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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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2
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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3
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Casarotto M, Lupato V, Giurato G, Guerrieri R, Sulfaro S, Salvati A, D’Angelo E, Furlan C, Menegaldo A, Baboci L, Montico B, Turturici I, Dolcetti R, Romeo S, Baggio V, Corrado S, Businello G, Guido M, Weisz A, Giacomarra V, Franchin G, Steffan A, Sigalotti L, Vaccher E, Boscolo-Rizzo P, Jerry P, Fanetti G, Fratta E. LINE-1 hypomethylation is associated with poor outcomes in locoregionally advanced oropharyngeal cancer. Clin Epigenetics 2022; 14:171. [PMID: 36503584 PMCID: PMC9743592 DOI: 10.1186/s13148-022-01386-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND PURPOSE Currently, human papillomavirus (HPV) positivity represents a strong prognostic factor for both reduced risk of relapse and improved survival in patients with oropharyngeal squamous cell carcinoma (OPSCC). However, a subset of HPV-positive OPSCC patients still experience poor outcomes. Furthermore, HPV-negative OPSCC patients, who have an even higher risk of relapse, are still lacking suitable prognostic biomarkers for clinical outcome. Here, we evaluated the prognostic value of LINE-1 methylation level in OPSCC patients and further addressed the relationship between LINE-1 methylation status and p53 protein expression as well as genome-wide/gene-specific DNA methylation. RESULTS In this study, DNA was extracted from 163 formalin-fixed paraffin-embedded tissue samples retrospectively collected from stage III-IVB OPSCC patients managed with curative intent with up-front treatment. Quantitative methylation-specific PCR revealed that LINE-1 hypomethylation was directly associated with poor prognosis (5-year overall survival-OS: 28.1% for LINE-1 methylation < 35% vs. 69.1% for ≥ 55%; p < 0.0001). When LINE-1 methylation was dichotomized as < 55% versus ≥ 55%, interaction with HPV16 emerged: compared with hypermethylated HPV16-positive patients, subjects with hypomethylated HPV16-negative OPSCC reported an adjusted higher risk of death (HR 4.83, 95% CI 2.24-10.38) and progression (HR 4.54, 95% CI 2.18-9.48). Tumor protein p53 (TP53) gene is often mutated and overexpressed in HPV-negative OPSCC. Since p53 has been reported to repress LINE-1 promoter, we then analyzed the association between p53 protein expression and LINE-1 methylation levels. Following p53 immunohistochemistry, results indicated that among HPV16-negative patients with p53 ≥ 50%, LINE-1 methylation levels declined and remained stable at approximately 43%; any HPV16-positive patient reported p53 ≥ 50%. Finally, DNA methylation analysis demonstrated that genome-wide average methylation level at cytosine-phosphate-guanine sites was significantly lower in HPV16-negative OPSCC patients who relapsed within two years. The subsequent integrative analysis of gene expression and DNA methylation identified 20 up-regulated/hypomethylated genes in relapsed patients, and most of them contained LINE-1 elements in their promoter sequences. CONCLUSIONS Evaluation of the methylation level of LINE-1 may help in identifying the subset of OPSCC patients with bad prognosis regardless of their HPV status. Aberrant LINE-1 hypomethylation might occur along with TP53 mutations and lead to altered gene expression in OPSCC.
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Affiliation(s)
- Mariateresa Casarotto
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Valentina Lupato
- grid.415199.10000 0004 1756 8284Division of Otolaryngology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Giorgio Giurato
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy
| | - Roberto Guerrieri
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Sandro Sulfaro
- grid.415199.10000 0004 1756 8284Division of Pathology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Annamaria Salvati
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Medical Genomics Program, AOU ‘SS. Giovanni di Dio e Ruggi d’Aragona’, University of Salerno, Salerno, Italy
| | - Elisa D’Angelo
- grid.413363.00000 0004 1769 5275Department of Radiation Oncology, University Hospital of Modena, Modena, Italy
| | - Carlo Furlan
- grid.415199.10000 0004 1756 8284Department of Radiation Oncology, General Hospital “San Martino”, Belluno, Italy
| | - Anna Menegaldo
- Unit of Otolaryngology, AULSS 2 - Marca Trevigiana, Treviso, Italy
| | - Lorena Baboci
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Barbara Montico
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Irene Turturici
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Riccardo Dolcetti
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010 Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Salvatore Romeo
- Department of Services of Diagnosis and Care, Santorso Hospital, Santorso, VI Italy
| | - Vittorio Baggio
- grid.413196.8Department of Radiation Oncology, Treviso Regional Hospital, Treviso, Italy
| | - Stefania Corrado
- grid.413363.00000 0004 1769 5275Department of Anatomy and Pathology, University Hospital of Modena, Modena, Italy
| | - Gianluca Businello
- grid.413196.8Department of Pathology, Treviso Regional Hospital, Treviso, Italy
| | - Maria Guido
- grid.413196.8Department of Pathology, Treviso Regional Hospital, Treviso, Italy ,grid.5608.b0000 0004 1757 3470Department of Medicine (DIMED), University of Padova, Padova, Italy
| | - Alessandro Weisz
- grid.11780.3f0000 0004 1937 0335Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Genome Research Center for Health, Campus of Medicine, University of Salerno, Baronissi, SA Italy ,grid.11780.3f0000 0004 1937 0335Medical Genomics Program, AOU ‘SS. Giovanni di Dio e Ruggi d’Aragona’, University of Salerno, Salerno, Italy
| | - Vittorio Giacomarra
- grid.415199.10000 0004 1756 8284Division of Otolaryngology, General Hospital “S. Maria Degli Angeli”, Pordenone, Italy
| | - Giovanni Franchin
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Agostino Steffan
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Luca Sigalotti
- grid.414603.4Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Emanuela Vaccher
- grid.414603.4Division of Medical Oncology A, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Paolo Boscolo-Rizzo
- grid.5608.b0000 0004 1757 3470Section of Otolaryngology, Department of Neurosciences, University of Padova, Treviso, Italy
| | - Polesel Jerry
- grid.414603.4Unit of Cancer Epidemiology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Giuseppe Fanetti
- grid.418321.d0000 0004 1757 9741Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, PN Italy
| | - Elisabetta Fratta
- grid.414603.4Unit of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy ,grid.418321.d0000 0004 1757 9741Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Via Franco Gallini, 2, 33081 Aviano, PN Italy
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Serth J, Peters I, Katzendorn O, Dang TN, Moog J, Balli Z, Reese C, Hennenlotter J, Grote A, Lafos M, Tezval H, Kuczyk MA. Identification of a Novel Renal Metastasis Associated CpG-Based DNA Methylation Signature (RMAMS). Int J Mol Sci 2022; 23:ijms231911190. [PMID: 36232491 PMCID: PMC9569431 DOI: 10.3390/ijms231911190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Approximately 21% of patients with renal cell cancer (RCC) present with synchronous metastatic disease at the time of diagnosis, and metachronous metastatic disease occurs in 20–50% of cases within 5 years. Recent advances in adjuvant treatment of aggressive RCC following surgery suggest that biomarker-based prediction of risk for distant metastasis could improve patient selection. Biometrical analysis of TCGA-KIRC data identified candidate loci in the NK6 homeobox 2 gene (NKX6-2) that are hypermethylated in primary metastatic RCC. Analyses of NKX6-2 DNA methylation in three gene regions including a total of 16 CpG sites in 154 tumor-adjacent normal tissue, 189 RCC, and 194 metastatic tissue samples from 95 metastasized RCC patients revealed highly significant tumor-specific, primary metastatic-specific, and metastatic tissue-specific hypermethylation of NKX6-2. Combined CpG site methylation data for NKX6-2 and metastasis-associated genes (INA, NHLH2, and THBS4) demonstrated similarity between metastatic tissues and metastatic primary RCC tissues. The random forest method and evaluation of an unknown test cohort of tissues using receiver operator characteristic curve analysis revealed that metastatic tissues can be differentiated by a median area under the curve of 0.86 (p = 1.7 × 10−8–7.5 × 10−3) in 1000 random runs. Analysis of variable importance demonstrated an above median contribution for decision-making of at least one CpG site in each of the genes, suggesting superior informativity for sites annotated to NHLH2 and NKX6-2. Thus, DNA methylation of NKX6-2 is associated with the metastatic state of RCC tissues and contributes to a four-gene-based statistical predictor of tumoral and metastatic renal tissues.
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Affiliation(s)
- Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence:
| | - Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Olga Katzendorn
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Tu N. Dang
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Joana Moog
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Zarife Balli
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Christel Reese
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Jörg Hennenlotter
- Department of Urology, University of Tübingen, 72076 Tübingen, Germany
| | - Alexander Grote
- Department of Neurosurgery, University Hospital Gießen und Marburg, 35043 Marburg, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, 30625 Hannover, Germany
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5
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Bücker L, Lehmann U. CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story. Cancers (Basel) 2022; 14:cancers14184377. [PMID: 36139537 PMCID: PMC9497067 DOI: 10.3390/cancers14184377] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used. Abstract Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.
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Affiliation(s)
| | - Ulrich Lehmann
- Correspondence: ; Tel.: +49-(0)511-532-4501; Fax: +49-(0)511-532-5799
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6
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Moonen L, Mangiante L, Leunissen DJG, Lap LMV, Gabriel A, Hillen LM, Roemen GM, Koch A, van Engeland M, Dingemans AC, Foll M, Alcala N, Fernandez‐Cuesta L, Derks JL, Speel EM. Differential Orthopedia Homeobox expression in pulmonary carcinoids is associated with changes in DNA methylation. Int J Cancer 2022; 150:1987-1997. [PMID: 35076935 PMCID: PMC9303689 DOI: 10.1002/ijc.33939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/26/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022]
Abstract
Limited number of tumor types have been examined for Orthopedia Homeobox (OTP) expression. In pulmonary carcinoids, loss of expression is a strong indicator of poor prognosis. Here, we investigated OTP expression in 37 different tumor types, and the association between OTP expression and DNA methylation levels in lung neuroendocrine neoplasms. We analyzed publicly available multi-omics data (whole-exome-, whole-genome-, RNA sequencing and Epic 850K-methylation array) of 58 typical carcinoids, 27 atypical carcinoids, 69 large cell neuroendocrine carcinoma and 51 small cell lung cancer patients and TCGA (The Cancer Genome Atlas) data of 33 tumor types. 850K-methylation analysis was cross-validated using targeted pyrosequencing on 35 carcinoids. We report bimodality of OTP expression in carcinoids (OTPhigh vs OTPlow group, likelihood-ratio test P = 1.5 × 10-2 ), with the OTPhigh group specific to pulmonary carcinoids while absent from all other cohorts analyzed. Significantly different DNA methylation levels were observed between OTPhigh and OTPlow carcinoids in 12/34 OTP infinium probes (FDR < 0.05 and β-value effect size > .2). OTPlow carcinoids harbor high DNA methylation levels as compared to OTPhigh carcinoids. OTPlow carcinoids showed a significantly worse overall survival (log-rank test P = .0052). Gene set enrichment analysis for somatically mutated genes associated with hallmarks of cancer showed robust enrichment of three hallmarks in the OTPlow group, that is, sustaining proliferative signaling, evading growth suppressor and genome instability and mutation. Together our data suggest that high OTP expression is a unique feature of pulmonary carcinoids with a favorable prognosis and that in poor prognostic patients, OTP expression is lost, most likely due to changes in DNA methylation levels.
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Affiliation(s)
- Laura Moonen
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Lise Mangiante
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM)International Agency for Research on Cancer/World Health Organisation (IARC/WHO)LyonFrance
| | - Daphne J. G. Leunissen
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Lisa M. V. Lap
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Aurelie Gabriel
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM)International Agency for Research on Cancer/World Health Organisation (IARC/WHO)LyonFrance
| | - Lisa M. Hillen
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Guido M. Roemen
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
- Epify BVMaastrichtThe Netherlands
| | - Manon van Engeland
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Anne‐Marie C. Dingemans
- Department of Pulmonary DiseasesGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
- Department of Pulmonary MedicineErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM)International Agency for Research on Cancer/World Health Organisation (IARC/WHO)LyonFrance
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM)International Agency for Research on Cancer/World Health Organisation (IARC/WHO)LyonFrance
| | - Lynnette Fernandez‐Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM)International Agency for Research on Cancer/World Health Organisation (IARC/WHO)LyonFrance
| | - Jules L. Derks
- Department of Pulmonary DiseasesGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Ernst‐Jan M. Speel
- Department of PathologyGROW School for Oncology and Developmental Biology, Maastricht University Medical CentreMaastrichtThe Netherlands
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7
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [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: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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8
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Mehrgou A, Teimourian S. Update of gene expression/methylation and MiRNA profiling in colorectal cancer; application in diagnosis, prognosis, and targeted therapy. PLoS One 2022; 17:e0265527. [PMID: 35333898 PMCID: PMC8956198 DOI: 10.1371/journal.pone.0265527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/02/2022] [Indexed: 01/22/2023] Open
Abstract
Background
Colorectal cancer is one of the most deadliest malignancies worldwide. Due to the dearth of appropriate biomarkers, the diagnosis of this mortal disease is usually deferred, in its turn, culminating in the failure of prevention. By the same token, proper biomarkers are at play in determining the quality of prognosis. In other words, the survival rate is contingent upon the regulation of such biomarkers.
Materials and methods
The information regarding expression (GSE41258, and GSE31905), methylation (GSE101764), and miRNA (dbDEMC) were downloaded. MEXPRESS and GEPIA confirmed the validated differentially expressed/methylated genes using TCGA data. Taking advantage of the correlation plots and receiver-operating-characteristic (ROC) curves, expression and methylation profiles were compared. The interactions between validated differentially expressed genes and differentially expressed miRNA were recognized and visualized by miRTarBase and Cytoscape, respectively. Then, the protein-protein interaction (PPI) network and hub genes were established via STRING and Cytohubba plugin. Utilizing R packages (DOSE, Enrichplot, and clusterProfiler) and DAVID database, the Functional Enrichment analysis and the detection of KEGG pathways were performed. Ultimately, in order to recognize the prognostic value of found biomarkers, they were evaluated through drawing survival plots for CRC patients.
Results
In this research, we found an expression profile (with 13 novel genes), a methylation profile (with two novel genes), and a miRNA profile with diagnostic value. Concerning diagnosis, the expression profile was evaluated more powerful in comparison with the methylation profile. Furthermore, a prognosis-related expression profile was detected.
Conclusion
In addition to diagnostic- and prognostic-applicability, the discerned profiles can assist in targeted therapy and current therapeutic strategies.
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Affiliation(s)
- Amir Mehrgou
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahram Teimourian
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- * E-mail:
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9
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Nasif D, Real S, Roqué M, Branham MT. CDC42 as an epigenetic regulator of ID4 in triple-negative breast tumors. Breast Cancer 2022; 29:562-573. [DOI: 10.1007/s12282-022-01334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/09/2022] [Indexed: 12/01/2022]
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10
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Alizadeh-Sedigh M, Fazeli MS, Mahmoodzadeh H, Sharif SB, Teimoori-Toolabi L. Methylation of FBN1, SPG20, ITF2, RUNX3, SNCA, MLH1, and SEPT9 genes in circulating cell-free DNA as biomarkers of colorectal cancer. Cancer Biomark 2021; 34:221-250. [PMID: 34957998 DOI: 10.3233/cbm-210315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Investigating aberrant tumor-specific methylation in plasma cell-free DNA provides a promising and noninvasive biomarker for cancer detection. OBJECTIVE We aimed to investigate methylation status of some promoter regions in the plasma and tumor tissues to find biomarkers for early detection of colorectal cancer. METHODS This case-control study on seventy colorectal cancer patients and fifty matched healthy controls used Methylation-Specific High-Resolution Melting Curve analysis to evaluate the methylation of the selected promoter regions in converted genomic tissue DNA and plasma cfDNA. RESULTS The methylation levels in selected regions of SPG20 (+24375 to +24680, +24209 to +24399, and +23625 to +23883), SNCA (+807 to +1013, +7 to +162, and -180 to +7), FBN1 (+223 to +429, +1 to +245, and -18 to -175), ITF2 (+296 to +436 and -180 to +55), SEPT9 (-914412 to -91590 and -99083 to -92264), and MLH1 (-13 to +22) were significantly higher in tumor tissues compared with normal adjacent tissues. The methylation levels of FBN1, ITF2, SNCA, and SPG20 promoters were significantly higher in the patient's plasma compared to patient's normal tissue and plasma of healthy control subjects. FBN1, SPG20, and SEPT9 promoter methylation had a good diagnostic performance for discriminating CRC tissues from normal adjacent tissues (AUC > 0.8). A panel of SPG20, FBN1, and SEPT9 methylation had a higher diagnostic value than that of any single biomarker and other panels in tissue-based assay (AUC > 0.9). The methylation of FBN1(a) and SPG20(a) regions, as the closest region to the first coding sequence (CDS), had a good diagnostic performance in plasma cfDNA (AUC > 0.8) while a panel consisted of FBN1(a) and SPG20(a) regions showed excellent diagnostic performance for CRC detection in plasma cfDNA (AUC > 0.9). CONCLUSION Methylation of FBN1(a) and SPG20(a) promoter regions in the plasma cfDNA can be an excellent simple, non-invasive blood-based test for early detection of CRC.
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Affiliation(s)
- Maryam Alizadeh-Sedigh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Division of Colorectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahin Behrouz Sharif
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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11
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Zhou S, Wang X, Ding J, Yang H, Xie Y. Increased ATG5 Expression Predicts Poor Prognosis and Promotes EMT in Cervical Carcinoma. Front Cell Dev Biol 2021; 9:757184. [PMID: 34901004 PMCID: PMC8655861 DOI: 10.3389/fcell.2021.757184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/22/2021] [Indexed: 01/06/2023] Open
Abstract
Cervical cancer has the second-highest incidence and mortality of female malignancy. The major causes of mortality in patients with cervical cancer are invasion and metastasis. The epithelial–mesenchymal transition (EMT) process plays a major role in the acquisition of metastatic potential and motility. Autophagy-related genes (ARGs) are implicated in the EMT process, and autophagy exerts a dual function in EMT management at different phases of tumor progression. However, the role of specific ARGs during the EMT process has not yet been reported in cervical cancer. Based on the data from the Cancer Genome Atlas (TCGA) cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) sequencing database, we performed the prognosis analysis for those ARGs obtained from the Human Autophagy database. ATG5 was identified as the only important harmful marker influencing survival of cervical cancer patients by univariate Cox regression (HR 1.7; 95% CI: 1.0–2.8, p = 0.047), and the 5-years survival rate for the high- and low-ATG5 expression groups was 0.486 (0.375–0.631) and 0.782 (0.708–0.863), respectively. TCGA CESC methylation data showed that eight methylation sites of ATG5 could also be significantly associated with the overall survival (OS) of cervical cancer patients. Single-sample gene-set enrichment and gene functional enrichment results showed that ATG5 was correlated with some cancer-related pathways, such as phagocytosis-related genes, endocytosis-related genes, immune-related genes, EMT score, and some EMT signature-related genes. Next, cell migration and invasion assay and Western blot were applied to detect the function of ATG5 in EMT of cervical cancer. In cervical cancer cells, ATG5 knockdown resulted in attenuation of migration and invasion. The functional study showed that knockdown of ATG5 could reverse EMT process by P-ERK, P-NFκBp65, P-mTOR pathways, and so on. In conclusion, the present study implies that ATG5 was a major contributor to EMT regulation and poor prognosis in cervical cancer.
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Affiliation(s)
- Suna Zhou
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Xuequan Wang
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Jiapei Ding
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
| | - Youyou Xie
- Laboratory of Cellular and Molecular Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China.,Department of Radiation Oncology, The Affiliated Taizhou Hospital, Wenzhou Medical University, Taizhou, China
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12
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Lin Z, Chang J, Li X, Wang J, Wu X, Liu X, Zhu Y, Yu XY. Association of DNA methylation and transcriptome reveals epigenetic etiology of heart failure. Funct Integr Genomics 2021; 22:89-112. [PMID: 34870779 DOI: 10.1007/s10142-021-00813-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/08/2023]
Abstract
Epigenetic modifications viz. DNA methylation, histone modifications, and RNA-based alterations play a crucial role in the development of cardiovascular diseases. In this study, we investigated DNA methylation with an aim to reveal the epigenetic etiology of heart failure. Sprague-Dawley rats surviving myocardial infarction developed acute heart failure in 1 week. Genomic DNA methylation changes were profiled by bisulfite sequencing, and gene expression levels were analyzed by RNA-seq in failing and sham-operation hearts. A total of 3480 differentially methylated genes in the promoter regions including transcriptional start site and 1934 transcriptome-altered genes were identified in the defected hearts. Common differential genes were enriched by the gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and protein-protein interaction for HF phenotypes. Among these, Mettl11b, HDAC3, HDAC11, ubiquitination-related genes, and snoRNAs are new epigenetic classifiers that had not been reported yet, which may be important regulators in HF.
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Affiliation(s)
- Zhongxiao Lin
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
- China State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- South China Center for Drug Clinical Evaluation and Guangzhou Medical University New Drug Research and Development Co., Ltd, Guangzhou, 511436, China
| | - Jishuo Chang
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
- South China Center for Drug Clinical Evaluation and Guangzhou Medical University New Drug Research and Development Co., Ltd, Guangzhou, 511436, China
| | - Xinzhi Li
- China State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jianglin Wang
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xiaodan Wu
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xiaoyan Liu
- China State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
- Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, No. 58, Pu Yu Dong Road, Shanghai, 200011, China
| | - YiZhun Zhu
- China State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
- South China Center for Drug Clinical Evaluation and Guangzhou Medical University New Drug Research and Development Co., Ltd, Guangzhou, 511436, China.
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13
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Kubiliute R, Zalimas A, Bakavicius A, Ulys A, Jankevicius F, Jarmalaite S. Clinical Significance of ADAMTS19, BMP7, SIM1, and SFRP1 Promoter Methylation in Renal Clear Cell Carcinoma. Onco Targets Ther 2021; 14:4979-4990. [PMID: 34675538 PMCID: PMC8502107 DOI: 10.2147/ott.s330341] [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: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney tumors, accounting for the majority of deaths from genitourinary cancers. The currently used nomograms for predicting patient outcomes are based on clinical-pathological characteristics only; however, a significant number of ccRCC survivors with similar radiological and histological features still demonstrate a different clinical course of the disease. This study aimed at the identification of novel DNA methylation biomarkers for the monitoring of patients with ccRCC. Methods Gene expression profiling by SurePrint G3 Human GE 8×60K Microarrays was performed in 4 ccRCC tissues and adjacent non-cancerous renal tissue (NRT) samples. Four down-regulated genes were selected for further DNA methylation status analysis in 123 ccRCC and 45 NRT samples using methylation-specific PCR (MSP). Results DNA methylation changes of ADAMTS19, BMP7, SIM1, and SFRP1 were cancer-specific with significantly (P<0.050) higher methylation frequency (37%, 20%, 18%, and 42%, respectively) in tumor tissues. The methylated status of at least one gene was significantly related to various clinical-pathological parameters, including tumor size, Fuhrman and WHO/ISUP grades, intravascular invasion, and necrosis. Moreover, the methylated status of multimarker panel ADAMTS19, BMP7 & SFRP1 was predictive for poorer overall survival (HR, 4.11; 95% CI, 1.22–13.86). Conclusion In conclusion, DNA methylation of the three-gene panel consisting of ADAMTS19, BMP7 & SFRP1 supposedly predicts the outcome of patients diagnosed with ccRCC and possibly might be used to enrich the current prognostic tools.
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Affiliation(s)
- Raimonda Kubiliute
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
| | - Algirdas Zalimas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
| | - Arnas Bakavicius
- National Cancer Institute, Vilnius, Lithuania.,Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.,Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Feliksas Jankevicius
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.,Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaite
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,National Cancer Institute, Vilnius, Lithuania
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14
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Vizoso M, van Rheenen J. Diverse transcriptional regulation and functional effects revealed by CRISPR/Cas9-directed epigenetic editing. Oncotarget 2021; 12:1651-1662. [PMID: 34434494 PMCID: PMC8378768 DOI: 10.18632/oncotarget.28037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/27/2021] [Indexed: 01/04/2023] Open
Abstract
DNA methylation is an epigenetic process that controls DNA accessibility and serves as a transcriptomic switch when deposited at regulatory regions. The adequate functioning of this process is indispensable for tissue homeostasis and cell fate determination. Conversely, altered DNA methylation patterns result in abnormal gene transcription profiles that contribute to tumor initiation and progression. However, whether the consequence of DNA methylation on gene expression and cell fate is uniform regardless of the cell type or state could so far not been tested due to the lack of technologies to target DNA methylation in-situ. Here, we have taken advantage of CRISPR/dCas9 technology adapted for epigenetic editing through site-specific targeting of DNA methylation to characterize the transcriptional changes of the candidate gene and the functional effects on cell fate in different tumor settings. As a proof-of-concept, we were able to induce de-novo site-specific methylation of the gene promoter of IGFBP2 up to 90% with long-term and bona-fide inheritance by daughter cells. Strikingly, this modification led to opposing expression profiles of the target gene in different cancer cell models and affected the expression of mesenchymal genes CDH1, VIM1, TGFB1 and apoptotic marker BCL2. Moreover, methylation-induced changes in expression profiles was also accompanied by a phenotypic switch in cell migration and cell morphology. We conclude that in different cell types the consequence of DNA methylation on gene expression and cell fate can be completely different.
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Affiliation(s)
- Miguel Vizoso
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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15
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Alcaraz J, Ikemori R, Llorente A, Díaz-Valdivia N, Reguart N, Vizoso M. Epigenetic Reprogramming of Tumor-Associated Fibroblasts in Lung Cancer: Therapeutic Opportunities. Cancers (Basel) 2021; 13:cancers13153782. [PMID: 34359678 PMCID: PMC8345093 DOI: 10.3390/cancers13153782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Lung cancer is the leading cause of cancer death among both men and women, partly due to limited therapy responses. New avenues of knowledge are indicating that lung cancer cells do not form a tumor in isolation but rather obtain essential support from their surrounding host tissue rich in altered fibroblasts. Notably, there is growing evidence that tumor progression and even the current limited responses to therapies could be prevented by rescuing the normal behavior of fibroblasts, which are critical housekeepers of normal tissue function. For this purpose, it is key to improve our understanding of the molecular mechanisms driving the pathologic alterations of fibroblasts in cancer. This work provides a comprehensive review of the main molecular mechanisms involved in fibroblast transformation based on epigenetic reprogramming, and summarizes emerging therapeutic approaches to prevent or overcome the pathologic effects of tumor-associated fibroblasts. Abstract Lung cancer is the leading cause of cancer-related death worldwide. The desmoplastic stroma of lung cancer and other solid tumors is rich in tumor-associated fibroblasts (TAFs) exhibiting an activated/myofibroblast-like phenotype. There is growing awareness that TAFs support key steps of tumor progression and are epigenetically reprogrammed compared to healthy fibroblasts. Although the mechanisms underlying such epigenetic reprogramming are incompletely understood, there is increasing evidence that they involve interactions with either cancer cells, pro-fibrotic cytokines such as TGF-β, the stiffening of the surrounding extracellular matrix, smoking cigarette particles and other environmental cues. These aberrant interactions elicit a global DNA hypomethylation and a selective transcriptional repression through hypermethylation of the TGF-β transcription factor SMAD3 in lung TAFs. Likewise, similar DNA methylation changes have been reported in TAFs from other cancer types, as well as histone core modifications and altered microRNA expression. In this review we summarize the evidence of the epigenetic reprogramming of TAFs, how this reprogramming contributes to the acquisition and maintenance of a tumor-promoting phenotype, and how it provides novel venues for therapeutic intervention, with a special focus on lung TAFs.
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Affiliation(s)
- Jordi Alcaraz
- Unit of Biophysics and Bioengineering, Department of Biomedicine, School of Medicine and Health Sciences, Universitat de Barcelona, 08036 Barcelona, Spain; (R.I.); (A.L.); (N.D.-V.)
- Thoracic Oncology Unit, Hospital Clinic Barcelona, 08036 Barcelona, Spain;
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain
- Correspondence: (J.A.); (M.V.)
| | - Rafael Ikemori
- Unit of Biophysics and Bioengineering, Department of Biomedicine, School of Medicine and Health Sciences, Universitat de Barcelona, 08036 Barcelona, Spain; (R.I.); (A.L.); (N.D.-V.)
| | - Alejandro Llorente
- Unit of Biophysics and Bioengineering, Department of Biomedicine, School of Medicine and Health Sciences, Universitat de Barcelona, 08036 Barcelona, Spain; (R.I.); (A.L.); (N.D.-V.)
| | - Natalia Díaz-Valdivia
- Unit of Biophysics and Bioengineering, Department of Biomedicine, School of Medicine and Health Sciences, Universitat de Barcelona, 08036 Barcelona, Spain; (R.I.); (A.L.); (N.D.-V.)
| | - Noemí Reguart
- Thoracic Oncology Unit, Hospital Clinic Barcelona, 08036 Barcelona, Spain;
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Miguel Vizoso
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Correspondence: (J.A.); (M.V.)
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16
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Joosten SC, Odeh SNO, Koch A, Buekers N, Aarts MJB, Baldewijns MMLL, Van Neste L, van Kuijk S, Schouten LJ, van den Brandt PA, Tjan-Heijnen VC, van Engeland M, Smits KM. Development of a prognostic risk model for clear cell renal cell carcinoma by systematic evaluation of DNA methylation markers. Clin Epigenetics 2021; 13:103. [PMID: 33947447 PMCID: PMC8094610 DOI: 10.1186/s13148-021-01084-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/19/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a head-to-head comparison of previously published DNA methylation markers and propose a potential prognostic model for clear cell RCC (ccRCC). PATIENTS AND METHODS Promoter methylation of PCDH8, BNC1, SCUBE3, GREM1, LAD1, NEFH, RASSF1A, GATA5, SFRP1, CDO1, and NEURL was determined by nested methylation-specific PCR. To identify clinically relevant methylated regions, The Cancer Genome Atlas (TCGA) was used to guide primer design. Formalin-fixed paraffin-embedded (FFPE) tissue samples from 336 non-metastatic ccRCC patients from the prospective Netherlands Cohort Study (NLCS) were used to develop a Cox proportional hazards model using stepwise backward elimination and bootstrapping to correct for optimism. For validation purposes, FFPE ccRCC tissue of 64 patients from the University Hospitals Leuven and a series of 232 cases from The Cancer Genome Atlas (TCGA) were used. RESULTS Methylation of GREM1, GATA5, LAD1, NEFH, NEURL, and SFRP1 was associated with poor ccRCC-specific survival, independent of age, sex, tumor size, TNM stage or tumor grade. Moreover, the association between GREM1, NEFH, and NEURL methylation and outcome was shown to be dependent on the genomic region. A prognostic biomarker model containing GREM1, GATA5, LAD1, NEFH and NEURL methylation in combination with clinicopathological characteristics, performed better compared to the model with clinicopathological characteristics only (clinical model), in both the NLCS and the validation population with a c-statistic of 0.71 versus 0.65 and a c-statistic of 0.95 versus 0.86 consecutively. However, the biomarker model had limited added prognostic value in the TCGA series with a c-statistic of 0.76 versus 0.75 for the clinical model. CONCLUSION In this study we performed a head-to-head comparison of potential prognostic methylation markers for ccRCC using a novel approach to guide primers design which utilizes the optimal location for measuring DNA methylation. Using this approach, we identified five methylation markers that potentially show prognostic value in addition to currently known clinicopathological factors.
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Affiliation(s)
- S C Joosten
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - S N O Odeh
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - A Koch
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - N Buekers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - M J B Aarts
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - L Van Neste
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - S van Kuijk
- Department of Clinical Epidemiology and Medical Technology Assessment, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - L J Schouten
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - P A van den Brandt
- Department of Epidemiology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - V C Tjan-Heijnen
- Department of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - M van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - K M Smits
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
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17
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Gissi DB, Gabusi A, Tarsitano A, Asioli S, Rossi R, Marchetti C, Montebugnoli L, Foschini MP, Morandi L. Application of a non-invasive oral brushing procedure based on bisulfite sequencing of a 13-gene panel to study high-risk OSCC patients. Cancer Biomark 2021; 28:499-510. [PMID: 32568174 DOI: 10.3233/cbm-190422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND A non-invasive sampling procedure for the early detection of Oral Squamous Cell Carcinoma (OSCC) based on DNA methylation analysis of a panel of 13 genes was applied in 4 different OSCC risk-group of patients. Aim of the study is to evaluate the between-group differences and the variables related to the methylation profile of each group. METHODS Oral brushing samples were collected from 54 healthy subjects, 31 Oral Leukoplakia (OL) patients, 18 Oral Lichen Planus (OLP) patients and 26 patients previously treated for OSCC. Each sample was considered positive or negative in relation to a predefined cut-off value. RESULTS None of the samples from 54 healthy subjects were positive, whereas 22/31 OL, 3/18 OLP and 8/26 surgically treated OSCC samples showed positive values with respect to the cut-off. In OL patients, dysplasia was the only variable significantly related to positive values: 10/10 OLs with high-grade dysplasia were positive with respect to 12/21 OLs without dysplasia (Chi 6.039, p< 0.05). CONCLUSION DNA methylation analysis in epithelial cells collected by oral brushing seems to be a promising genetic method to distinguish lesions at high risk of developing OSCC. Larger population studies and an adequate follow-up period are necessary to confirm these preliminary data.
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Affiliation(s)
- Davide B Gissi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Andrea Gabusi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Section of Maxillo-facial Surgery at Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Roberto Rossi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Claudio Marchetti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Section of Maxillo-facial Surgery at Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - Lucio Montebugnoli
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Maria P Foschini
- Department of Biomedical and Neuromotor Sciences, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Luca Morandi
- Department of Biomedical and Neuromotor Sciences, Functional MR Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, University of Bologna, Bologna, Italy
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Diagnostic DNA Methylation Biomarkers for Renal Cell Carcinoma: A Systematic Review. Eur Urol Oncol 2021; 4:215-226. [DOI: 10.1016/j.euo.2019.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/23/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023]
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Mallisetty Y, Mukherjee N, Jiang Y, Chen S, Ewart S, Arshad SH, Holloway JW, Zhang H, Karmaus W. Epigenome-Wide Association of Infant Feeding and Changes in DNA Methylation from Birth to 10 Years. Nutrients 2020; 13:E99. [PMID: 33396735 PMCID: PMC7824231 DOI: 10.3390/nu13010099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetic factors have been suggested as mediators of early-life nutrition to future health. Prior studies focused on breastfeeding effects on DNA methylation (DNAm), ignoring other feeding modes. In this analysis of the Isle of Wight birth cohort, feeding modes were categorized as exclusive breastfeeding (EBF), exclusive formula feeding (EFF), and mixed feeding based on whether the respective feeding mode lasted for at least 3 months. In addition, in the past, infant feeding modes were assessed using DNAm at one time point in childhood, not changes of DNAm. In this paper, methylation differences (delta DNAm) were calculated by subtracting residual methylation values at birth from age 10 years (adjusting for cell types and season of blood collection at both ages). These deltas were estimated for all methylation sites where cytosine was followed by guanine (cytosine guanine dinucleotide (CpG) sites). Then, we performed an epigenome-wide association study contrasting EBF, EFF, and mixed feeding with delta DNAm that represents changes in methylation from birth to 10 years. A total of 87 CpGs (EBF: 27 CpGs, EFF: 48 CpGs, mixed: 12 CpGs) were identified using separate linear regression models adjusting for confounders and multiple testing. The sum of all changes in methylation from birth to age 10 years was significantly lower in the EFF group. Correspondingly, the number of CpGs with a methylation decline was 4.7% higher reflecting 13,683 CpGs. Lower methylation related to exclusive formula feeding and its adverse potential for the child's development needs future research to reduce adverse health effects.
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Affiliation(s)
- Yamini Mallisetty
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Robison Hall, Memphis, TN 38152, USA; (Y.M.); (N.M.); (Y.J.); (H.Z.)
| | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Robison Hall, Memphis, TN 38152, USA; (Y.M.); (N.M.); (Y.J.); (H.Z.)
| | - Yu Jiang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Robison Hall, Memphis, TN 38152, USA; (Y.M.); (N.M.); (Y.J.); (H.Z.)
| | - Su Chen
- Department of Mathematical Science, University of Memphis, Dunn Hall, Memphis, TN 38152, USA;
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; (S.H.A.); (J.W.H.)
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Isle of Wight PO30 5TG, UK
| | - John W. Holloway
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK; (S.H.A.); (J.W.H.)
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Robison Hall, Memphis, TN 38152, USA; (Y.M.); (N.M.); (Y.J.); (H.Z.)
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Robison Hall, Memphis, TN 38152, USA; (Y.M.); (N.M.); (Y.J.); (H.Z.)
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20
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Dong Z, Dai L, Zhang Y, Fang C, Shi G, Chen Y, Li J, Wang Q, Fu J, Yu Y, Wang W, Cheng L, Liu Y, Lin Y, Wang Y, Wang Q, Wang H, Zhang H, Zhang Y, Su X, Zhang S, Wang F, Qiu M, Zhou Z, Deng H. Hypomethylation of GDNF family receptor alpha 1 promotes epithelial-mesenchymal transition and predicts metastasis of colorectal cancer. PLoS Genet 2020; 16:e1009159. [PMID: 33175846 PMCID: PMC7682896 DOI: 10.1371/journal.pgen.1009159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/23/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Tumor metastasis is the major cause of poor prognosis and mortality in colorectal cancer (CRC). However, early diagnosis of highly metastatic CRC is currently difficult. In the present study, we screened for a novel biomarker, GDNF family receptor alpha 1 (GFRA1) based on the expression and methylation data in CRC patients from The Cancer Genome Altlas (TCGA), followed by further analysis of the correlation between the GFRA1 expression, methylation, and prognosis of patients. Our results show DNA hypomethylation-mediated upregulation of GFRA1 in invasive CRC, and it was found to be correlated with poor prognosis of CRC patients. Furthermore, GFRA1 methylation-modified sequences were found to have potential as methylation diagnostic markers of highly metastatic CRC. The targeted demethylation of GFRA1 by dCas9-TET1CD and gRNA promoted CRC metastasis in vivo and in vitro. Mechanistically, demethylation of GFRA1 induces epithelial-mesenchymal transition (EMT) by promoting AKT phosphorylation and increasing c-Jun expression in CRC cells. Collectively, our findings indicate that GFRA1 hypomethylation can promote CRC invasion via inducing EMT, and thus, GFRA1 methylation can be used as a biomarker for the early diagnosis of highly metastasis CRC. Abnormal DNA methylation, one of important characteristics in tumor cells, is exploited as biomarkers for cancer diagnosis and prognosis prediction. Early diagnosis of highly metastatic CRC will be helpful for the clinical management, thus prolongs patient survival. However, it is currently difficult to make early diagnosis of highly metastatic CRC in clinical practice. Currently, we screened a novel biomarker gene, GFRA1, which associated with the invasion and poor prognosis of CRC. The targeted demethylation of GFRA1 exerted a significant promoting effect on CRC metastasis, and GFRA1 methylation-modified sequences are valuable diagnostic biomarker for CRC metastasis risk assessment. Mechanically, demethylation of GFRA1 induced epithelial-mesenchymal transition (EMT) by upregulating AKT phosphorylation and c-Jun expression in CRC cells. Our results demonstrate the promoting effect of GFRA1 demethylation on CRC invasion and GFRA1 methylation may be a potential prognostic marker for predicting metastasis of CRC.
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Affiliation(s)
- Zhexu Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Gang Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Ye Chen
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Junshu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Qin Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Jiamei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yan Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Wenshuang Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Lin Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yi Lin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yuan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Qingnan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Huiling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Hantao Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yujing Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Xiaolan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Shuang Zhang
- Department of biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Meng Qiu
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Zongguang Zhou
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
- * E-mail:
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Xu G, Zhou X, Xing J, Xiao Y, Jin B, Sun L, Yang H, Du S, Xu H, Mao Y. Identification of RASSF1A promoter hypermethylation as a biomarker for hepatocellular carcinoma. Cancer Cell Int 2020; 20:547. [PMID: 33292241 PMCID: PMC7653745 DOI: 10.1186/s12935-020-01638-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Background RAS association domain family protein 1A (RASSF1A) promoter hypermethylation is suggested to be linked to hepatocellular carcinoma (HCC), but the results remained controversial. Methods We evaluated how RASSF1A promoter hypermethylation affects HCC risk and its clinicopathological characteristics through meta-analysis. Data on DNA methylation in HCC and relevant clinical data were also collected based on The Cancer Genome Atlas (TCGA) database to investigate the prognostic role of RASSF1A promoter hypermethylation in HCC. Results Forty-four articles involving 4777 individuals were enrolled in the pooled analyses. The RASSF1A promoter methylation rate was notably higher in the HCC cases than the non-tumor cases and healthy individuals, and was significantly related to hepatitis B virus (HBV) infection-positivity and large tumor size. Kaplan–Meier survival analysis revealed that HCC cases with RASSF1A promoter hypermethylation had worse outcomes. Receiver operating characteristic curves confirmed that RASSF1A promoter methylation may be a marker of HCC-related prognoses. Conclusions RASSF1A promoter hypermethylation is a promising biomarker for the diagnosis of HCC from tissue and peripheral blood, and is an emerging therapeutic target against HCC.
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Affiliation(s)
- Gang Xu
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaoxiang Zhou
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jiali Xing
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yao Xiao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Bao Jin
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lejia Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Huayu Yang
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haifeng Xu
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Olbromski M, Podhorska-Okołów M, Dzięgiel P. Role of SOX Protein Groups F and H in Lung Cancer Progression. Cancers (Basel) 2020; 12:cancers12113235. [PMID: 33152990 PMCID: PMC7692225 DOI: 10.3390/cancers12113235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The expression of SOX proteins has been demonstrated in many tissues at various stages of embryogenesis, where they play the role of transcription factors. The SOX18 protein (along with SOX7 and SOX17) belongs to the SOXF group and is mainly involved in the development of the cardiovascular system, where its expression was found in the endothelium. SOX18 expression was also demonstrated in neoplastic lines of gastric, pancreatic and colon adenocarcinomas. The prognostic role of SOX30 expression has only been studied in lung adenocarcinomas, where a low expression of this factor in the stromal tumor was associated with a worse prognosis for patients. Because of the complexity of non-small-cell lung cancer (NSCLC) development, the role of the SOX proteins in this malignancy is still not fully understood. Many recently published papers show that SOX family protein members play a crucial role in the progression of NSCLC. Abstract The SOX family proteins are proved to play a crucial role in the development of the lymphatic ducts and the cardiovascular system. Moreover, an increased expression level of the SOX18 protein has been found in many malignances, such as melanoma, stomach, pancreatic breast and lung cancers. Another SOX family protein, the SOX30 transcription factor, is responsible for the development of male germ cells. Additionally, recent studies have shown its proapoptotic character in non-small cell lung cancer cells. Our preliminary studies showed a disparity in the amount of mRNA of the SOX18 gene relative to the amount of protein. This is why our attention has been focused on microRNA (miRNA) molecules, which could regulate the SOX18 gene transcript level. Recent data point to the fact that, in practically all types of cancer, hundreds of genes exhibit an abnormal methylation, covering around 5–10% of the thousands of CpG islands present in the promoter sequences, which in normal cells should not be methylated from the moment the embryo finishes its development. It has been demonstrated that in non-small-cell lung cancer (NSCLC) cases there is a large heterogeneity of the methylation process. The role of the SOX18 and SOX30 expression in non-small-cell lung cancers (NSCLCs) is not yet fully understood. However, if we take into account previous reports, these proteins may be important factors in the development and progression of these malignancies.
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Affiliation(s)
- Mateusz Olbromski
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
- Correspondence: ; Tel.: +48-717-841-354; Fax: +48-717-840-082
| | - Marzenna Podhorska-Okołów
- Department of Ultrastructural Research, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
| | - Piotr Dzięgiel
- Department of Histology and Embryology, Department of Human Morphology and Embryology, Medical University, 50-368 Wroclaw, Poland;
- Department of Physiotherapy, University School of Physical Education, 51-612 Wroclaw, Poland
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Vordenbäumen S, Rosenbaum A, Gebhard C, Raithel J, Sokolowski A, Düsing C, Chehab G, Richter JG, Brinks R, Rehli M, Schneider M. Associations of site-specific CD4 +-T-cell hypomethylation within CD40-ligand promotor and enhancer regions with disease activity of women with systemic lupus erythematosus. Lupus 2020; 30:45-51. [PMID: 33081589 DOI: 10.1177/0961203320965690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To comprehensively assess associations of site-specific CD4+-T-cell hypomethylation of the CD40-Ligand gene (CD40L) with disease activity of women with systemic lupus erythematosus (SLE). METHODS CpG-sites within the DNA of the promotor and two enhancer regions (n = 22) of CD40L were identified and numbered consecutively. The rate of methylated DNA in isolated CD4+-T-cells of women with SLE were quantified for each methylation site by MALDI-TOF. Disease activity was assessed by SLE Disease Activity Index (SLEDAI). Associations of site-specific methylation rates with the SLEDAI scores were assessed by linear regression modelling. P values were adjusted according to Bonferroni-Holm as indicated. RESULTS 60 female SLE patients participated in the study (age 45.7 ± 11.1 years, disease duration 17.0 ± 8.3 years). Significant associations to the SLEDAI were noted for CpG22 hypomethylation of the promotor (β = -40.1, p = 0.017, adjusted p = 0.027), trends were noted for CpG17 hypomethylation of the promotor (β = -30.5, p = 0.032, adjusted p = 0.6), and for CpG11 hypermethylation of the second enhancer (β = 15.0, p = 0.046, adjusted p = 0.8). CONCLUSION Site-specific hypomethylation of the CD40L promotor in CD4+-T-cells show associations with disease activity in female SLE patients.
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Affiliation(s)
- Stefan Vordenbäumen
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany.,Rheinisches Rheuma-Zentrum St. Elisabeth-Hospital, Meerbusch-Lank, Germany
| | - Anna Rosenbaum
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Claudia Gebhard
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
| | - Johanna Raithel
- Rheinisches Rheuma-Zentrum St. Elisabeth-Hospital, Meerbusch-Lank, Germany.,Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Sokolowski
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christina Düsing
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Gamal Chehab
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jutta G Richter
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ralph Brinks
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael Rehli
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
| | - Matthias Schneider
- Medical Faculty, Department & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany
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Zappe K, Cichna-Markl M. Aberrant DNA Methylation of ABC Transporters in Cancer. Cells 2020; 9:cells9102281. [PMID: 33066132 PMCID: PMC7601986 DOI: 10.3390/cells9102281] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
ATP-binding cassette (ABC) transporters play a crucial role in multidrug resistance (MDR) of cancers. They function as efflux pumps, resulting in limited effectiveness or even failure of therapy. Increasing evidence suggests that ABC transporters are also involved in tumor initiation, progression, and metastasis. Tumors frequently show multiple genetic and epigenetic abnormalities, including changes in histone modification and DNA methylation. Alterations in the DNA methylation status of ABC transporters have been reported for a variety of cancer types. In this review, we outline the current knowledge of DNA methylation of ABC transporters in cancer. We give a brief introduction to structure, function, and gene regulation of ABC transporters that have already been investigated for their DNA methylation status in cancer. After giving an overview of the applied methodologies and the CpGs analyzed, we summarize and discuss the findings on aberrant DNA methylation of ABC transporters by cancer types. We conclude our review with the discussion of the potential to target aberrant DNA methylation of ABC transporters for cancer therapy.
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An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species. Cells 2020; 9:cells9092092. [PMID: 32933205 PMCID: PMC7565279 DOI: 10.3390/cells9092092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Ultra-conserved non-coding elements (UCNEs) are genomic sequences that exhibit > 95% sequence identity between humans, mammals, birds, reptiles, and fish. Recent findings reported their functional role in cancer. The aim of this study was to evaluate the DNA methylation modifications of UNCEs in squamous cell carcinoma (SCC) from different mammal species. Methods: Fifty SCCs from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger, and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite next generation sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, and uc.328). Results: 57/59 CpGs were significantly different according to the Kruskal–Wallis test (p < 0.05) comparing normal samples with SCC. A common DNA hypermethylation pattern was observed in SCCs from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC. Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.
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26
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Liu P, Tian W. Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 2020; 8:e9654. [PMID: 32832275 PMCID: PMC7409785 DOI: 10.7717/peerj.9654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 12/30/2022] Open
Abstract
Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratification (hazard ratio (HR) > 4; log-rank test, p-value < 0.01). Based on independent datasets and seven additional cancers, the diagnostic and prognostic classifiers also had better robustness and stability. The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction. Conclusion The present study provides a comprehensive analysis of ccRCC using multi-omics data. These findings indicated that multi-omics analysis could identify some novel epigenetic factors, which were the most important causes of advanced cancer and poor clinical prognosis. Diagnostic and prognostic biomarkers were identified, which provided a promising avenue to develop effective therapies for ccRCC.
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Affiliation(s)
- Pengfei Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
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27
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Potential of RASSF1A promoter methylation as a biomarker for colorectal cancer: Meta-analysis and TCGA analysis. Pathol Res Pract 2020; 216:153009. [PMID: 32703486 DOI: 10.1016/j.prp.2020.153009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/16/2020] [Accepted: 05/10/2020] [Indexed: 12/24/2022]
Abstract
The RAS association domain family protein 1A (RASSF1A) is a tumor suppressor in colorectal cancer (CRC), and is often inactived by hypermethylation. Therefore, we evaluated the association between RASSF1A hypermethylation and the risk and prognosis in CRC. We identified literature through searching PubMed and China National Knowledge Infrastructure databases, and then validated and supplemented the meta-analysis with TCGA analysis. Twenty-three studies involving 2886 subjects of CRC were examined. The meta-analysis showed that RASSF1A promoter methylation inferred high CRC risk (odds ratio, 6.53, 95% confidence interval 3.88-11.01, P < .001) and poor overall survival (hazard ratio 2.85, 95% CI 1.88-4.31, P < .001). The TCGA analysis suggested that effect of RASSF1A promotor methylation was affected by tumor localization (colon vs. rectum). RASSF1A promoter methylation was a predictor of high risk (OR 2.38, 95%CI 1.02-5.6, P = .046) and poor disease free survival(HR 2.25, 95%CI 1.27-3.99, P = .006)in colon adenocarcinoma, but the association was statistically insignificant in rectum adenocarcinoma(HR 1.58, 95% CI 0.69-3.59, P = .28). These results suggested RASSF1A hypermethylation is a risk and a potential prognostic biomarker in CRC.
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Renzi A, Morandi L, Lenzi J, Rigillo A, Bettini G, Bellei E, Giacomini A, Tinto D, Sabattini S. Analysis of DNA methylation and TP53 mutational status for differentiating feline oral squamous cell carcinoma from non-neoplastic mucosa: A preliminary study. Vet Comp Oncol 2020; 18:825-837. [PMID: 32506786 DOI: 10.1111/vco.12624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022]
Abstract
Feline oral squamous cell carcinoma (FOSCC) is characterized by high local invasiveness and early bone lysis. The late diagnosis largely limits the efficacy of therapy and increases treatment-related morbidity. The aim of this exploratory study was to assess the methylation pattern of 10 candidate genes and TP53 mutational status in histologic samples of FOSCC. Results were compared with normal oral mucosa and oral inflammatory lesions, in order to establish a gene panel for FOSCC detection. For 10 cats, the above analyses were also performed on oral brushing samples, in order to explore the utility of these methods for screening purposes. Thirty-one FOSCC, 25 chronic inflammatory lesions and 12 controls were included. TP53 mutations were significantly more frequent in the FOSCC (68%) than in the non-neoplastic oral mucosa (3%; P <.001). Based on lasso regression analysis, a step-wise algorithm including TP53, FLI1, MiR124-1, KIF1A and MAGEC2 was proposed. The algorithm allowed to differentiate FOSCC with 94% sensitivity and 100% specificity (accuracy, 97%). When applying the proposed algorithm on 10 brushing samples, accuracy decreased to 80%. These results indicate that the altered DNA methylation of specific genes is present in FOSCC, together with a significant proportion of TP53 mutations. Such alterations are infrequent in normal oral mucosa and chronic stomatitis in cats, suggesting their involvement in feline oral carcinogenesis and their utility as diagnostic biomarkers. Further studies on a high number of brushing samples will be needed to assess the utility of a screening test for the early detection of FOSCC.
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Affiliation(s)
- Andrea Renzi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Luca Morandi
- Department of Biomedical and Neuromotor Sciences, Functional MR Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Jacopo Lenzi
- Department of Biomedical and Neuromotor Sciences, Section of Hygiene, Public Health and Medical Statistics, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Antonella Rigillo
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Giuliano Bettini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Emma Bellei
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Alessandra Giacomini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Debora Tinto
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Silvia Sabattini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
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de Ruijter TC, van der Heide F, Smits KM, Aarts MJ, van Engeland M, Heijnen VCG. Prognostic DNA methylation markers for hormone receptor breast cancer: a systematic review. Breast Cancer Res 2020; 22:13. [PMID: 32005275 PMCID: PMC6993426 DOI: 10.1186/s13058-020-1250-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In patients with hormone receptor-positive breast cancer, differentiating between patients with a low and a high risk of recurrence is an ongoing challenge. In current practice, prognostic clinical parameters are used for risk prediction. DNA methylation markers have been proven to be of additional prognostic value in several cancer types. Numerous prognostic DNA methylation markers for breast cancer have been published in the literature. However, to date, none of these markers are used in clinical practice. METHODS We conducted a systematic review of PubMed and EMBASE to assess the number and level of evidence of published DNA methylation markers for hormone receptor-positive breast cancer. To obtain an overview of the reporting quality of the included studies, all were scored according to the REMARK criteria that were established as reporting guidelines for prognostic biomarker studies. RESULTS A total of 74 studies were identified reporting on 87 different DNA methylation markers. Assessment of the REMARK criteria showed variation in reporting quality of the studies. Eighteen single markers and one marker panel were studied in multiple independent populations. Hypermethylation of the markers RASSF1, BRCA, PITX2, CDH1, RARB, PCDH10 and PGR, and the marker panel GSTP1, RASSF1 and RARB showed a statistically significant correlation with poor disease outcome that was confirmed in at least one other, independent study. CONCLUSION This systematic review provides an overview on published prognostic DNA methylation markers for hormone receptor-positive breast cancer and identifies eight markers that have been independently validated. Analysis of the reporting quality of included studies suggests that future research on this topic would benefit from standardised reporting guidelines.
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Affiliation(s)
- Tim C. de Ruijter
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Frank van der Heide
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M. Smits
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Maureen J. Aarts
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Manon van Engeland
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C. G. Heijnen
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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Lin L, Lin DC. Biological Significance of Tumor Heterogeneity in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2019; 11:cancers11081156. [PMID: 31409002 PMCID: PMC6721624 DOI: 10.3390/cancers11081156] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common and aggressive malignancy, with hitherto dismal clinical outcome. Genomic analyses of patient samples reveal a complex heterogeneous landscape for ESCC, which presents in both intertumor and intratumor forms, manifests at both genomic and epigenomic levels, and contributes significantly to tumor evolution, drug resistance, and metastasis. Here, we review the important molecular characteristics underlying ESCC heterogeneity, with an emphasis on genomic aberrations and their functional contribution to cancer evolutionary trajectories. We further discuss how novel experimental tools, including single-cell sequencing and three-dimensional organoids, may advance our understanding of tumor heterogeneity. Lastly, we suggest that deciphering the mechanisms governing tumor heterogeneity holds the potential to developing precision therapeutics for ESCC patients.
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Affiliation(s)
- Lehang Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen University, Guangzhou 510120, China
| | - De-Chen Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen University, Guangzhou 510120, China.
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Abstract
Changes in DNA methylation in cancer have been heralded as promising targets for the development of powerful diagnostic, prognostic, and predictive biomarkers. Despite the existence of more than 14,000 scientific publications describing DNA methylation-based biomarkers and their clinical associations in cancer, only 14 of these biomarkers have been translated into a commercially available clinical test. Methodological and experimental obstacles are both major causes of this disparity, but the genomic location of a DNA methylation-based biomarker is an intrinsic and essential property that also has an important and often overlooked role. Here, we examine the importance of the location of DNA methylation for the development of cancer biomarkers, and take a detailed look at the genomic location and other relevant characteristics of the various biomarkers with commercially available tests. We also emphasize the value of publicly available databases for the development of DNA methylation-based biomarkers and the importance of accurate reporting of the full methodological details of research findings.
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Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun 2019; 10:2188. [PMID: 31097695 PMCID: PMC6522544 DOI: 10.1038/s41467-019-09937-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 04/09/2019] [Indexed: 02/08/2023] Open
Abstract
Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation. In tumours aberrant epigenetic modifications can alter the transcriptional state. Here, the authors identify a common tumour-specific shift to transcriptional repression associated with DNA methylation and chromatin dysregulation at the transcription start site.
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Ibrahim J, Op de Beeck K, Fransen E, Croes L, Beyens M, Suls A, Vanden Berghe W, Peeters M, Van Camp G. Methylation analysis of Gasdermin E shows great promise as a biomarker for colorectal cancer. Cancer Med 2019; 8:2133-2145. [PMID: 30993897 PMCID: PMC6536921 DOI: 10.1002/cam4.2103] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
In addition to its implication in hereditary hearing loss, the Gasdermin E (GSDME) gene is also a tumor suppressor involved in cancer progression through programmed cell death. GSDME epigenetic silencing through methylation has been shown in some cancer types, but studies are yet to fully explore its diagnostic/prognostic potential in colorectal cancer on a large-scale. We used public data from The Cancer Genome Atlas (TCGA) to investigate differences in GSDME methylation and expression between colorectal cancer and normal colorectal tissue, and between left- and right-sided colorectal cancers in 432 samples. We also explored GSDME's diagnostic capacity as a biomarker for colorectal cancer. We observed differential methylation in all 22 GSDME CpGs between tumor and normal tissues, and in 18 CpGs between the left- and right-sided groups. In the cancer tissue, putative promoter probes were hypermethylated and gene body probes were hypomethylated, while this pattern was inversed in normal tissues. Both putative promoter and gene body CpGs correlated well together but formed distinct methylation patterns with the putative promoter exhibiting the most pronounced methylation differences between tumor and normal tissues. Clinicopathological parameters, excluding age, did not show any effect on CpG methylation. Although the methylation of 5 distinct probes was a good predictor of gene expression, we could not identify an association between GSDME methylation and expression in general. Survival analysis showed no association between GSDME methylation and expression on 5-year patient survival. Through logistic regression, we identified a combination of 2 CpGs, that can discriminate between cancer and normal tissue with high accuracy (AUC = 0.95) irrespective of age and tumor stage. We also validated our model in 3 external methylation datasets, from the Gene Expression Omnibus database, and similar results were reached. Our results suggest that GSDME is a promising biomarker for the detection of colorectal cancer.
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Affiliation(s)
- Joe Ibrahim
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Ken Op de Beeck
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Erik Fransen
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- StatUa Centre for StatisticsUniversity of AntwerpAntwerpBelgium
| | - Lieselot Croes
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Matthias Beyens
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Arvid Suls
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling, Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Marc Peeters
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Department of Medical OncologyAntwerp University HospitalEdegemBelgium
| | - Guy Van Camp
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
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Roy R, Chatterjee A, Das D, Ray A, Singh R, Chattopadhyay E, Sarkar ND, Eccles M, Pal M, Maitra A, Roy B. Genome-wide miRNA methylome analysis in oral cancer: possible biomarkers associated with patient survival. Epigenomics 2019; 11:473-487. [PMID: 30875235 DOI: 10.2217/epi-2018-0078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM The methylome associated with miRNA loci was investigated in oral cancer to explore tobacco specific methylation and potential biomarkers for patient survival. METHODS Methylome data was generated from 16 pairs of cancer-normal tissues by reduced representation bisulfite sequencing method. Differentially methylated regions were identified using the DMAP pipeline. In silico validation and Kaplan-Meier survival analyses were performed on The Cancer Genome Atlas data based on our miRNA methylome data. RESULTS A total of 4310 unique differentially methylated regions, mapping to 144 miRNA loci, were identified. Three distinct groups of miRNAs were differentially methylated in cancer tissues from smokers, chewers and mixed habitués. Hypermethylation of miR-503, miR-200a/b, miR-320b and miR-489 was associated with worse 5-year survival. CONCLUSION Differential methylation patterns in miRNA loci are associated with poor survival underscoring their potential as predictive and prognostic biomarkers in oral cancer.
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Affiliation(s)
- Roshni Roy
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Aniruddha Chatterjee
- HB Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109-1024, USA
| | - Debasis Das
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Anindita Ray
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Richa Singh
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Esita Chattopadhyay
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
| | - Navonil De Sarkar
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand.,Department of Oral & Maxillofacial Pathology, Guru Nanak Institute of Dental Science & Research, Kolkata, India
| | - Michael Eccles
- HB Division, Fred Hutchinson Cancer Research Centre, Seattle, WA 98109-1024, USA
| | - Mousumi Pal
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Arindam Maitra
- Human Genetics Unit, Indian Statistical Institute, 205 B.T. Road, Kolkata 700108, India
| | - Bidyut Roy
- Department of Pathology, Division of Health Science, University of Otago, Dunedin, Otago, MD 20892, New Zealand
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Priesterbach-Ackley LP, Wesseling P, Snijders TJ, de Vos FYFL, de Leng WWJ. Molecular tools for the pathologic diagnosis of central nervous system tumors. Neurooncol Pract 2019; 6:4-16. [PMID: 31386041 PMCID: PMC6656323 DOI: 10.1093/nop/npy041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Molecular diagnostics currently has a crucial role in neuro-oncological patient care. (Epi)genetic assays testing for point mutations, copy number variations, gene fusions, translocations, and methylation status are of main diagnostic interest in neuro-oncology. Multiple assays have been developed for this purpose, ranging from single gene tests to high-throughput, integrated techniques enabling detection of multiple genetic aberrations in a single workflow. This review describes the nature of the simpler and more complex assays for molecular diagnostics of tumors of the central nervous system and briefly discusses their strengths and weaknesses.
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Affiliation(s)
| | - Pieter Wesseling
- Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, The Netherlands
- Department of Pathology, VU University Medical Center/Brain Tumor Center Amsterdam, The Netherlands
| | - Tom J Snijders
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, The Netherlands
| | - Filip Y F L de Vos
- Department of Medical Oncology, University Medical Center Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, The Netherlands
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Ashktorab H, Rahi H, Nouraie M, Shokrani B, Lee E, Haydari T, Laiyemo AO, Siegel P, Brim H. GPNMB methylation: a new marker of potentially carcinogenic colon lesions. BMC Cancer 2018; 18:1068. [PMID: 30400781 PMCID: PMC6219212 DOI: 10.1186/s12885-018-4903-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 10/04/2018] [Indexed: 01/09/2023] Open
Abstract
Background Epigenetic plays an important role in colorectal neoplasia process. There is a need to determine sound biomarkers of colorectal cancer (CRC) progression with clinical and therapeutic implications. Therefore, we aimed to examine the role and methylation status of Glyco Protein Non-Metastatic GPNM B (GPNMB) gene in normal, adenoma and CRC in African American (AA) patients. Methods The methylation status of 13 CpG sites (chr7: 23287345–23,287,426) in GPNMB gene’s promoter, was analyzed by pyrosequencing in human CRC cell lines (HCT116, SW480, and HT29) and microdissected African American paraffin embedded samples (20 normal, 21 non-advanced adenoma (NA), 48 advanced adenoma (AD), and 20 cancer tissues. GPNMB expression was analyzed by immunohistochemistry (IHC) on tissue microarrays (TMA). Correlations between GPNMB methylation and expression with clinicopathological features were analyzed. GPNMB functional analysis was performed in triplicates using cell proliferation, migration and invasion assays in HCT116 colon cell line after stable transfection with a GPNMB-cDNA expression vector. Results GPNMB methylation was lower in normal mucosa compared to CRC samples (1/20 [5%] vs. 18/20 [90%]; P < 0.001). AD also had a significantly higher GPNMB methylation frequency than normal colon samples (42/48 [88%] vs 1/20 [5%]; P < 0.001). GPNMB was more frequently methylated in AD than in matched normal mucosa from three patients (3/3 [100%] vs 1/3 [33.3%]; P < 0.001). The frequency of GPNMB methylation in NA differed significantly from that in the normal mucosa (16/21 [76%] vs 1/20 [5%]; P = 0.008). There was statistically significant correlation of higher methylation at advanced stages and lower methylation at stage 1 CRCs (P < 0.05). In agreement with these findings, GPNMB protein expression decreased in CRC tissues compared with AD and NA colon mucosa (p < 0.05). GPNMB overexpression in HCT116 colon cancer cell line decreased cell proliferation [(24 h, P = 0.02), (48 h, P < 0.001, 72 h, P = 0.007)], invasion (p < 0.05) and migration (p > 0.05) compared to the mock-transfected cells. Conclusion Our data indicate a high methylation profile leading to a lower GPNMB expression in adenoma and CRC samples. The functional analysis established GPNMB as a potential tumor suppressor gene. As such, GPNMB might be useful as a biomarker of adenomas with high carcinogenic potential.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA.
| | - Hamed Rahi
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Babak Shokrani
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Edward Lee
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Tahmineh Haydari
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Adeyinka O Laiyemo
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
| | - Peter Siegel
- Goodman Cancer Research Centre, Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Hassan Brim
- Department of Medicine, Department of Pathology and Cancer Center, Howard University College of Medicine, 2041 Georgia Avenue, N.W, Washington, D.C, 20060, USA
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Zhou Y, Li Z, Ding Y, Zhang P, Wang J, Zhang J, Wang H. Promoter methylation of WNT inhibitory factor-1 may be associated with the pathogenesis of multiple human tumors. J Cancer Res Ther 2018; 14:S381-S387. [PMID: 29970693 DOI: 10.4103/0973-1482.235357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Aim We investigated the association of WNT inhibitory factor-1 (WIF-1) gene methylation with the pathogenesis of multiple human tumors, using a meta-analysis based approach. Materials and Methods Electronic databases and manual search was additionally employed to retrieve relevant published literature. The cohort studies relating to tumor and WIF-1 were screened based on predefined selection criteria, and all extracted data from the selected studies were analyzed through STATA software. Results Sixteen studies were finally enrolled in our study involved 1112 tumor samples and 612 adjacent normal samples. The study result showed that WIF-1 gene methylations in tumor tissues were significantly higher compared with adjacent/normal tissues. The result of subgroup analysis on ethnicity revealed that in the Caucasians, Asians, and Africans, the methylation status of WIF-1 gene in tumor tissues was higher than adjacent/normal tissues. Further subgroup analysis on disease types revealed that WIF-1 gene methylation status is a widespread phenomenon that is, observed in tumor tissues of patients with multiple human tumors compared with that in adjacent/normal tissues. Interestingly, there was no significant difference in WIF-1 gene methylation between tumor tissues among patients with lung cancer, gastric cancer, astrocytoma, and adjacent/normal tissues, indicating the WIF-1 gene methylation not a general nonspecific phenomenon. Conclusion WIF-1 gene methylation in tumor tissues was significantly more frequent as compared to that in adjacent normal tissues, indicating that WIF-1 gene methylation may be an important event in the pathogenesis of multiple human tumors.
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Affiliation(s)
- Yong Zhou
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Zhaohua Li
- Department of Medical Imaging, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Yinlu Ding
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Peng Zhang
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Jinqing Wang
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Jianliang Zhang
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
| | - Hao Wang
- Department of General Surgery, The Second Hospital of Shandong University, Jinan 250033, P. R. China
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El Sherbini MA, Mansour AA, Sallam MM, Shaban EA, Shehab ElDin ZA, El-Shalakany AH. KLK10 exon 3 unmethylated PCR product concentration: a new potential early diagnostic marker in ovarian cancer? - A pilot study. J Ovarian Res 2018; 11:32. [PMID: 29690914 PMCID: PMC5913797 DOI: 10.1186/s13048-018-0407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND KLK10 exon 3 hypermethylation correlated to tumor-specific lack of KLK10 expression in cancer cell lines and primary tumors. In the present study we investigate the possible role of KLK10 exon 3 methylation in ovarian tumor diagnosis and prognosis. RESULTS Qualitative methylation-specific PCR (MSP) results did not show statistically significant differences in patient group samples (normal and tumor) where all samples were positive only for the unmethylated-specific PCR except for two malignant samples that were either doubly positive (serous carcinoma) or doubly negative (Sertoli-Leydig cell tumor) for the two MSP tests. However, KLK10 exon 3 unmethylated PCR product concentration (ng/μl) showed statistically significant differences in benign and malignant patient group samples; mean ± SD (n): tumor: 0.077 ± 0.035 (14) and 0.047 ± 0.021 (15), respectively, p-value = 0.011; and normal: 0.094 ± 0.039 (7) and 0.046 ± 0.027 (6), respectively, p-value = 0.031. Moreover, ROC curve analysis of KLK10 exon 3 unmethylated PCR product concentration in overall patient group samples showed good diagnostic ability (AUC = 0.778; p-value = 0.002). Patient survival (living and died) showed statistically significant difference according to preoperative serum CA125 concentration (U/ml); median (n): 101.25 (10) and 1252 (5), respectively, p-value = 0.037, but not KLK10 exon 3 unmethylated PCR product concentration (ng/μl) in overall malignant patient samples; mean ± SD (n): 0.042 ± 0.015 (14) and 0.055 ± 0.032 (7), p-value = 0.228. CONCLUSION To the best of our knowledge, this is the first report on KLK10 exon 3 unmethylated PCR product concentration as potential early epigenetic diagnostic marker in primary ovarian tumors. Taken into account the limitations in our study (small sample size and semi-quantitative PCR product analysis) further studies are strongly recommended.
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Affiliation(s)
- Mustafa A El Sherbini
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Amal A Mansour
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Maha M Sallam
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Emtiaz A Shaban
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Amr H El-Shalakany
- Gynecologic Oncology Unit, Ain Shams University Maternity Hospital, Cairo, Egypt
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40
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Wei J, Li G, Zhang J, Zhou Y, Dang S, Chen H, Wu Q, Liu M. Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer. Oncotarget 2018; 7:62547-62558. [PMID: 27566576 PMCID: PMC5308745 DOI: 10.18632/oncotarget.11534] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
DNA methylation was regarded as the promising biomarker for rectal cancer diagnosis. However, the optimal methylation biomarkers with ideal diagnostic performance for rectal cancer are still limited. To identify new molecular markers for rectal cancer, we mapped DNA methylation and transcriptomic profiles in the six rectal cancer and paired normal samples. Further analysis revealed the hypermethylated probes in cancer prone to be located in gene promoter. Meanwhile, transcriptome analysis presented 773 low-expressed and 1,161 over-expressed genes in rectal cancer. Correction analysis identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels, including 10 known colorectal cancer related genes. From the other 26 novel marker genes, GFRA1 and GSTM2 were selected for further analysis on the basis of their biological functions. Further experiment analysis confirmed their methylation and expression status in a larger number (44) of rectal cancer samples, and ROC curves showed higher AUC than SEPT9, which has been used as a biomarker in rectal cancer. Our data suggests that aberrant DNA methylation of contiguous CpG sites in methylation array may be potential diagnostic markers of rectal cancer.
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Affiliation(s)
- Jiufeng Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Jinning Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Yuhui Zhou
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Shuwei Dang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, P.R. China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
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Prognostic DNA methylation markers for sporadic colorectal cancer: a systematic review. Clin Epigenetics 2018; 10:35. [PMID: 29564023 PMCID: PMC5851322 DOI: 10.1186/s13148-018-0461-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Background Biomarkers that can predict the prognosis of colorectal cancer (CRC) patients and that can stratify high-risk early stage patients from low-risk early stage patients are urgently needed for better management of CRC. During the last decades, a large variety of prognostic DNA methylation markers has been published in the literature. However, to date, none of these markers are used in clinical practice. Methods To obtain an overview of the number of published prognostic methylation markers for CRC, the number of markers that was validated independently, and the current level of evidence (LoE), we conducted a systematic review of PubMed, EMBASE, and MEDLINE. In addition, we scored studies based on the REMARK guidelines that were established in order to attain more transparency and complete reporting of prognostic biomarker studies. Eighty-three studies reporting on 123 methylation markers fulfilled the study entry criteria and were scored according to REMARK. Results Sixty-three studies investigated single methylation markers, whereas 20 studies reported combinations of methylation markers. We observed substantial variation regarding the reporting of sample sizes and patient characteristics, statistical analyses, and methodology. The median (range) REMARK score for the studies was 10.7 points (4.5 to 17.5) out of a maximum of 20 possible points. The median REMARK score was lower in studies, which reported a p value below 0.05 versus those, which did not (p = 0.005). A borderline statistically significant association was observed between the reported p value of the survival analysis and the size of the study population (p = 0.051). Only 23 out of 123 markers (17%) were investigated in two or more study series. For 12 markers, and two multimarker panels, consistent results were reported in two or more study series. For four markers, the current LoE is level II, for all other markers, the LoE is lower. Conclusion This systematic review reflects that adequate reporting according to REMARK and validation of prognostic methylation markers is absent in the majority of CRC methylation marker studies. However, this systematic review provides a comprehensive overview of published prognostic methylation markers for CRC and highlights the most promising markers that have been published in the last two decades. Electronic supplementary material The online version of this article (10.1186/s13148-018-0461-8) contains supplementary material, which is available to authorized users.
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Moraes L, Galrão ALR, Rubió I, Cerutti JM. Transcriptional regulation of the potential tumor suppressor ABI3 gene in thyroid carcinomas: interplay between methylation and NKX2-1 availability. Oncotarget 2018; 7:25960-70. [PMID: 27036019 PMCID: PMC5041957 DOI: 10.18632/oncotarget.8416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/12/2016] [Indexed: 12/05/2022] Open
Abstract
We previously reported that ABI3 expression was decreased in thyroid cancer tissues and that ectopic expression of ABI3 in a follicular thyroid carcinoma cell line delayed cell cycle progression and inhibited cell proliferation, invasion, migration and tumor formation in athymic mice. These data indicated that ABI3 is a tumor suppressor gene; however the mechanism through which ABI3 is silenced in thyroid carcinomas is unknown. We here show that treatment of four follicular thyroid carcinoma cell lines with 5-aza-dC induced demethylation of a specific region of the ABI3 promoter and restored ABI3 expression. In contrast, 5-aza-dC treatment did not restore ABI3 expression in a non-thyroid cell line, suggesting a tissue-specific regulation. We additionally show that 8 CpG sites located within the ABI3 promoter are hypermethylated in most thyroid carcinoma samples and the degree of methylation correlated with ABI3 expression. Narrowing the region to specific CpG sites, the CpG4-6 sites showed the largest difference between benign and malignant lesions. In silico analysis revealed that these CpG sites flank a canonical binding site for NKX2-1, a thyroid specific transcriptional factor. Analysis of thyroid samples shows a correlation between NKX2-1 and ABI3 expression. In vitro assays demonstrate that NKX2-1 was required for ABI3 expression. Luciferase assay further confirmed the promoter activity of this region, which was increased when the cells were co-transfected with NKX2-1. Our study shows that the transcriptional silencing of ABI3 in cancer cells occurs via methylation and uncovered a previously unrecognized role for NKX2-1 in the regulation of ABI3.
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Affiliation(s)
- Lais Moraes
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
| | - Ana Luiza R Galrão
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
| | - Ileana Rubió
- Department of Biological Sciences, Universidade Federal de São Paulo, SP, Brazil
| | - Janete M Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, SP, Brazil
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43
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Long HK, Rose NR, Blackledge NP, Klose RJ. Biochemical Identification of Nonmethylated DNA by BioCAP-Seq. Methods Mol Biol 2018; 1766:15-29. [PMID: 29605845 DOI: 10.1007/978-1-4939-7768-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
CpG islands are regions of vertebrate genomes that often function as gene regulatory elements and are associated with most gene promoters. CpG island elements usually contain nonmethylated CpG dinucleotides, while the remainder of the genome is pervasively methylated. We developed a biochemical approach called biotinylated CxxC affinity purification (BioCAP) to unbiasedly isolate regions of the genome that contain nonmethylated CpG dinucleotides. The resulting highly pure nonmethylated DNA is easily analyzed by quantitative PCR to interrogate specific loci or via massively parallel sequencing to yield genome-wide profiles.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nathan R Rose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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44
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Sun Y, Sun Y, Tian W, Liu C, Gao K, Li Z. A novel restriction endonuclease GlaI for rapid and highly sensitive detection of DNA methylation coupled with isothermal exponential amplification reaction. Chem Sci 2017; 9:1344-1351. [PMID: 29675182 PMCID: PMC5887237 DOI: 10.1039/c7sc04975g] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/09/2017] [Indexed: 12/22/2022] Open
Abstract
Sensitive and accurate detection of site-specific DNA methylation is of critical significance for early diagnosis of human diseases, especially cancers. Herein, for the first time we employ a novel methylation-dependent restriction endonuclease GlaI to detect site-specific DNA methylation in a highly specific and sensitive way by coupling with isothermal exponential amplification reaction (EXPAR). GlaI can only cut the methylated target site with excellent selectivity but leave the unmethylated DNA intact. Then the newly exposed end fragments of methylated DNA can trigger EXPAR for highly efficient signal amplification while the intact unmethylated DNA will not initiate EXPAR at all. As such, only the methylated DNA is quantitatively and faithfully reflected by the real-time fluorescence signal of the GlaI-EXPAR system, and the potential false positive interference from unmethylated DNA can be effectively eliminated. Therefore, by integrating the unique features of GlaI for highly specific methylation discrimination and EXPAR for rapid and powerful signal amplification, the elegant GlaI-EXPAR assay allows the direct quantification of methylated DNA with ultrahigh sensitivity and accuracy. The detection limit of methylated DNA target has been pushed down to the aM level and the whole detection process of GlaI-EXPAR can be accomplished within a short time of 2 h. More importantly, ultrahigh specificity is achieved and as low as 0.01% methylated DNA can be clearly identified in the presence of a large excess of unmethylated DNA. This GlaI-EXPAR is also demonstrated to be capable of determining site-specific DNA methylations in real genomic DNA samples. Sharing the distinct advantages of ultrahigh sensitivity, outstanding specificity and facile operation, this new GlaI-EXPAR strategy may provide a robust and reliable platform for the detection of site-specific DNA methylations with low abundances.
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Affiliation(s)
- Yueying Sun
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Yuanyuan Sun
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Weimin Tian
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Kejian Gao
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
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Karpinski P, Pesz K, Sasiadek MM. Pan-cancer analysis reveals presence of pronounced DNA methylation drift in CpG island methylator phenotype clusters. Epigenomics 2017; 9:1341-1352. [PMID: 28960094 DOI: 10.2217/epi-2017-0070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences. Pronounced epigenetic drift observed in majority of CIMP-H subgroups may be related to increased cell division rate, which leads to expansion of DNA methylation errors. This may explain pan-cancer mechanism of establishing CIMP-H in majority of tissue types.
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Affiliation(s)
- Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Karolina Pesz
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
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Morandi L, Gissi D, Tarsitano A, Asioli S, Gabusi A, Marchetti C, Montebugnoli L, Foschini MP. CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel. Clin Epigenetics 2017; 9:85. [PMID: 28814981 PMCID: PMC5558660 DOI: 10.1186/s13148-017-0386-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/07/2017] [Indexed: 02/08/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is usually diagnosed at an advanced stage and is commonly preceded by oral premalignant lesions. The mortality rates have remained unchanged (50% within 5 years after diagnosis), and it is related to tobacco smoking and alcohol intake. Novel molecular markers for early diagnosis are urgently needed. The purpose of this study was to evaluate the diagnostic value of methylation level in a set of 18 genes by bisulfite next-generation sequencing. Methods With minimally invasive oral brushing, 28 consecutive OSCC, one squamous cell carcinoma with sarcomatoid features, six high-grade squamous intraepithelial lesions (HGSIL), 30 normal contralateral mucosa from the same patients, and 65 healthy donors were evaluated for DNA methylation analyzing 18 target genes by quantitative bisulfite next-generation sequencing. We further evaluated an independent cohort (validation dataset) made of 20 normal donors, one oral fibroma, 14 oral lichen planus (OLP), three proliferative verrucous leukoplakia (PVL), and two OSCC. Results Comparing OSCC with normal healthy donors and contralateral mucosa in 355 CpGs, we identified the following epigenetically altered genes: ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MIR193, LINC00599, PAX1, and MIR137HG showing hypermethylation and MIR296, TERT, and GP1BB showing hypomethylation. The behavior of ZAP70, GP1BB, H19, EPHX3, and MIR193 fluctuated among different interrogated CpGs. The gap between normal and OSCC samples remained mostly the same (Kruskal-Wallis P values < 0.05), but the absolute values changed conspicuously. ROC curve analysis identified the most informative CpGs, and we correctly stratified OSCC and HGSIL from normal donors using a multiclass linear discriminant analysis in a 13-gene panel (AUC 0.981). Only the OSCC with sarcomatoid features was negative. Three contralateral mucosa were positive, a sign of a possible field cancerization. Among imprinted genes, only MIR296 showed loss of imprinting. DNMT1, TERC, and H19 together with the global methylation of long interspersed element 1 were unchanged. In the validation dataset, values over the threshold were detected in 2/2 OSCC, in 3/3 PVL, and in 2/14 OLP. Conclusions Our data highlight the importance of CpG location and correct estimation of DNA methylation level for highly accurate early diagnosis of OSCC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0386-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luca Morandi
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Davide Gissi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Sofia Asioli
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Andrea Gabusi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Claudio Marchetti
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Lucio Montebugnoli
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Maria Pia Foschini
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
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Joosten SC, Deckers IA, Aarts MJ, Hoeben A, van Roermund JG, Smits KM, Melotte V, van Engeland M, Tjan-Heijnen VC. Prognostic DNA methylation markers for renal cell carcinoma: a systematic review. Epigenomics 2017; 9:1243-1257. [PMID: 28803494 DOI: 10.2217/epi-2017-0040] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM Despite numerous published prognostic methylation markers for renal cell carcinoma (RCC), none of these have yet changed patient management. Our aim is to systematically review and evaluate the literature on prognostic DNA methylation markers for RCC. MATERIALS & METHODS We conducted an exhaustive search of PubMed, EMBASE and MEDLINE up to April 2017 and identified 49 publications. Studies were reviewed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, assessed for their reporting quality using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criteria, and were graded to determine the level of evidence (LOE) for each biomarker. RESULTS We identified promoter methylation of BNC1, SCUBE3, GATA5, SFRP1, GREM1, RASSF1A, PCDH8, LAD1 and NEFH as promising prognostic markers. Extensive methodological heterogeneity across the included studies was observed, which hampers comparability and reproducibility of results, providing a possible explanation why these biomarkers do not reach the clinic. CONCLUSION Potential prognostic methylation markers for RCC have been identified, but they require further validation in prospective studies to determine their true clinical value.
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Affiliation(s)
- Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ivette Ag Deckers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Joep G van Roermund
- Department of Urology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M Smits
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands.,Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C Tjan-Heijnen
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
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Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD. Targeted DNA methylation in human cells using engineered dCas9-methyltransferases. Sci Rep 2017; 7:6732. [PMID: 28751638 PMCID: PMC5532369 DOI: 10.1038/s41598-017-06757-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Mammalian genomes exhibit complex patterns of gene expression regulated, in part, by DNA methylation. The advent of engineered DNA methyltransferases (MTases) to target DNA methylation to specific sites in the genome will accelerate many areas of biological research. However, targeted MTases require clear design rules to direct site-specific DNA methylation and minimize the unintended effects of off-target DNA methylation. Here we report a targeted MTase composed of an artificially split CpG MTase (sMTase) with one fragment fused to a catalytically-inactive Cas9 (dCas9) that directs the functional assembly of sMTase fragments at the targeted CpG site. We precisely map RNA-programmed DNA methylation to targeted CpG sites as a function of distance and orientation from the protospacer adjacent motif (PAM). Expression of the dCas9-sMTase in mammalian cells led to predictable and efficient (up to ~70%) DNA methylation at targeted sites. Multiplexing sgRNAs enabled targeting methylation to multiple sites in a single promoter and to multiple sites in multiple promoters. This programmable de novo MTase tool might be used for studying mechanisms of initiation, spreading and inheritance of DNA methylation, and for therapeutic gene silencing.
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Affiliation(s)
- Tina Xiong
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Glenna E Meister
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nathaniel C Kato
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael J Spellberg
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA
| | - Fulya Turker
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA
- Boston University, Boston, MA, 02215, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Carl D Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA.
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Lind GE, van Engeland M. Details matter: the role of genomic location and assay standardization in DNA methylation analyses. Epigenomics 2017; 9:933-935. [PMID: 28617096 DOI: 10.2217/epi-2017-0053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research & Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Manon van Engeland
- Department of Pathology, GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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50
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Bartosch C, Lopes JM, Jerónimo C. Epigenetics in endometrial carcinogenesis - part 1: DNA methylation. Epigenomics 2017; 9:737-755. [PMID: 28470096 DOI: 10.2217/epi-2016-0166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. The present review is the first part of this work, in which we examined the contribution of DNA methylation alterations for endometrial carcinogenesis.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - José Manuel Lopes
- Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Department of Pathology, Centro Hospitalar São João (CHSJ), Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology & Immunology, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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