeutic drug Temozolomide. In contrast, stably overexpressing MGMT in parental BEAS-2B cells reverses chronic low dose of Cr(VI) exposure-caused DNA damage repair deficiency and significantly reduces cell transformation by Cr(VI). Further mechanistical studies revealed that chronic low dose of Cr(VI) exposure down-regulates MGMT expression through epigenetic mechanisms by increasing DNA methylation and histone H3 repressive modifications. Taken together, these findings suggest that epigenetic down-regulation of a crucial DNA damage repair protein MGMT contributes significantly to the genotoxic effect and cell transformation caused by chronic low dose of Cr(VI) exposure.
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Affiliation(s)
- Zhishan Wang
- Stony Brook Cancer Center, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, 101 Nicolls Road, Stony Brook, NY 11794, USA.
| | - Zulong Liu
- Stony Brook Cancer Center, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Po-Shun Wang
- Stony Brook Cancer Center, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Hsuan-Pei Lin
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Matthew Rea
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Kazuya Kondo
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima City 770-8509, Japan
| | - Chengfeng Yang
- Stony Brook Cancer Center, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, 101 Nicolls Road, Stony Brook, NY 11794, USA
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Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Hogstrand C, (Ron) Hoogenboom L, Leblanc J, Nebbia CS, Nielsen E, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Romualdo B, Cristina F, Stephen H, Marco I, Mosbach‐Schulz O, Riolo F, Christodoulidou A, Grasl‐Kraupp B. Risk assessment of N-nitrosamines in food. EFSA J 2023; 21:e07884. [PMID: 36999063 PMCID: PMC10043641 DOI: 10.2903/j.efsa.2023.7884] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
EFSA was asked for a scientific opinion on the risks to public health related to the presence of N-nitrosamines (N-NAs) in food. The risk assessment was confined to those 10 carcinogenic N-NAs occurring in food (TCNAs), i.e. NDMA, NMEA, NDEA, NDPA, NDBA, NMA, NSAR, NMOR, NPIP and NPYR. N-NAs are genotoxic and induce liver tumours in rodents. The in vivo data available to derive potency factors are limited, and therefore, equal potency of TCNAs was assumed. The lower confidence limit of the benchmark dose at 10% (BMDL10) was 10 μg/kg body weight (bw) per day, derived from the incidence of rat liver tumours (benign and malignant) induced by NDEA and used in a margin of exposure (MOE) approach. Analytical results on the occurrence of N-NAs were extracted from the EFSA occurrence database (n = 2,817) and the literature (n = 4,003). Occurrence data were available for five food categories across TCNAs. Dietary exposure was assessed for two scenarios, excluding (scenario 1) and including (scenario 2) cooked unprocessed meat and fish. TCNAs exposure ranged from 0 to 208.9 ng/kg bw per day across surveys, age groups and scenarios. 'Meat and meat products' is the main food category contributing to TCNA exposure. MOEs ranged from 3,337 to 48 at the P95 exposure excluding some infant surveys with P95 exposure equal to zero. Two major uncertainties were (i) the high number of left censored data and (ii) the lack of data on important food categories. The CONTAM Panel concluded that the MOE for TCNAs at the P95 exposure is highly likely (98-100% certain) to be less than 10,000 for all age groups, which raises a health concern.
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Multiomics characteristics and immunotherapeutic potential of EZH2 in pan-cancer. Biosci Rep 2023; 43:232355. [PMID: 36545914 PMCID: PMC9842950 DOI: 10.1042/bsr20222230] [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: 11/03/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is a significant epigenetic regulator that plays a critical role in the development and progression of cancer. However, the multiomics features and immunological effects of EZH2 in pan-cancer remain unclear. Transcriptome and clinical raw data of pan-cancer samples were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and subsequent data analyses were conducted by using R software (version 4.1.0). Furthermore, numerous bioinformatics analysis databases also reapplied to comprehensively explore and elucidate the oncogenic mechanism and therapeutic potential of EZH2 from pan-cancer insight. Finally, quantitative reverse transcription polymerase chain reaction and immunohistochemical assays were performed to verify the differential expression of EZH2 gene in various cancers at the mRNA and protein levels. EZH2 was widely expressed in multiple normal and tumor tissues, predominantly located in the nucleoplasm. Compared with matched normal tissues, EZH2 was aberrantly expressed in most cancers either at the mRNA or protein level, which might be caused by genetic mutations, DNA methylation, and protein phosphorylation. Additionally, EZH2 expression was correlated with clinical prognosis, and its up-regulation usually indicated poor survival outcomes in cancer patients. Subsequent analysis revealed that EZH2 could promote tumor immune evasion through T-cell dysfunction and T-cell exclusion. Furthermore, expression of EZH2 exhibited a strong correlation with several immunotherapy-associated responses (i.e., immune checkpoint molecules, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) status, and neoantigens), suggesting that EZH2 appeared to be a novel target for evaluating the therapeutic efficacy of immunotherapy.
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5
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Pan-cancer analysis based on epigenetic modification explains the value of HJURP in the tumor microenvironment. Sci Rep 2022; 12:20871. [PMID: 36460821 PMCID: PMC9718852 DOI: 10.1038/s41598-022-25439-0] [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: 05/22/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
To analyze the expression levels, prognostic value and immune infiltration association of Holliday junction protein (HJURP) as well as its feasibility as a pan-cancer biomarker for different cancers. The Protter online tool was utilized to obtain the localization of HJURP, then the methylation of HJURP in tumors were further explored. Thereafter, the mRNA data and clinical characteristics of 33 tumor types from TCGA database were obtained to investigate the expression and prognostic relationship of HJURP in different tumor types. Finally, the composition pattern and immune infiltration of HJURP in different tumors were detected in Tumor Immune Estimation Resource. HJURP was abnormally expressed in most of the cancer types and subtypes in TCGA database. Also, it was associated with poor prognosis of different cohorts. At the same time, the results also showed that HJURP was related to tumor immune evasion through different mechanisms, including T cell rejection and methylation in different cancer types. Besides, the methylation of HJURP was inversely proportional to mRNA expression levels, which mediated the dysfunctional phenotypes of T cells and poor prognosis of different cancer types. Alternatively, our results indicated that HJURP expression was associated with immune cell infiltration in a variety of cancers. HJURP may serve as an oncogenic molecule, and its expression and immune infiltration characteristics can be used as a biomarker for cancer detection, prognosis, treatment design and follow-up.
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Li XY, Hou L, Zhang LY, Zhang L, Wang D, Wang Z, Wen MZ, Yang XT. OAS3 is a Co-Immune Biomarker Associated With Tumour Microenvironment, Disease Staging, Prognosis, and Treatment Response in Multiple Cancer Types. Front Cell Dev Biol 2022; 10:815480. [PMID: 35592250 PMCID: PMC9110822 DOI: 10.3389/fcell.2022.815480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/28/2022] [Indexed: 11/15/2022] Open
Abstract
2′,5′-oligoadenylate synthase (OAS) is a class of enzymes induced by interferons and mainly encoded by the OAS1, OAS2, and OAS3 genes, which activate the potential RNA enzymes to degrade viral mRNA, inhibit viral protein synthesis and promote apoptosis in virus-infected cells. OAS3 is associated with breast cancer prognosis. However, the expression and prognosis of OAS3 and tumour-infiltrating lymphocytes in pan-cancer remain unknown. In the present study, we have systematically investigated and confirmed the role of OAS3 in tumour immune infiltration, immune escape, tumour progression, response to treatment, and prognosis of different cancer types using various bioinformatics methods. The findings suggest that OAS3 is aberrantly expressed in almost all TCGA cancer types and subtypes and is associated with tumour staging, metastasis, and prognostic deterioration in different tumours. In addition, OAS3 expression is associated with the prognosis and chemotherapeutic outcomes of various cancers. In terms of immune-infiltrating levels, OAS3 expression is positively associated with the infiltration of immunosuppressive cells. These findings suggest that OAS3 is correlated with prognosis and immune-infiltrating levels.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Lei Hou
- Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Lu-yu Zhang
- Department of Urologic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Zhang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deming Wang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenfeng Wang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Zhe Wen
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi-tao Yang,
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Zhao H, Lu J, Yan T, Han F, Sun J, Yin X, Chen L, Shen C, Wunderlich M, Yun W, Yang L, Chen L, Su D, Bohlander SK, Wang F, Mulloy JC, Li C, Chen J, Huang H, Jiang X. Opioid receptor signaling suppresses leukemia through both catalytic and non-catalytic functions of TET2. Cell Rep 2022; 38:110253. [DOI: 10.1016/j.celrep.2021.110253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/24/2021] [Accepted: 12/21/2021] [Indexed: 01/12/2023] Open
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8
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Watanabe Y, Oikawa R, Agawa S, Matsuo Y, Oda I, Futagami S, Yamamoto H, Tada T, Itoh F. Combination of artificial intelligence-based endoscopy and miR148a methylation for gastric indefinite dysplasia diagnosis. J Clin Lab Anal 2021; 36:e24122. [PMID: 34811809 PMCID: PMC8761468 DOI: 10.1002/jcla.24122] [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: 10/03/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AND AIM Gastrointestinal endoscopy and biopsy-based pathological findings are needed to diagnose early gastric cancer. However, the information of biopsy specimen is limited because of the topical procedure; therefore, pathology doctors sometimes diagnose as gastric indefinite for dysplasia (GIN). METHODS We compared the accuracy of physician-performed endoscopy (trainee, n = 3; specialists, n = 3), artificial intelligence (AI)-based endoscopy, and/or molecular markers (DNA methylation: BARHL2, MINT31, TET1, miR-148a, miR-124a-3, NKX6-1; mutations: TP53; and microsatellite instability) in diagnosing GIN lesions. We enrolled 24,388 patients who underwent endoscopy, and 71 patients were diagnosed with GIN lesions. Thirty-two cases of endoscopic submucosal dissection (ESD) in 71 GIN lesions and 32 endoscopically resected tissues were assessed by endoscopists, AI, and molecular markers to identify benign or malignant lesions. RESULTS The board-certified endoscopic physicians group showed the highest accuracy in the receiver operative characteristic curve (area under the curve [AUC]: 0.931), followed by a combination of AI and miR148a DNA methylation (AUC: 0.825), and finally trainee endoscopists (AUC: 0.588). CONCLUSION AI with miR148s DNA methylation-based diagnosis is a potential modality for diagnosing GIN.
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Affiliation(s)
- Yoshiyuki Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan.,Department of Internal Medicine, Kawasaki Rinko General Hospital, Kanagawa, Japan.,Division of Gastroenterology, Department of Internal Medicine, Nippon Medical School, Tokyo, Japan
| | - Ritsuko Oikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Shuhei Agawa
- Division of Gastroenterology, Department of Internal Medicine, Nippon Medical School, Tokyo, Japan
| | - Yasumasa Matsuo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Ichiro Oda
- Department of Internal Medicine, Kawasaki Rinko General Hospital, Kanagawa, Japan
| | - Seiji Futagami
- Division of Gastroenterology, Department of Internal Medicine, Nippon Medical School, Tokyo, Japan
| | - Hiroyuki Yamamoto
- Department of Bioinformatics, St. Marianna University Graduate School of Medicine, Kanagawa, Japan
| | - Tomohiro Tada
- Tada Tomohiro Institute of Gastroenterology and Proctology, Saitama, Japan
| | - Fumio Itoh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
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9
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Wu SY, Lin KC, Lawal B, Wu ATH, Wu CZ. MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types. Comput Struct Biotechnol J 2021; 19:4970-4983. [PMID: 34584637 PMCID: PMC8441106 DOI: 10.1016/j.csbj.2021.08.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
MAX dimerization (MXD) protein 3 (MXD3) is a member of the MXD family of basic-helix-loop-helix-leucine-zipper (bHLHZ) transcription factors that plays pivotal roles in cell cycle progression and cell proliferation. However, there is insufficient scientific evidence on the pathogenic roles of MXD3 in various cancers and whether MXD3 plays a role in the immuno-oncology context of the tumor microenvironment, pathogenesis, prognosis, and therapeutic response of different tumors through certain common molecular mechanisms; thus, we saw a need to conduct the present in silico pan-cancer study. Using various computational tools, we interrogated the role of MXD3 in tumor immune infiltration, immune evasion, tumor progression, therapy response, and prognosis of cohorts from various cancer types. Our results indicated that MXD3 was aberrantly expressed in almost all The Cancer Genome Atlas (TCGA) cancer types and subtypes and was associated with the tumor stage, metastasis, and worse prognoses of various cohorts. Our results also suggested that MXD3 is associated with tumor immune evasion via different mechanisms involving T-cell exclusion in different cancer types and by tumor infiltration of immune cells in thymoma (THYM), liver hepatocellular carcinoma (LIHC), and head and neck squamous cell carcinoma (HNSC). Methylation of MXD3 was inversely associated with messenger (m)RNA expression levels and mediated dysfunctional T-cell phenotypes and worse prognoses of cohorts from different cancer types. Finally, we found that genetic alterations and oncogenic features of MXD3 were concomitantly associated with deregulation of the DBN1, RAB24, SLC34A1, PRELID1, LMAN2, F12, GRK6, RGS14, PRR7, and PFN3 genes and were connected to phospholipid transport and ion homeostasis. Our results also suggested that MXD3 expression is associated with immune or chemotherapeutic outcomes in various cancers. In addition, higher MXD3 expression levels were associated with decreased sensitivity of cancer cell lines to several mitogen-activated protein kinase kinase (MEK) inhibitors but led to increased activities of other kinase inhibitors, including Akt inhibitors. Interestingly, MXD3 exhibited higher predictive power for response outcomes and overall survival of immune checkpoint blockade sub-cohorts than three of seven standardized biomarkers. Altogether, our study strongly suggests that MXD3 is an immune-oncogenic molecule and could serve as a biomarker for cancer detection, prognosis, therapeutic design, and follow-up.
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Affiliation(s)
- Szu-Yuan Wu
- Department of Food Nutrition and Health Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.,Big Data Center, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan.,Division of Radiation Oncology, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan.,Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung, Taiwan.,Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan.,Centers for Regional Anesthesia and Pain Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan
| | - Kuan-Chou Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Oral and Maxillofacial Surgery, Department of Dentistry, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Bashir Lawal
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan.,Taipei Heart Institute (THI), Taipei Medical University, Taipei, Taiwan
| | - Ching-Zong Wu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Dentistry, Lotung Poh-Ai hospital, Yilan, Taiwan
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10
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Tomicic MT, Dawood M, Efferth T. Epigenetic Alterations Upstream and Downstream of p53 Signaling in Colorectal Carcinoma. Cancers (Basel) 2021; 13:cancers13164072. [PMID: 34439227 PMCID: PMC8394868 DOI: 10.3390/cancers13164072] [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] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) belongs to the most common tumor types, and half of all CRC harbor missense mutations in the TP53 tumor suppressor gene. In addition to genetically caused loss of function of p53, epigenetic alterations (DNA methylation, histone modifications, micro-RNAs) contribute to CRC development. In this review, we focused on epigenetic alterations related to the entire p53 signaling pathway upstream and downstream of p53. Methylation of genes which activate p53 function has been reported, and methylation of APC and MGMT was associated with increased mutation rates of TP53. The micro-RNA 34a activates TP53 and was methylated in CRC. Proteins that regulate TP53 DNA methylation, mutations, and acetylation of TP53-related histones were methylated in CRC. P53 regulates the activity of numerous downstream proteins. Even if TP53 is not mutated, the function of wildtype p53 may be compromised if corresponding downstream genes are epigenetically inactivated. Thus, the role of p53 for CRC development, therapy response, and survival prognosis of patients may be much more eminent than previously estimated. Therefore, we propose that novel diagnostic devices measuring the entirety of genetic and epigenetic changes in the "p53 signalome" have the potential to improve the predictive and prognostic power in CRC diagnostics and management.
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Affiliation(s)
- Maja T. Tomicic
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany;
| | - Mona Dawood
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128 Mainz, Germany;
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128 Mainz, Germany;
- Correspondence: ; Tel.: +49-6131-3925751; Fax: +49-6131-3923752
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11
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Gao A, Guo M. Epigenetic based synthetic lethal strategies in human cancers. Biomark Res 2020; 8:44. [PMID: 32974031 PMCID: PMC7493427 DOI: 10.1186/s40364-020-00224-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023] Open
Abstract
Over the past decades, it is recognized that loss of DNA damage repair (DDR) pathways is an early and frequent event in tumorigenesis, occurring in 40-50% of many cancer types. The basis of synthetic lethality in cancer therapy is DDR deficient cancers dependent on backup DNA repair pathways. In cancer, the concept of synthetic lethality has been extended to pairs of genes, in which inactivation of one by deletion or mutation and pharmacological inhibition of the other leads to death of cancer cells whereas normal cells are spared the effect of the drug. The paradigm study is to induce cell death by inhibiting PARP in BRCA1/2 defective cells. Since the successful application of PARP inhibitor, a growing number of developed DDR inhibitors are ongoing in preclinical and clinical testing, including ATM, ATR, CHK1/2 and WEE1 inhibitors. Combination of PARP inhibitors and other DDR inhibitors, or combination of multiple components of the same pathway may have great potential synthetic lethality efficiency. As epigenetics joins Knudson’s two hit theory, silencing of DDR genes by aberrant epigenetic changes provide new opportunities for synthetic lethal therapy in cancer. Understanding the causative epigenetic changes of loss-of-function has led to the development of novel therapeutic agents in cancer. DDR and related genes were found frequently methylated in human cancers, including BRCA1/2, MGMT, WRN, MLH1, CHFR, P16 and APC. Both genetic and epigenetic alterations may serve as synthetic lethal therapeutic markers.
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Affiliation(s)
- Aiai Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,Henan Key Laboratory for Esophageal Cancer Research, Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052 Henan China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
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12
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Ta TV, Nguyen QN, Chu HH, Truong VL, Vuong LD. RAS/RAF mutations and their associations with epigenetic alterations for distinct pathways in Vietnamese colorectal cancer. Pathol Res Pract 2020; 216:152898. [PMID: 32089414 DOI: 10.1016/j.prp.2020.152898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
KRAS, NRAS, and BRAF are potential tumor-driven genes that are involved in the RAS/RAF/MAPK signaling pathway. RAS/RAF mutations importantly contribute to colorectal tumorigenesis since they remain the activated status of downstream pathways without regulation of the upstream EGFR signal. However, it has not been unclear how epigenetic alterations involved in colorectal tumorigenesis mediated by KRAS, NRAS, or BRAF mutations. Therefore, in this study, we investigated the frequency and distribution of KRAS/NRAS/BRAF mutations in Vietnamese colorectal cancer (CRC) and explored the relationship between genetic and epigenetic abnormalities in 156 tumors of CRC. Somatic mutations of KRAS (exon 2, codon 12/13; exon 3, codon 61), NRAS (exon 2, codon 12/13; exon 3, codon 61), and BRAF (exon 15, codon 600) was determined by Cobas® KRAS Mutation Test, Therascreen NRAS Pyro Kit and Cobas® 4800 BRAF V600 Mutation Test, respectively. Methylation status of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC was detected by methylation-specific PCR. Distribution of each abnormality in clinicopathological features was also analyzed. Results showed the mutation rates of KRAS, NRAS, and BRAF were 41.0 %, 9.6 %, 8.3 % respectively, while the methylation rates of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC were 16.7 %, 16.7 %, 32.7 %, 30.1 %, 30.1 %, and 37.2 % respectively. The distribution of KRAS mutation was mutually exclusive against that of NRAS (p < 0.001) and BRAF (p < 0.001) mutations in CRC. RAS/RAF mutations were more common in adenocarcinoma subtype (p = 0.020), whereas RASSF1A methylation was more frequent in mucinous adenocarcinoma subtype (p = 0.007). In addition, the frequency of having KRAS mutations was significantly higher in MGMT (p = 0.035) or RASSF1A (p = 0.043) methylated cases than in those without methylation. BRAF mutations were positively associated with MLH1 hypermethylation (p = 0.028) but were inversely associated with APC hypermethylation (p = 0.032). Overall, our results show specific interactions of genetic and epigenetic alterations and suggest the presence of independent oncogenic pathways in tumorigenesis of CRC.
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Affiliation(s)
- To Van Ta
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Quang Ngoc Nguyen
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Ha Hoang Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Viet Nam
| | - Van-Long Truong
- Department of Smart Food and Drug, College of BNIT, Inje University, Gimhae 50834, South Korea.
| | - Linh Dieu Vuong
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam.
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13
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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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14
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Köhler F, Rodríguez-Paredes M. DNA Methylation in Epidermal Differentiation, Aging, and Cancer. J Invest Dermatol 2019; 140:38-47. [PMID: 31427190 DOI: 10.1016/j.jid.2019.05.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
Abstract
The formation and maintenance of the epidermis depend on epidermal stem cell differentiation and must be tightly regulated. Epigenetic mechanisms such as DNA methylation allow the precise gene expression cascade needed during cellular differentiation. However, these mechanisms become deregulated during aging and tumorigenesis, where cellular function and identity become compromised. Here we provide a review of this rapidly developing field. We discuss recent discoveries related to epidermal homeostasis, aging, and cancer, including the functional role of DNA methyltransferases, the methylation clock, and the determination of tumor cells-of-origin. Finally, we focus on future advances, greatly influenced by single-cell sequencing technologies.
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Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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15
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Zhang D, Liu H, Lin J, Ye D. Hepatitis B Virus Infection Dampens CtIP Expression in Hepatoma Cell. J Cancer 2018; 9:1182-1187. [PMID: 29675099 PMCID: PMC5907666 DOI: 10.7150/jca.23649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/28/2018] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a leading cause for hepatocellular carcinoma (HCC). Dysregulation of DNA double-strand break (DSB) repair may explain the pathogenesis of HBV-related HCC. Tumor suppressor CtIP plays a critical role in DSB repair. The purpose of present study was to clarify whether HBV affects CtIP expression in DSB repair of hepatoma cell. HepG2.2.15 was selected as the HBV positive hepatoma cell line, while HepG2 as the HBV negative hepatoma cell line. The two cell lines were treated with bleomycin to induce DSB. Bleomycin treatment could result in DSB by γ-H2AX detection. CtIP gene expression was significantly upregulated after DSB in both HepG2 and HepG2.2.15, while CtIP expression of HepG2.2.15 was higher than that observed in HepG2 before and after DSB. CtIP protein expression was the same pattern as its gene expression. Phosphorylated CtIP (p-CtIP, serine site) was even lower than detectable limit in both HepG2 and HepG2.2.15 before DSB. However, p-CtIP of HepG2.2.15 was significantly lower than that of HepG2 after DSB. These results suggest that HBV could interfere CtIP via enhancing its expression while dampening its phosphorylation, which may disrupt DSB repair pathways and implicate CtIP dysfunction in HBV-related HCC.
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Affiliation(s)
- Dongxin Zhang
- Department of Clinical Laboratory, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430033, People's Republic of China.,Department of Pathophysiology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Haojing Liu
- Department of Internal Medicine, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430033, People's Republic of China.,Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jusheng Lin
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Duyun Ye
- Department of Pathophysiology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
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16
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Gao D, Herman JG, Guo M. The clinical value of aberrant epigenetic changes of DNA damage repair genes in human cancer. Oncotarget 2018; 7:37331-37346. [PMID: 26967246 PMCID: PMC5095080 DOI: 10.18632/oncotarget.7949] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/20/2016] [Indexed: 12/22/2022] Open
Abstract
The stability and integrity of the human genome are maintained by the DNA damage repair (DDR) system. Unrepaired DNA damage is a major source of potentially mutagenic lesions that drive carcinogenesis. In addition to gene mutation, DNA methylation occurs more frequently in DDR genes in human cancer. Thus, DNA methylation may play more important roles in DNA damage repair genes to drive carcinogenesis. Aberrant methylation patterns in DNA damage repair genes may serve as predictive, diagnostic, prognostic and chemosensitive markers of human cancer. MGMT methylation is a marker for poor prognosis in human glioma, while, MGMT methylation is a sensitive marker of glioma cells to alkylating agents. Aberrant epigenetic changes in DNA damage repair genes may serve as therapeutic targets. Treatment of MLH1-methylated colon cancer cell lines with the demethylating agent 5′-aza-2′-deoxycytidine induces the expression of MLH1 and sensitizes cancer cells to 5-fluorouracil. Synthetic lethality is a more exciting approach in patients with DDR defects. PARP inhibitors are the most effective anticancer reagents in BRCA-deficient cancer cells.
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Affiliation(s)
- Dan Gao
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China.,Medical College of NanKai University, Tianjin, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
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17
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Sadeghi MR, Jeddi F, Soozangar N, Somi MH, Samadi N. The role of Nrf2-Keap1 axis in colorectal cancer, progression, and chemoresistance. Tumour Biol 2017. [PMID: 28621229 DOI: 10.1177/1010428317705510] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is the third common cancer after lung and genital cancers worldwide with more than 1.2 million new cases diagnosed annually. Although extensive progress has been made in the treatment of colorectal cancer, finding novel targets for early diagnosis and effective treatment of these patients is an urgent need. Nuclear factor-erythroid 2-kelch-like ECH-associated protein 1 signaling pathway plays a key role in protecting cells from the damage of intracellular oxidative stress and extracellular oxidizing agents. Nuclear factor-erythroid 2 is a transcription factor that creates intracellular redox homeostasis via transcriptional activity and interaction with kelch-like ECH-associated protein 1. Furthermore, it contributes to survival and chemoresistance of colorectal cancer cells which is mediated by overexpression of cytoprotective and multidrug resistance genes. In this review, the dual role of nuclear factor-erythroid 2 signaling in induction of colorectal cancer cell survival and death as well as the possibility of targeting nuclear factor-erythroid 2-kelch-like ECH-associated protein 1 axis as an advanced strategy in prevention and effective treatment of colorectal cancer patients have been discussed.
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Affiliation(s)
- Mohammad Reza Sadeghi
- 1 Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- 2 Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- 3 Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Jeddi
- 1 Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- 2 Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Narges Soozangar
- 1 Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- 2 Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- 1 Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- 1 Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- 2 Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- 4 Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-016-0115-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.
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19
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Greenlee H, Ogden Gaffney A, Aycinena AC, Koch P, Contento I, Karmally W, Richardson JM, Shi Z, Lim E, Tsai WY, Santella RM, Blaner WS, Clugston RD, Cremers S, Pollak S, Sirosh I, Crew KD, Maurer M, Kalinsky K, Hershman DL. Long-term Diet and Biomarker Changes after a Short-term Intervention among Hispanic Breast Cancer Survivors: The ¡Cocinar Para Su Salud! Randomized Controlled Trial. Cancer Epidemiol Biomarkers Prev 2016; 25:1491-1502. [PMID: 27461049 DOI: 10.1158/1055-9965.epi-15-1334] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Among Hispanic breast cancer survivors, we examined the long-term effects of a short-term culturally based dietary intervention on increasing fruits/vegetables (F/V), decreasing fat, and changing biomarkers associated with breast cancer recurrence risk. METHODS Spanish-speaking women (n = 70) with a history of stage 0-III breast cancer who completed treatment were randomized to ¡Cocinar Para Su Salud! (n = 34), a culturally based 9-session program (24 hours over 12 weeks, including nutrition education, cooking classes, and food-shopping field trips), or a control group (n = 36, written dietary recommendations for breast cancer survivors). Diet recalls, fasting blood, and anthropometric measures were collected at baseline, 6, and 12 months. We report changes between groups at 12 months in dietary intake and biomarkers using 2-sample Wilcoxon t tests and generalized estimating equation (GEE) models. RESULTS At 12 months, the intervention group compared with the control group reported higher increases in mean daily F/V servings (total: +2.0 vs. -0.4; P < 0.01), and nonsignificant decreases in the percentage of calories from fat (-2.2% vs. -1.1%; P = 0.69) and weight (-2.6 kg vs. -1.5 kg; P = 0.56). Compared with controls, participants in the intervention group had higher increases in plasma lutein (+20.4% vs. -11.5%; P < 0.01), and borderline significant increases in global DNA methylation (+0.8% vs. -0.5%; P = 0.06). CONCLUSIONS The short-term ¡Cocinar Para Su Salud! program was effective at increasing long-term F/V intake in Hispanic breast cancer survivors and changed biomarkers associated with breast cancer recurrence risk. IMPACT It is possible for short-term behavioral interventions to have long-term effects on behaviors and biomarkers in minority cancer patient populations. Results can inform future study designs. Cancer Epidemiol Biomarkers Prev; 25(11); 1491-502. ©2016 AACR.
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Affiliation(s)
- Heather Greenlee
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | | | - A Corina Aycinena
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Health and Behavior Studies, Teachers College, Columbia University, New York, New York
| | - Pam Koch
- Department of Health and Behavior Studies, Teachers College, Columbia University, New York, New York
| | - Isobel Contento
- Department of Health and Behavior Studies, Teachers College, Columbia University, New York, New York
| | - Wahida Karmally
- Irving Institute for Clinical and Translational Research, Columbia University, New York, New York
| | - John M Richardson
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Zaixing Shi
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Emerson Lim
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Wei-Yann Tsai
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - William S Blaner
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Robin D Clugston
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Serge Cremers
- Irving Institute for Clinical and Translational Research, Columbia University, New York, New York
| | - Susan Pollak
- Irving Institute for Clinical and Translational Research, Columbia University, New York, New York
| | - Iryna Sirosh
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Katherine D Crew
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Matthew Maurer
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Kevin Kalinsky
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Dawn L Hershman
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
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20
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Iannone A, Losurdo G, Pricci M, Girardi B, Massaro A, Principi M, Barone M, Ierardi E, Di Leo A. Stool Investigations for Colorectal Cancer Screening: From Occult Blood Test to DNA Analysis. J Gastrointest Cancer 2016; 47:143-51. [PMID: 26922358 DOI: 10.1007/s12029-016-9810-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE We report an update of current methods for colorectal cancer (CRC) screening based on fecal sample analysis. METHODS A systematic review of the literature was performed in MEDLINE, EMBASE, and Science Direct electronic databases. RESULTS Blood in the stools is the first and most used strategy. Fecal occult blood test (FOBT) and fecal immunochemical test (FIT) are the main methods. Both are economic, easy to perform with high specificity, and low sensitivity. Based on CRC multi-step process with genetic and epigenetic alterations in large bowel cell DNA, single mutations or panels of alterations have been detected. These tests have the advantage of a marked improvement of the sensitivity when compared to fecal blood. However, high costs, poor availability, and correct choice of marker panel represent the major limits. A specific sDNA panel including aberrantly methylated BMP3 and NDRG4 promoter regions, mutant k-ras and β-actin (a reference gene for human DNA quantity), and an immunochemical assay for human hemoglobin has been recently approved by Food and Drug Administration. Novel promising biomarkers for CRC screening are represented by microRNAs (miRNAs), a group of 18-25 nucleotide non-coding RNA molecules that regulate gene expression. Reports on these fecal biomarkers are case-control studies, and each of them evaluates single miRNAs or multi-target panels. On the other hand, some fecal proteins have been studied as possible CRC screening markers, even though they demonstrated poor results. Finally, alterations of estrogen receptor-beta (i.e., dramatic reduction in the early stage of CRC) have been demonstrated in tissue samples. CONCLUSIONS Specific investigations are warranted in order to add further noninvasive markers to the panel of CRC screening tools.
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Affiliation(s)
- Andrea Iannone
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Giuseppe Losurdo
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Maria Pricci
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Bruna Girardi
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Antonio Massaro
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Mariabeatrice Principi
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Michele Barone
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Enzo Ierardi
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Alfredo Di Leo
- Section of Gastroenterology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
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21
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Hocher B, Haumann H, Rahnenführer J, Reichetzeder C, Kalk P, Pfab T, Tsuprykov O, Winter S, Hofmann U, Li J, Püschel GP, Lang F, Schuppan D, Schwab M, Schaeffeler E. Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner. Epigenetics 2016; 11:539-52. [PMID: 27175980 PMCID: PMC4939931 DOI: 10.1080/15592294.2016.1184800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood.
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Affiliation(s)
- Berthold Hocher
- a Department of Basic Medicine , Medical College of Hunan Normal University , Changsha , China.,b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany.,c IFLb, Laboratoriumsmedizin Berlin GmbH , Berlin , Germany
| | - Hannah Haumann
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Jan Rahnenführer
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany
| | | | - Philipp Kalk
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Thiemo Pfab
- d Department of Internal Medicine IV/Nephrology (UKBF) , Charité Campus Benjamin Franklin , Berlin , Germany.,f Diaverum Deutschland , Potsdam , Germany
| | - Oleg Tsuprykov
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany.,e Center for Cardiovascular Research, Charité Campus Mitte , Berlin , Germany
| | - Stefan Winter
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
| | - Ute Hofmann
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
| | - Jian Li
- a Department of Basic Medicine , Medical College of Hunan Normal University , Changsha , China
| | - Gerhard P Püschel
- b Institute of Nutritional Science, University of Potsdam , Nuthetal , Germany
| | - Florian Lang
- i Institute of Physiology, University of Tübingen , Tübingen , Germany
| | - Detlef Schuppan
- j Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany.,k Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , MA , USA
| | - Matthias Schwab
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,l Department of Clinical Pharmacology , University Hospital Tübingen , Tübingen , Germany.,m Department of Pharmacy and Biochemistry , University Tübingen , Tübingen , Germany
| | - Elke Schaeffeler
- g Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology , Stuttgart , Germany.,h University of Tübingen , Tübingen , Germany
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22
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Singh MD, Thomas P, Owens J, Hague W, Fenech M. Potential role of folate in pre-eclampsia. Nutr Rev 2015; 73:694-722. [PMID: 26359215 DOI: 10.1093/nutrit/nuv028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Dietary deficiencies of folate and other B vitamin cofactors involved in one-carbon metabolism, together with genetic polymorphisms in key folate-methionine metabolic pathway enzymes, are associated with increases in circulating plasma homocysteine, reduction in DNA methylation patterns, and genome instability events. All of these biomarkers have also been associated with pre-eclampsia. The aim of this review was to explore the literature and identify potential knowledge gaps in relation to the role of folate at the genomic level in either the etiology or the prevention of pre-eclampsia. A systematic search strategy was designed to identify citations in electronic databases for the following terms: folic acid supplementation AND pre-eclampsia, folic acid supplementation AND genome stability, folate AND genome stability AND pre-eclampsia, folic acid supplementation AND DNA methylation, and folate AND DNA methylation AND pre-eclampsia. Forty-three articles were selected according to predefined selection criteria. The studies included in the present review were not homogeneous, which made pooled analysis of the data very difficult. The present review highlights associations between folate deficiency and certain biomarkers observed in various tissues of women at risk of pre-eclampsia. Further investigation is required to understand the role of folate in either the etiology or the prevention of pre-eclampsia.
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Affiliation(s)
- Mansi Dass Singh
- M.D. Singh, J. Owens, and W. Hague are with the School of Pediatrics and Reproductive Health, Discipline of Obstetrics and Gynecology, Faculty of Health Sciences, Robinson Institute, Australian Research Centre for Health of Women and Babies, The University of Adelaide, Adelaide, South Australia, Australia. M.D. Singh, P. Thomas and M. Fenech are with the Genome Health and Personalized Nutrition Laboratory Commonwealth Scientific and Industrial Research Organization (CSIRO), Food and Nutrition Flagship, Adelaide, South Australia, Australia
| | - Philip Thomas
- M.D. Singh, J. Owens, and W. Hague are with the School of Pediatrics and Reproductive Health, Discipline of Obstetrics and Gynecology, Faculty of Health Sciences, Robinson Institute, Australian Research Centre for Health of Women and Babies, The University of Adelaide, Adelaide, South Australia, Australia. M.D. Singh, P. Thomas and M. Fenech are with the Genome Health and Personalized Nutrition Laboratory Commonwealth Scientific and Industrial Research Organization (CSIRO), Food and Nutrition Flagship, Adelaide, South Australia, Australia
| | - Julie Owens
- M.D. Singh, J. Owens, and W. Hague are with the School of Pediatrics and Reproductive Health, Discipline of Obstetrics and Gynecology, Faculty of Health Sciences, Robinson Institute, Australian Research Centre for Health of Women and Babies, The University of Adelaide, Adelaide, South Australia, Australia. M.D. Singh, P. Thomas and M. Fenech are with the Genome Health and Personalized Nutrition Laboratory Commonwealth Scientific and Industrial Research Organization (CSIRO), Food and Nutrition Flagship, Adelaide, South Australia, Australia
| | - William Hague
- M.D. Singh, J. Owens, and W. Hague are with the School of Pediatrics and Reproductive Health, Discipline of Obstetrics and Gynecology, Faculty of Health Sciences, Robinson Institute, Australian Research Centre for Health of Women and Babies, The University of Adelaide, Adelaide, South Australia, Australia. M.D. Singh, P. Thomas and M. Fenech are with the Genome Health and Personalized Nutrition Laboratory Commonwealth Scientific and Industrial Research Organization (CSIRO), Food and Nutrition Flagship, Adelaide, South Australia, Australia
| | - Michael Fenech
- M.D. Singh, J. Owens, and W. Hague are with the School of Pediatrics and Reproductive Health, Discipline of Obstetrics and Gynecology, Faculty of Health Sciences, Robinson Institute, Australian Research Centre for Health of Women and Babies, The University of Adelaide, Adelaide, South Australia, Australia. M.D. Singh, P. Thomas and M. Fenech are with the Genome Health and Personalized Nutrition Laboratory Commonwealth Scientific and Industrial Research Organization (CSIRO), Food and Nutrition Flagship, Adelaide, South Australia, Australia.
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Bobola MS, Alnoor M, Chen JYS, Kolstoe DD, Silbergeld DL, Rostomily RC, Blank A, Chamberlain MC, Silber JR. O 6-methylguanine-DNA methyltransferase activity is associated with response to alkylating agent therapy and with MGMT promoter methylation in glioblastoma and anaplastic glioma. BBA CLINICAL 2015; 3:1-10. [PMID: 25558448 PMCID: PMC4280839 DOI: 10.1016/j.bbacli.2014.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background CpG methylation in the O6-methylguanine-DNA methyltransferase (MGMT) promoter is associated with better outcome following alkylating agent chemotherapy in glioblastoma (GBM) and anaplastic glioma (AG). To what extent improved response reflects low or absent MGMT activity in glioma tissue has not been unequivocally assessed. This information is central to developing anti-resistance therapies. Methods We examined the relationship of MGMT activity in 91 GBMs and 84 AGs with progression-free survival (PFS) following alkylator therapy and with promoter methylation status determined by methylation-specific PCR (MSP). Results Cox regression analysis revealed that GBMs with high activity had a significantly greater risk for progression in dichotomous (P ≤ 0.001) and continuous (P ≤ 0.003) models, an association observed for different alkylator regimens, including concurrent chemo-radiation with temozolomide. Analysis of MGMT promoter methylation status in 47 of the GBMs revealed that methylated tumors had significantly lower activity (P ≤ 0.005) and longer PFS (P ≤ 0.036) compared to unmethylated tumors, despite overlapping activities. PFS was also significantly greater in methylated vs. unmethylated GBMs with comparable activity (P ≤ 0.005), and among unmethylated tumors with less than median activity (P ≤ 0.026), suggesting that mechanisms in addition to MGMT promote alkylator resistance. Similar associations of MGMT activity with PFS and promoter methylation status were observed for AGs. Conclusions Our results provide strong support for the hypotheses that MGMT activity promotes alkylator resistance and reflects promoter methylation status in malignant gliomas. General significance MGMT activity is an attractive target for anti-resistance therapy regardless of methylation status. Largest study to date of association of MGMT activity with treatment response. MGMT activity is inversely associated with alkylator response in malignant gliomas. Mean activity is significantly lower in MGMT promoter-methylated tumors. Better response in methylated tumors is unlikely due to lower MGMT activity alone. Supports the use of MGMT inhibitors to improve responsiveness to alkylator therapy.
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Affiliation(s)
- Michael S Bobola
- Department of Neurological Surgery, University of Washington, Seattle, WA
| | - Mohammad Alnoor
- Department of Neurological Surgery, University of Washington, Seattle, WA
| | - John Y-S Chen
- Taipei Medical University Hospital, Department of Neurosurgery, 252 Wu-Xin Street, Taipei, Taiwan 110
| | - Douglas D Kolstoe
- Department of Neurological Surgery, University of Washington, Seattle, WA
| | | | - Robert C Rostomily
- Department of Neurological Surgery, University of Washington, Seattle, WA
| | - A Blank
- Department of Neurological Surgery, University of Washington, Seattle, WA
| | - Marc C Chamberlain
- Department of Neurological Surgery, University of Washington, Seattle, WA ; Department of Neurology, University of Washington, Seattle, WA
| | - John R Silber
- Department of Neurological Surgery, University of Washington, Seattle, WA
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24
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Delgado-Cruzata L, Zhang W, McDonald JA, Tsai WY, Valdovinos C, Falci L, Wang Q, Crew KD, Santella RM, Hershman DL, Greenlee H. Dietary modifications, weight loss, and changes in metabolic markers affect global DNA methylation in Hispanic, African American, and Afro-Caribbean breast cancer survivors. J Nutr 2015; 145:783-90. [PMID: 25833781 PMCID: PMC4381766 DOI: 10.3945/jn.114.202853] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/30/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Lower levels of global DNA methylation in tissue and blood have been associated with increased cancer risk. Conversely, cross-sectional analyses of healthier lifestyle patterns have been associated with higher levels of global DNA methylation. OBJECTIVE In this trial, we explored the associations between changes in lifestyle modifications (diet, weight loss), metabolic markers, and global epigenetic biomarkers in white blood cells. METHODS Study participants were Hispanic, African American, and Afro-Caribbean overweight and sedentary female breast cancer survivors (n = 24) who participated in a larger randomized, crossover, pilot study of a 6-mo weight loss intervention and who had available blood specimens. Anthropometric measures, a food-frequency questionnaire, and peripheral blood were collected at baseline, 6 mo, and 12 mo. Plasma samples were analyzed for metabolic markers (insulin, glucose). We measured DNA methylation of long interspersed nucleotide element 1 (LINE-1) and satellite 2 by pyrosequencing and MethyLight, respectively, and global DNA methylation by the luminometric methylation assay (LUMA). RESULTS DNA methylation of LINE-1 was statistically significantly elevated at 6 mo [75.5% vs. 78.5% (P < 0.0001)] and 12 mo [75.5% vs. 77.7% (P < 0.0001)], compared to baseline. Over a 12-mo period, changes in percentage body fat and plasma glucose concentrations were positively associated with LINE-1 DNA methylation (β = 0.19, P = 0.001) and LUMA DNA methylation levels (β = 0.24, P = 0.02), respectively. Similarly, 12-mo changes in dietary measures such as vegetable (β = 0.009, P = 0.048), protein (β = 0.04, P = 0.001), and total caloric (β = 0.05, P = 0.01) intake were positively associated with changes in LUMA DNA methylation, as was intake of fruit positively associated with changes in LINE-1 DNA methylation (β = 0.004, P = 0.02). CONCLUSIONS Our hypothesis-generating results suggest that lifestyle modifications may be associated with changes in global DNA methylation detectable at 6 and 12 mo. These biomarkers may be useful intermediate biomarkers to use in future intervention trials. This trial was registered at clinicaltrials.gov as NCT00811824.
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Affiliation(s)
- Lissette Delgado-Cruzata
- Departments of Environmental Health Sciences,,Department of Sciences, John Jay College of Criminal Justice, City University of New York, New York, NY
| | | | | | | | | | - Laura Falci
- Epidemiology, Mailman School of Public Health
| | - Qiao Wang
- Departments of Environmental Health Sciences
| | - Katherine D Crew
- Epidemiology, Mailman School of Public Health,,Herbert Irving Comprehensive Cancer Center, and,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY; and
| | - Regina M Santella
- Departments of Environmental Health Sciences,,Herbert Irving Comprehensive Cancer Center, and
| | - Dawn L Hershman
- Epidemiology, Mailman School of Public Health,,Herbert Irving Comprehensive Cancer Center, and,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY; and
| | - Heather Greenlee
- Epidemiology, Mailman School of Public Health, Herbert Irving Comprehensive Cancer Center, and
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25
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Zhang W, Spector TD, Deloukas P, Bell JT, Engelhardt BE. Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. Genome Biol 2015; 16:14. [PMID: 25616342 PMCID: PMC4389802 DOI: 10.1186/s13059-015-0581-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific methylation levels is critical to enable genome-wide analyses, but current approaches tackle average methylation within a locus and are often limited to specific genomic regions. RESULTS We characterize genome-wide DNA methylation patterns, and show that correlation among CpG sites decays rapidly, making predictions solely based on neighboring sites challenging. We built a random forest classifier to predict methylation levels at CpG site resolution using features including neighboring CpG site methylation levels and genomic distance, co-localization with coding regions, CpG islands (CGIs), and regulatory elements from the ENCODE project. Our approach achieves 92% prediction accuracy of genome-wide methylation levels at single-CpG-site precision. The accuracy increases to 98% when restricted to CpG sites within CGIs and is robust across platform and cell-type heterogeneity. Our classifier outperforms other types of classifiers and identifies features that contribute to prediction accuracy: neighboring CpG site methylation, CGIs, co-localized DNase I hypersensitive sites, transcription factor binding sites, and histone modifications were found to be most predictive of methylation levels. CONCLUSIONS Our observations of DNA methylation patterns led us to develop a classifier to predict DNA methylation levels at CpG site resolution with high accuracy. Furthermore, our method identified genomic features that interact with DNA methylation, suggesting mechanisms involved in DNA methylation modification and regulation, and linking diverse epigenetic processes.
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Affiliation(s)
- Weiwei Zhang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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26
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Godschalk RWL, Verhofstad N, Verheijen M, Yauk CL, Linschooten JO, van Steeg H, van Oostrom CT, van Benthem J, van Schooten FJ. Effects of benzo[a]pyrene on mouse germ cells: heritable DNA mutation, testicular cell hypomethylation and their interaction with nucleotide excision repair. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00114a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Benzo[a]pyrene induces heritable mutations in male germ cells.
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Affiliation(s)
- Roger W. L. Godschalk
- Dept. Toxicology
- School for Nutrition
- toxicology and metabolism (NUTRIM)
- Maastricht University
- 6200 MD Maastricht
| | - Nicole Verhofstad
- Dept. Toxicology
- School for Nutrition
- toxicology and metabolism (NUTRIM)
- Maastricht University
- 6200 MD Maastricht
| | - Marcha Verheijen
- Dept. Toxicology
- School for Nutrition
- toxicology and metabolism (NUTRIM)
- Maastricht University
- 6200 MD Maastricht
| | - Carole Lyn Yauk
- Environmental Health Science and Research Bureau
- Health Canada
- Ottawa
- Canada
| | - Joost O. Linschooten
- Dept. Toxicology
- School for Nutrition
- toxicology and metabolism (NUTRIM)
- Maastricht University
- 6200 MD Maastricht
| | - Harry van Steeg
- Laboratory for Health Protection Research
- National Institute for Public Health and the Environment (RIVM)
- 3720 BA Bilthoven
- The Netherlands
| | - Conny T. van Oostrom
- Laboratory for Health Protection Research
- National Institute for Public Health and the Environment (RIVM)
- 3720 BA Bilthoven
- The Netherlands
| | - Jan van Benthem
- Laboratory for Health Protection Research
- National Institute for Public Health and the Environment (RIVM)
- 3720 BA Bilthoven
- The Netherlands
| | - Frederik J. van Schooten
- Dept. Toxicology
- School for Nutrition
- toxicology and metabolism (NUTRIM)
- Maastricht University
- 6200 MD Maastricht
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27
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Kolybaba A, Classen AK. Sensing cellular states--signaling to chromatin pathways targeting Polycomb and Trithorax group function. Cell Tissue Res 2014; 356:477-93. [PMID: 24728925 DOI: 10.1007/s00441-014-1824-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/22/2014] [Indexed: 02/06/2023]
Abstract
Cells respond to extra- and intra-cellular signals by dynamically changing their gene expression patterns. After termination of the original signal, new expression patterns are maintained by epigenetic DNA and histone modifications. This represents a powerful mechanism that enables long-term phenotypic adaptation to transient signals. Adaptation of epigenetic landscapes is important for mediating cellular differentiation during development and allows adjustment to altered environmental conditions throughout life. Work over the last decade has begun to elucidate the way that extra- and intra-cellular signals lead to changes in gene expression patterns by directly modulating the function of chromatin-associated proteins. Here, we review key signaling-to-chromatin pathways that are specifically thought to target Polycomb and Trithorax group complexes, a classic example of epigenetically acting gene silencers and activators important in development, stem cell differentiation and cancer. We discuss the influence that signals triggered by kinase cascades, metabolic fluctuations and cell-cycle dynamics have on the function of these protein complexes. Further investigation into these pathways will be important for understanding the mechanisms that maintain epigenetic stability and those that promote epigenetic plasticity.
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Affiliation(s)
- Addie Kolybaba
- Ludwig Maximilians University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany
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28
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Molinari C, Casadio V, Foca F, Zingaretti C, Giannini M, Avanzolini A, Lucci E, Saragoni L, Passardi A, Amadori D, Calistri D, Zoli W. Gene methylation in rectal cancer: predictive marker of response to chemoradiotherapy? J Cell Physiol 2014; 228:2343-9. [PMID: 23702823 DOI: 10.1002/jcp.24405] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/09/2013] [Indexed: 01/11/2023]
Abstract
Although numerous studies have focused on the link between CpG island methylator phenotypes and the development of colorectal cancer, few studies have dealt specifically with methylation profiling in rectal cancer and its role in predicting response to neoadjuvant chemoradiotherapy (NCRT). We characterized methylation profiles in normal and neoplastic tissue samples from patients with rectal cancer and assessed the role of this molecular profile in predicting chemoradioactivity. We evaluated 74 pretreatment tumor samples and 16 apparently normal tissue biopsies from rectal cancer patients submitted to NCRT. The methylation profile of 24 different tumor suppressor genes was analyzed from FFPE samples by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Methylation status was studied in relation to tissue type and clinical pathological parameters, in particular, pathological response evaluated by tumor regression grade (TRG). ESR1, CDH13, RARB, IGSF4, and APC genes showed high methylation levels in tumor samples (range 18.92-49.77) with respect to normal tissue. Methylation levels of the remaining genes were low and similar in both normal (range 1.91-14.56) and tumor tissue (range 1.84-11). Analysis of the association between methylation and response to therapy in tumor samples showed that only TIMP3 methylation status differed significantly within the four TRG classes (ANOVA, P < 0.05). Results from the present explorative study suggest that quantitative epigenetic classification of rectal cancer by MS-MLPA clearly distinguishes tumor tissue from apparently normal mucosa. Conversely, with the exception of TIMP3 gene, the methylation of selected genes does not seem to correlate with response to NCRT.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), Meldola, Italy
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Abstract
DNA damage response genes play vital roles in the maintenance of a healthy genome. Defects in cell cycle checkpoint and DNA repair genes, especially mutation or aberrant downregulation, are associated with a wide spectrum of human disease, including a predisposition to the development of neurodegenerative conditions and cancer. On the other hand, upregulation of DNA damage response and repair genes can also cause cancer, as well as increase resistance of cancer cells to DNA damaging therapy. In recent years, it has become evident that many of the genes involved in DNA damage repair have additional roles in tumorigenesis, most prominently by acting as transcriptional (co-)factors. Although defects in these genes are causally connected to tumor initiation, their role in tumor progression is more controversial and it seems to depend on tumor type. In some tumors like melanoma, cell cycle checkpoint/DNA repair gene upregulation is associated with tumor metastasis, whereas in a number of other cancers the opposite has been observed. Several genes that participate in the DNA damage response, such as RAD9, PARP1, BRCA1, ATM and TP53 have been associated with metastasis by a number of in vitro biochemical and cellular assays, by examining human tumor specimens by immunohistochemistry or by DNA genome-wide gene expression profiling. Many of these genes act as transcriptional effectors to regulate other genes implicated in the pathogenesis of cancer. Furthermore, they are aberrantly expressed in numerous human tumors and are causally related to tumorigenesis. However, whether the DNA damage repair function of these genes is required to promote metastasis or another activity is responsible (e.g., transcription control) has not been determined. Importantly, despite some compelling in vitro evidence, investigations are still needed to demonstrate the role of cell cycle checkpoint and DNA repair genes in regulating metastatic phenotypes in vivo.
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Affiliation(s)
- Constantinos G. Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032
| | - Howard B. Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032
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30
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Coppedè F, Migheli F, Lopomo A, Failli A, Legitimo A, Consolini R, Fontanini G, Sensi E, Servadio A, Seccia M, Zocco G, Chiarugi M, Spisni R, Migliore L. Gene promoter methylation in colorectal cancer and healthy adjacent mucosa specimens: correlation with physiological and pathological characteristics, and with biomarkers of one-carbon metabolism. Epigenetics 2014; 9:621-33. [PMID: 24500500 DOI: 10.4161/epi.27956] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We evaluated the promoter methylation levels of the APC, MGMT, hMLH1, RASSF1A and CDKN2A genes in 107 colorectal cancer (CRC) samples and 80 healthy adjacent tissues. We searched for correlation with both physical and pathological features, polymorphisms of folate metabolism pathway genes (MTHFR, MTRR, MTR, RFC1, TYMS, and DNMT3B), and data on circulating folate, vitamin B12 and homocysteine, which were available in a subgroup of the CRC patients. An increased number of methylated samples were found in CRC respect to adjacent healthy tissues, with the exception of APC, which was also frequently methylated in healthy colonic mucosa. Statistically significant associations were found between RASSF1A promoter methylation and tumor stage, and between hMLH1 promoter methylation and tumor location. Increasing age positively correlated with both hMLH1 and MGMT methylation levels in CRC tissues, and with APC methylation levels in the adjacent healthy mucosa. Concerning gender, females showed higher hMLH1 promoter methylation levels with respect to males. In CRC samples, the MTR 2756AG genotype correlated with higher methylation levels of RASSF1A, and the TYMS 1494 6bp ins/del polymorphism correlated with the methylation levels of both APC and hMLH1. In adjacent healthy tissues, MTR 2756AG and TYMS 1494 6bp del/del genotypes correlated with APC and MGMT promoter methylation, respectively. Low folate levels were associated with hMLH1 hypermethylation. Present results support the hypothesis that DNA methylation in CRC depends from both physiological and environmental factors, with one-carbon metabolism largely involved in this process.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery; Division of Medical Genetics; University of Pisa; Pisa, Italy; Istituto Toscano Tumori (ITT); Florence, Italy; Research Center Nutraceuticals and Food for Health-Nutrafood; University of Pisa; Pisa, Italy
| | - Francesca Migheli
- Department of Translational Research and New Technologies in Medicine and Surgery; Division of Medical Genetics; University of Pisa; Pisa, Italy; Istituto Toscano Tumori (ITT); Florence, Italy
| | - Angela Lopomo
- Department of Translational Research and New Technologies in Medicine and Surgery; Division of Medical Genetics; University of Pisa; Pisa, Italy; Doctoral School in Genetics, Oncology, and Clinical Medicine; University of Siena; Siena, Italy
| | - Alessandra Failli
- Istituto Toscano Tumori (ITT); Florence, Italy; Department of Clinical and Experimental Medicine; University of Pisa; Pisa, Italy
| | - Annalisa Legitimo
- Department of Clinical and Experimental Medicine; University of Pisa; Pisa, Italy
| | - Rita Consolini
- Department of Clinical and Experimental Medicine; University of Pisa; Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Elisa Sensi
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Adele Servadio
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Massimo Seccia
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Giuseppe Zocco
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Massimo Chiarugi
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Roberto Spisni
- Department of Surgery, Medical, Molecular, and Critical Area Pathology; University of Pisa; Pisa, Italy
| | - Lucia Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery; Division of Medical Genetics; University of Pisa; Pisa, Italy; Istituto Toscano Tumori (ITT); Florence, Italy; Research Center Nutraceuticals and Food for Health-Nutrafood; University of Pisa; Pisa, Italy
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Coppedè F, Lopomo A, Spisni R, Migliore L. Genetic and epigenetic biomarkers for diagnosis, prognosis and treatment of colorectal cancer. World J Gastroenterol 2014; 20:943-56. [PMID: 24574767 PMCID: PMC3921546 DOI: 10.3748/wjg.v20.i4.943] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/21/2013] [Accepted: 12/05/2013] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancer worldwide and results from the accumulation of mutations and epimutations in colonic mucosa cells ultimately leading to cell proliferation and metastasis. Unfortunately, CRC prognosis is still poor and the search of novel diagnostic and prognostic biomarkers is highly desired to prevent CRC-related deaths. The present article aims to summarize the most recent findings concerning the use of either genetic or epigenetic (mainly related to DNA methylation) biomarkers for CRC diagnosis, prognosis, and response to treatment. Recent large-scale DNA methylation studies suggest that CRC can be divided into several subtypes according to the frequency of DNA methylation and those of mutations in key CRC genes, and that this is reflected by different prognostic outcomes. Increasing evidence suggests that the analysis of DNA methylation in blood or fecal specimens could represent a valuable non-invasive diagnostic tool for CRC. Moreover, a broad spectrum of studies indicates that the inter-individual response to chemotherapeutic treatments depends on both epigenetic modifications and genetic mutations occurring in colorectal cancer cells, thereby opening the way for a personalized medicine. Overall, combining genetic and epigenetic data might represent the most promising tool for a proper diagnostic, prognostic and therapeutic approach.
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Stefanoli M, La Rosa S, Sahnane N, Romualdi C, Pastorino R, Marando A, Capella C, Sessa F, Furlan D. Prognostic relevance of aberrant DNA methylation in g1 and g2 pancreatic neuroendocrine tumors. Neuroendocrinology 2014; 100:26-34. [PMID: 25011998 DOI: 10.1159/000365449] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND/AIMS The occurrence and clinical relevance of DNA hypermethylation and global hypomethylation in pancreatic neuroendocrine tumours (PanNETs) are still unknown. We evaluated the frequency of both epigenetic alterations in PanNETs to assess the relationship between methylation profiles and chromosomal instability, tumour phenotypes and prognosis. METHODS In a well-characterized series of 56 sporadic G1 and G2 PanNETs, methylation-sensitive multiple ligation-dependent probe amplification was performed to assess hypermethylayion of 33 genes and copy number alterations (CNAs) of 53 chromosomal regions. Long interspersed nucleotide element-1 (LINE-1) hypomethylation was quantified by pyrosequencing. RESULTS Unsupervised hierarchical clustering allowed to identify a subset of 22 PanNETs (39%) exhibiting high frequency of gene-specific methylation and low CNA percentages. This tumour cluster was significantly associated with stage IV (p = 0.04) and with poor prognosis in univariable analysis (p = 0.004). LINE-1 methylation levels in PanNETs were significantly lower than in normal samples (p < 0.01) and were approximately normally distributed. 12 tumours (21%) were highly hypomethylated, showing variable levels of CNA. Interestingly, only 5 PanNETs (9%) were observed to show simultaneously LINE-1 hypomethylation and high frequency of gene-specific methylation. LINE-1 hypomethylation was strongly correlated with advanced stage (p = 0.002) and with poor prognosis (p < 0.0001). In the multivariable analysis, low LINE-1 methylation status and methylation clusters were the only independent significant predictors of outcome (p = 0.034 and p = 0.029, respectively). CONCLUSION The combination of global DNA hypomethylation and gene hypermethylation analyses may be useful to define distinct subsets of PanNETs. Both alterations are common in PanNETs and could be directly correlated with tumour progression.
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Affiliation(s)
- Michele Stefanoli
- Section of Anatomic Pathology, Department of Surgical and Morphological Sciences, University of Insubria and Ospedale di Circolo, Varese, Italy
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Failli A, Legitimo A, Migheli F, Coppedè F, Mathers JC, Spisni R, Miccoli P, Migliore L, Consolini R. Efficacy and feasibility of the epithelial cell adhesion molecule (EpCAM) immunomagnetic cell sorter for studies of DNA methylation in colorectal cancer. Int J Mol Sci 2013; 15:44-57. [PMID: 24362576 PMCID: PMC3907797 DOI: 10.3390/ijms15010044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/10/2013] [Accepted: 12/13/2013] [Indexed: 12/28/2022] Open
Abstract
The aim of this work was to assess the impact on measurements of methylation of a panel of four cancer gene promoters of purifying tumor cells from colorectal tissue samples using the epithelial cell adhesion molecule (EpCAM)-immunomagnetic cell enrichment approach. We observed that, on average, methylation levels were higher in enriched cell fractions than in the whole tissue, but the difference was significant only for one out of four studied genes. In addition, there were strong correlations between methylation values for individual samples of whole tissue and the corresponding enriched cell fractions. Therefore, assays on whole tissue are likely to provide reliable estimates of tumor-specific methylation of cancer genes. However, tumor cell tissue separation using immunomagnetic beads could, in some cases, give a more accurate value of gene promoter methylation than the analysis of the whole cancer tissue, although relatively expensive and time-consuming. The efficacy and feasibility of the immunomagnetic cell sorting for methylation studies are discussed.
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Affiliation(s)
- Alessandra Failli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy; E-Mails: (A.F.); (A.L.)
| | - Annalisa Legitimo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy; E-Mails: (A.F.); (A.L.)
| | - Francesca Migheli
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Pisa 56126, Italy; E-Mails: (F.M.); (F.C.); (L.M.)
| | - Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Pisa 56126, Italy; E-Mails: (F.M.); (F.C.); (L.M.)
- Department of Laboratory Medicine, Pisa University Hospital (AOUP), Pisa 56126, Italy
| | - John C. Mathers
- Human Nutrition Research Centre, Institute for Ageing & Health, Biomedical Research Building, Campus for Ageing & Vitality, Newcastle University, Newcastle upon Tyne NE4 5PL, UK; E-Mail:
| | - Roberto Spisni
- Department of Surgery, Medical, Molecular, and Critical Area Pathology, University of Pisa, Pisa 56124, Italy; E-Mails: (R.S.); (P.M.)
| | - Paolo Miccoli
- Department of Surgery, Medical, Molecular, and Critical Area Pathology, University of Pisa, Pisa 56124, Italy; E-Mails: (R.S.); (P.M.)
| | - Lucia Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Pisa 56126, Italy; E-Mails: (F.M.); (F.C.); (L.M.)
- Department of Laboratory Medicine, Pisa University Hospital (AOUP), Pisa 56126, Italy
| | - Rita Consolini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy; E-Mails: (A.F.); (A.L.)
- Author to whom correspondence should be addressed; E-mail: ; Tel.: +39-50-992-222; Fax: +39-50-993-044
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Deming DA, Ninan J, Bailey HH, Kolesar JM, Eickhoff J, Reid JM, Ames MM, McGovern RM, Alberti D, Marnocha R, Espinoza-Delgado I, Wright J, Wilding G, Schelman WR. A Phase I study of intermittently dosed vorinostat in combination with bortezomib in patients with advanced solid tumors. Invest New Drugs 2013; 32:323-9. [PMID: 24114123 DOI: 10.1007/s10637-013-0035-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/11/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Accumulating evidence shows evidence of efficacy with the combination of vorinostat and bortezomib in solid tumors. We previously examined a once-daily continuous dosing schedule of vorinostat in combination with bortezomib which was well tolerated in cycles 1 and 2; however, there was concern regarding the tolerability through multiple cycles. This study was conducted to evaluate an intermittent dosing schedule of vorinostat with bortezomib. METHODS Vorinostat was initially administered orally twice daily on days 1-14 with bortezomib IV on days 1, 4, 8, and 11 of a 21 day cycle. Two DLTs (elevated ALT and fatigue) were observed at dose level 1, thus the protocol was amended to administer vorinostat intermittently twice daily on days 1-4 and 8-11. RESULTS 29 patients were enrolled; 13 men and 16 women. Common cancer types included sarcoma, pancreatic, colorectal, GIST, and breast. The most common Grade 3-4 toxicities at any dose level included thrombocytopenia, fatigue, increased ALT, elevated INR, and diarrhea. DLTs in the intermittent dosing scheduled included thrombocytopenia and fatigue. The Cmax and AUC for the intermittent dosing regimen were similar to those observed in the daily dosing. In this heavily pretreated population, stable disease was observed in patients with sarcoma, colorectal adenocarcinoma and GIST. CONCLUSIONS The MTD was established at vorinostat 300 mg BID on days 1-4 and 8-11 and bortezomib 1.3 mg/m(2) IV on days 1, 4, 8, and 11 of a 21 day cycle. Tolerability was not improved with the intermittent dosing schedule of vorinostat when compared to continuous dosing.
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Affiliation(s)
- Dustin A Deming
- University of Wisconsin Carbone Cancer Center, 600 Highland Avenue, K4/530 CSC, Madison, WI, 53792, USA
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Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Genome Res 2013; 23:1109-17. [PMID: 23737375 PMCID: PMC3698504 DOI: 10.1101/gr.145706.112] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Microsatellite instability (MSI) is a critical mechanism that drives genetic aberrations in cancer. To identify the entire MS mutation, we performed the first comprehensive genome- and transcriptome-wide analyses of mutations associated with MSI in Korean gastric cancer cell lines and primary tissues. We identified 18,377 MS mutations of five or more repeat nucleotides in coding sequences and untranslated regions of genes, and discovered 139 individual genes whose expression was down-regulated in association with UTR MS mutation. In addition, we found that 90.5% of MS mutations with deletions in gene regions occurred in UTRs. This analysis emphasizes the genetic diversity of MSI-H gastric tumors and provides clues to the mechanistic basis of instability in microsatellite unstable gastric cancers.
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Abstract
Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the greatest clonal advantage. These traits can be acquired and stably maintained by either genetic or epigenetic means. Here, we explore the ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation. Disruption of epigenomic control is pervasive in malignancy and can be classified as an enabling characteristic of cancer cells, akin to genome instability and mutation.
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Affiliation(s)
- Hui Shen
- USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA
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Chen W, Xiang J, Chen DF, Ni BB, Chen H, Fan XJ, Wang PN, Song SX, Fang LK, Xiao HY, Wang L, Wang JP. Screening for differentially methylated genes among human colorectal cancer tissues and normal mucosa by microarray chip. Mol Biol Rep 2013; 40:3457-64. [PMID: 23471507 DOI: 10.1007/s11033-012-2338-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 10/01/2012] [Indexed: 01/04/2023]
Abstract
UNLABELLED High density DNA methylation microarrays were used to study the differences of gene methylation level in six pairs of colorectal cancer (CRC) and adjacent normal mucosa. We analyzed the profile of methylated genes by NimbleGen Microarray and the biologic functions by NIH-NAVID. In addition, preliminary validation studies were done in six pairs of samples by MSP (methylation-specific PCR). A total of 4,644 genes had a difference in methylation levels. Among them 2,296 were hypermethylated (log2ratio > 1), 2,348 genes were hypomethylated (log2ratio < -1), in which 293 hypermethylated and 313 hypomethylated genes were unmapped according to the NIH-NAVID. All these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most of the hypermethylated genes (232 genes), followed by chromosome 19 (149 genes), chromosome 11 (144 genes), chromosome 2 (141 genes), chromosomes 3 (127 genes). Through the analysis of the statistics, There were 2 hypermethylated/3 hypomethylated genes involved in six pairs of samples simultaneously, followed by 10/14 in five samples, 34/37 in four samples, 101/113 in three samples, 341/377 in two samples, 1,808/1,804 in one sample. According to gene ontology analysis, some physiological processes play important roles in the cell division and the development of tumor, such as apoptosis, DNA repair, immune, cell cycle, cell cycle checkpoint, cell adhesion and invasion etc. Through Preliminary validation, there were two genes (St3gal6, Opcml) in thirty top-ranking genes shown hypermethylated in six pairs of CRC and adjacent normal mucosa. CONCLUSIONS High density DNA methylation microarrays is an effective method for screening aberrantly methylated genes in CRC. The methylated genes should be further studied for diagnostic or prognostic markers for CRC.
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Affiliation(s)
- Wei Chen
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancunerheng Rd, Guangzhou, Guangdong 510655, People's Republic of China
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siRNA screening identifies differences in the Fanconi anemia pathway in BALB/c-Trp53+/- with susceptibility versus C57BL/6-Trp53+/- mice with resistance to mammary tumors. Oncogene 2013; 32:5458-70. [PMID: 23435420 PMCID: PMC3898496 DOI: 10.1038/onc.2013.38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 12/18/2012] [Accepted: 12/27/2012] [Indexed: 12/24/2022]
Abstract
BALB/c mice heterozygous for Trp53 develop a high proportion of spontaneous mammary tumors, a phenotype distinct from other mouse strains. BALB/c-Trp53+/- female mice, thus, resemble the hereditary Li-Fraumeni syndrome (LFS) characterized by early-onset of breast cancer, even though LFS involves TP53 mutations, which may involve not only loss- but also gain-of-function. Previous analysis of tumors in BALB/c-Trp53+/- females showed frequent loss of heterozygosity involving the wild-type allele of Trp53 and displayed characteristics indicative of mitotic recombination. Critical involvement of DNA double-strand break (DSB) repair dysfunction, particularly of homologous recombination (HR), was also noticed in the etiology of human breast cancer. To better define functional alterations in BALB/c-Trp53+/- mice, we applied a fluorescence-based DSB repair assay on mouse embryonic fibroblasts (MEFs) from BALB/c-Trp53+/- versus C57BL/6J-Trp53+/- mice. This approach revealed deregulation of HR but not non-homologous end-joining (NHEJ) in BALB/c-Trp53+/-, which was further confirmed for mammary epithelial cells. Screening of a small interfering RNA-library targeting DSB repair, recombination, replication and signaling genes, identified 25 genes causing differences between homologous DSB repair in the two strains upon silencing. Interactome analysis of the hits revealed clustering of replication-related and fanconi anemia (FA)/breast cancer susceptibility (BRCA) genes. Further dissection of the functional change in BALB/c-Trp53+/- by immunofluorescence microscopy of nuclear 53BP1, Replication protein A (RPA) and Rad51 foci uncovered differences in crosslink and replication-associated repair. Chromosome breakage, G2 arrest and biochemical analyses indicated a FA pathway defect downstream of FancD2 associated with reduced levels of BRCA2. Consistent with polygenic models for BRCA, mammary carcinogenesis in BALB/c-Trp53+/- mice may, therefore, be promoted by a BRCA modifier allele in the FA pathway in the context of partial p53 loss-of-function.
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Arzumanyan A, Reis HMGPV, Feitelson MA. Pathogenic mechanisms in HBV- and HCV-associated hepatocellular carcinoma. Nat Rev Cancer 2013; 13:123-35. [PMID: 23344543 DOI: 10.1038/nrc3449] [Citation(s) in RCA: 599] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly lethal cancer, with increasing worldwide incidence, that is mainly associated with chronic hepatitis B virus (HBV) and/or hepatitis C virus (HCV) infections. There are few effective treatments partly because the cell- and molecular-based mechanisms that contribute to the pathogenesis of this tumour type are poorly understood. This Review outlines pathogenic mechanisms that seem to be common to both viruses and which suggest innovative approaches to the prevention and treatment of HCC.
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Affiliation(s)
- Alla Arzumanyan
- Department of Biology and Sbarro Health Research Organization, College of Science and Technology, Temple University, 1900 N. 12th Street, Philadelphia, Pennsylvania 19122, USA
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McCarrey JR. The epigenome as a target for heritable environmental disruptions of cellular function. Mol Cell Endocrinol 2012; 354:9-15. [PMID: 21970811 DOI: 10.1016/j.mce.2011.09.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/07/2011] [Accepted: 09/08/2011] [Indexed: 02/07/2023]
Abstract
The environment is a well-established source of damaging or disrupting influences on cellular function. In the past, studies of the mechanisms by which such disruptions occur have focused largely on either direct toxic effects on cellular function at the protein or cell signaling level, or mutagenic effects that impact the genome. In recent years there has been a growing appreciation for the potential for environmental influences to disrupt the epigenome and mechanisms of epigenetic regulation within the cell. Indeed, because of the inherent lability of the epigenome, this represents a primary target for environmentally induced disruption. This review summarizes the manner in which the epigenome normally regulates cellular function, the effects of disruptions on this function, and the manner in which such disruptions may or may not be corrected within the organism and/or transmitted to subsequent generations.
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Affiliation(s)
- John R McCarrey
- Department of Biology, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA.
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Brun P, Brun P, Vono M, Venier P, Tarricone E, Deligianni V, Martines E, Zuin M, Spagnolo S, Cavazzana R, Cardin R, Castagliuolo I, Valerio ALG, Leonardi A. Disinfection of ocular cells and tissues by atmospheric-pressure cold plasma. PLoS One 2012; 7:e33245. [PMID: 22432007 PMCID: PMC3303808 DOI: 10.1371/journal.pone.0033245] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 02/13/2012] [Indexed: 01/05/2023] Open
Abstract
Background Low temperature plasmas have been proposed in medicine as agents for tissue disinfection and have received increasing attention due to the frequency of bacterial resistance to antibiotics. This study explored whether atmospheric-pressure cold plasma (APCP) generated by a new portable device that ionizes a flow of helium gas can inactivate ocular pathogens without causing significant tissue damage. Methodology/Principal Findings We tested the APCP effects on cultured Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Candida albicans, Aspergillus fumigatus and Herpes simplex virus-1, ocular cells (conjunctival fibroblasts and keratocytes) and ex-vivo corneas. Exposure to APCP for 0.5 to 5 minutes significantly reduced microbial viability (colony-forming units) but not human cell viability (MTT assay, FACS and Tunel analysis) or the number of HSV-1 plaque-forming units. Increased levels of intracellular reactive oxygen species (ROS) in exposed microorganisms and cells were found using a FACS-activated 2′,7′-dichlorofluorescein diacetate probe. Immunoassays demonstrated no induction of thymine dimers in cell cultures and corneal tissues. A transient increased expression of 8-OHdG, genes and proteins related to oxidative stress (OGG1, GPX, NFE2L2), was determined in ocular cells and corneas by HPLC, qRT-PCR and Western blot analysis. Conclusions A short application of APCP appears to be an efficient and rapid ocular disinfectant for bacteria and fungi without significant damage on ocular cells and tissues, although the treatment of conjunctival fibroblasts and keratocytes caused a time-restricted generation of intracellular ROS and oxidative stress-related responses.
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Affiliation(s)
- Paola Brun
- Histology Unit, Department of Biomedical Sciences, University of Padua, Padua, Italy.
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Tournier B, Chapusot C, Courcet E, Martin L, Lepage C, Faivre J, Piard F. Why do results conflict regarding the prognostic value of the methylation status in colon cancers? The role of the preservation method. BMC Cancer 2012; 12:12. [PMID: 22243995 PMCID: PMC3293017 DOI: 10.1186/1471-2407-12-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 01/13/2012] [Indexed: 11/12/2022] Open
Abstract
Background In colorectal carcinoma, extensive gene promoter hypermethylation is called the CpG island methylator phenotype (CIMP). Explaining why studies on CIMP and survival yield conflicting results is essential. Most experiments to measure DNA methylation rely on the sodium bisulfite conversion of unmethylated cytosines into uracils. No study has evaluated the performance of bisulfite conversion and methylation levels from matched cryo-preserved and Formalin-Fixed Paraffin Embedded (FFPE) samples using pyrosequencing. Methods Couples of matched cryo-preserved and FFPE samples from 40 colon adenocarcinomas were analyzed. Rates of bisulfite conversion and levels of methylation of LINE-1, MLH1 and MGMT markers were measured. Results For the reproducibility of bisulfite conversion, the mean of bisulfite-to-bisulfite standard deviation (SD) was 1.3%. The mean of run-to-run SD of PCR/pyrosequencing was 0.9%. Of the 40 DNA couples, only 67.5%, 55.0%, and 57.5% of FFPE DNA were interpretable for LINE-1, MLH1, and MGMT markers, respectively, after the first analysis. On frozen samples the proportion of well converted samples was 95.0%, 97.4% and 87.2% respectively. For DNA showing a total bisulfite conversion, 8 couples (27.6%) for LINE-1, 4 couples (15.4%) for MLH1 and 8 couples (25.8%) for MGMT displayed significant differences in methylation levels. Conclusions Frozen samples gave reproducible results for bisulfite conversion and reliable methylation levels. FFPE samples gave unsatisfactory and non reproducible bisulfite conversions leading to random results for methylation levels. The use of FFPE collections to assess DNA methylation by bisulfite methods must not be recommended. This can partly explain the conflicting results on the prognosis of CIMP colon cancers.
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Affiliation(s)
- Benjamin Tournier
- Institut National de la Sante et de la Recherche Médicale, Université de Bourgogne, Dijon, France.
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González-Barrios R, Soto-Reyes E, Herrera LA. Assembling pieces of the centromere epigenetics puzzle. Epigenetics 2012; 7:3-13. [PMID: 22207360 PMCID: PMC3329500 DOI: 10.4161/epi.7.1.18504] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The centromere is a key region for cell division where the kinetochore assembles, recognizes and attaches to microtubules so that each sister chromatid can segregate to each daughter cell. The centromeric chromatin is a unique rigid chromatin state promoted by the presence of the histone H3 variant CENP-A, in which epigenetic histone modifications of both heterochromatin or euchromatin states and associated protein elements are present. Although DNA sequence is not regarded as important for the establishment of centromere chromatin, it has become clear that this structure is formed as a result of a highly regulated epigenetic event that leads to the recruitment and stability of kinetochore proteins. We describe an integrative model for epigenetic processes that conform regional chromatin interactions indispensable for the recruitment and stability of kinetochore proteins. If alterations of these chromatin regions occur, chromosomal instability is promoted, although segregation may still take place.
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Affiliation(s)
- Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F., México
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Shigetomi H, Oonogi A, Tsunemi T, Tanase Y, Yamada Y, Kajihara H, Yoshizawa Y, Furukawa N, Haruta S, Yoshida S, Sado T, Oi H, Kobayashi H. The role of components of the chromatin modification machinery in carcinogenesis of clear cell carcinoma of the ovary (Review). Oncol Lett 2011; 2:591-597. [PMID: 22848233 DOI: 10.3892/ol.2011.316] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 04/27/2011] [Indexed: 12/19/2022] Open
Abstract
Recent data have provided information regarding the profiles of clear cell carcinoma of the ovary (CCC) with adenine-thymine rich interactive domain 1A (ARID1A) mutations. The purpose of this review was to summarize current knowledge regarding the molecular mechanisms involved in CCC tumorigenesis and to describe the central role played by the aberrant chromatin remodeling. The present article reviews the English-language literature for biochemical studies on the ARID1A mutation and chromatin remodeling in CCC. ARID1A is responsible for directing the SWI/SNF complex to target promoters and regulates the transcription of certain genes by altering the chromatin structure around those genes. The mutation spectrum of ARID1A was enriched for C to T transitions. CCC and clear cell renal cell carcinoma (ccRCC) resemble each other pathogenetically. Dysfunction of the ARID1A protein, which occurs with VHL mutations in ccRCC, is responsible for loss of the assembly of the ARID1A-mediated histone H2B complex. Therefore, ARID1A acts as a chromatin remodeling modifier, which stimulates cell signaling that can lead to cell cycle arrest and cell death in the event of DNA damage. The dysfunction of ARID1A may result in susceptibility to CCC carcinogenesis through a defect in the repair or replication of damaged DNA.
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Affiliation(s)
- Hiroshi Shigetomi
- Department of Obstetrics and Gynecology, Nara Medical University, Nara, Japan
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Furness DLF, Dekker GA, Roberts CT. DNA damage and health in pregnancy. J Reprod Immunol 2011; 89:153-62. [PMID: 21511343 DOI: 10.1016/j.jri.2011.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 02/07/2011] [Accepted: 02/24/2011] [Indexed: 01/08/2023]
Abstract
In healthy pregnancy reactive oxygen species and antioxidants remain in balance and DNA damage is repaired effectively. However, pregnancy is an inflammatory state exhibiting increased susceptibility to oxidative stress such that this balance can be easily disrupted. Increased DNA damage has been shown to be involved in many pathological states including pregnancy complications. Modern lifestyles including exposure to pollutants, poor diet, and lack of exercise cause excess inflammation, oxidative stress, and ultimately DNA damage. There is a growing body of literature providing evidence that these lifestyle changes are increasing our risk of infertility, miscarriage, and late-gestation pregnancy complications. Moreover, baseline DNA damage rises with age and couples in developed societies are delaying childbirth, placing them at further risk. In order to understand the effect of lifestyle and DNA damage on pregnancy health we require large prospective studies, with the collection of samples prior to conception and endpoints of time-to-pregnancy, early pregnancy loss, and late-gestation maternal and fetal health.
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Affiliation(s)
- D L F Furness
- The University of Adelaide, Robinson Institute, Research Centre for Reproductive Health, Adelaide, South Australia 5005, Australia.
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Meng HX, Hackett JA, Nestor C, Dunican DS, Madej M, Reddington JP, Pennings S, Harrison DJ, Meehan RR. Apoptosis and DNA methylation. Cancers (Basel) 2011; 3:1798-820. [PMID: 24212783 PMCID: PMC3757391 DOI: 10.3390/cancers3021798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 03/11/2011] [Accepted: 03/11/2011] [Indexed: 01/05/2023] Open
Abstract
Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.
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Affiliation(s)
- Huan X. Meng
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James A. Hackett
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Colm Nestor
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Donncha S. Dunican
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Monika Madej
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - James P. Reddington
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
| | - Sari Pennings
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; E-Mail: (S.P.)
| | - David J. Harrison
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
| | - Richard R. Meehan
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mails: (H.X.M.); (J.A.H.); (C.N.); (D.S.D.); (M.M.); (J.P.R.)
- Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; E-Mail: (D.J.H.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44 (0)-332-2471; Fax: +44 (0) 131 467 8456
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