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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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2
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Wu Y, Ren L, Tang Y, Zhu Z, Liu S, Jiang Y, Zhang S, Zhuang X, Chen Y. Immunobiological signatures and the emerging role of SPP1 in predicting tumor heterogeneity, malignancy, and clinical outcomes in stomach adenocarcinoma. Aging (Albany NY) 2023; 15:11588-11610. [PMID: 37889539 PMCID: PMC10637809 DOI: 10.18632/aging.205148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Immunotherapy, as a form of immunobiological therapy, represents a promising approach for enhancing patients' immune responses. This work aims to present innovative ideas and insights for prognostic assessment and clinical treatment of stomach adenocarcinoma (STAD) by leveraging immunobiological signatures. METHODS We employed weighted gene co-expression network analysis (WGCNA) and unsupervised clustering analysis to identify hub genes. These hub genes were utilized to construct a prognostic risk model, and their impact on the tumor microenvironment (TME) and DNA variations was assessed using large-scale STAD patient cohorts. Additionally, we conducted transfection experiments with plasmids to investigate the influence of SPP1 on the malignancy of HGC27 and NCI-N87 cells. RESULTS Unsupervised clustering of 12 immune-related genes (IRGs) revealed three distinct alteration patterns with unique molecular phenotypes, clinicopathological characteristics, prognosis, and TME features. Using LASSO and multivariate Cox regression analyses, we identified three hub genes (MMP12, SPP1, PLAU) from the IRGs to establish a risk signature. This IRG-related risk model significantly stratified the prognosis risk among STAD patients in the training (n = 522), testing (n = 521), and validation (n = 300) cohorts. Notably, there were discernible differences in therapy responses and TME characteristics, such as tumor purity and lymphocyte infiltration, between the risk model groups. Subsequently, a nomogram that incorporates the IRG signature and clinicopathological factors demonstrated superior sensitivity and specificity in predicting outcomes for STAD patients. Furthermore, down-regulation of SPP1, as observed after siRNA transfection, significantly inhibited the proliferation and migration abilities of HGC27 and NCI-N87 cells. CONCLUSIONS In summary, this study highlights the critical role of immune-related signatures in STAD and offers novel insights into prognosis indicators and immunotherapeutic targets for this condition. SPP1 emerges as an independent prognostic factor for STAD and appears to regulate STAD progression by influencing the immune microenvironment.
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Affiliation(s)
- Yanan Wu
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Lingyu Ren
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Yichun Tang
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Zhu Zhu
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Shifan Liu
- Department of Medical Imaging, Medical School of Nantong University, Nantong, China
| | - Yan Jiang
- Department of Engineering Training Center, Nantong University, Nantong, China
| | - Siming Zhang
- Cancer Research Center Nantong, Nantong Tumor Hospital and Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Xiaocan Zhuang
- Department of Gastroenterology, Rudong People’s Hospital, Rudong Hospital Affiliated to Nantong University, Nantong, China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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3
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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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4
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Larsen M, He F, Kawasawa YI, Berg A, Vgontzas AN, Liao D, Bixler EO, Fernandez-Mendoza J. Objective and subjective measures of sleep initiation are differentially associated with DNA methylation in adolescents. Clin Epigenetics 2023; 15:136. [PMID: 37634000 PMCID: PMC10464279 DOI: 10.1186/s13148-023-01553-2] [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] [Received: 01/19/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
INTRODUCTION The onset of puberty is associated with a shift in the circadian timing of sleep, leading to delayed sleep initiation [i.e., later sleep onset time (SOT)] due to later bedtimes and/or longer sleep onset latency (SOL). Several genome-wide association studies (GWAS) have identified genes that may be involved in the etiology of sleep phenotypes. However, circadian rhythms are also epigenetically regulated; therefore, epigenetic biomarkers may provide insight into the physiology of the pubertal sleep onset shift and the pathophysiology of prolonged or delayed sleep initiation. RESULTS The gene-wide analysis indicated differential methylation within or around 1818 unique genes across the sleep initiation measurements using self-report, actigraphy (ACT), and polysomnography (PSG), while GWAS-informed analysis yielded 67 genes. Gene hits were identified for bedtime (PSG), SOL (subjective, ACT and PSG) and SOT (subjective and PSG). DNA methylation within 12 genes was associated with both subjective and PSG-measured SOL, 31 with both ACT- and PSG-measured SOL, 19 with both subjective and ACT-measured SOL, and one gene (SMG1P2) had methylation sites associated with subjective, ACT- and PSG-measured SOL. CONCLUSIONS Objective and subjective sleep initiation in adolescents is associated with altered DNA methylation in genes previously identified in adult GWAS of sleep and circadian phenotypes. Additionally, our data provide evidence for a potential epigenetic link between habitual (subjective and ACT) SOL and in-lab SOT and DNA methylation in and around genes involved in circadian regulation (i.e., RASD1, RAI1), cardiometabolic disorders (i.e., FADS1, WNK1, SLC5A6), and neuropsychiatric disorders (i.e., PRR7, SDK1, FAM172A). If validated, these sites may provide valuable targets for early detection and prevention of disorders involving prolonged or delayed SOT, such as insomnia, delayed sleep phase, and their comorbidity.
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Affiliation(s)
- Michael Larsen
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Fan He
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yuka Imamura Kawasawa
- Departments of Biochemistry and Molecular Biology and Pharmacology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Arthur Berg
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Alexandros N Vgontzas
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Duanping Liao
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Edward O Bixler
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Julio Fernandez-Mendoza
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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Wang M, Li Q, Liu L. Factors and Methods for the Detection of Gene Expression Regulation. Biomolecules 2023; 13:biom13020304. [PMID: 36830673 PMCID: PMC9953580 DOI: 10.3390/biom13020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Gene-expression regulation involves multiple processes and a range of regulatory factors. In this review, we describe the key factors that regulate gene expression, including transcription factors (TFs), chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. In addition, we also describe methods that can be used to detect these regulatory factors.
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6
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Martin EM, Grimm SA, Xu Z, Taylor JA, Wade PA. Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing. Epigenomics 2023; 15:115-129. [PMID: 37020391 PMCID: PMC10131490 DOI: 10.2217/epi-2023-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.
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Affiliation(s)
- Elizabeth M Martin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Sara A Grimm
- Integrative Bioinformatics, Biostatistics & Computational Biology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Jack A Taylor
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Paul A Wade
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
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7
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Durmus S, Gelisgen R, Uzun H. DNA Methylation Biomarkers in Cancer: Current Clinical Utility and Future Perspectives. Biomark Med 2022. [DOI: 10.2174/9789815040463122010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Epigenetic alterations are related to inherited but reversible changes in
modifications that regulate gene activity beyond the DNA sequence. DNA methylation
is the best characterized epigenetic modification, controlling DNA stability, DNA
structure, transcription, and regulation, contributing to normal development and
differentiation. In this section, we first discuss the cellular functions of DNA
methylation and focus on how this fundamental biological process is impaired in
cancer. Changes in DNA methylation status in cancer have been heralded as promising
targets for the development of diagnostic, prognostic, and predictive biomarkers due to
their noninvasive accessibility in bodily fluids (such as blood, urine, stool),
reversibility, stability, and frequency. The absence of markers for definitive diagnosis
of most types of cancer and, in some cases, DNA methylation biomarkers being more
specific and sensitive than commonly used protein biomarkers indicate a strong need
for continued research to expand DNA methylation markers. Although the information
on changes in DNA methylation status in cancer and research on its clinical relevance
is rapidly increasing, the number of DNA methylation biomarkers currently available
as commercial tests is very small. Here, we focus on the importance of DNA
methylation location and target genes likely to be developed in the future for the
development of biomarkers in addition to existing commercial tests. Following a
detailed study of possible target genes, we summarize the current clinical application
status of the most studied and validated DNA methylation biomarkers, including
SEPT9, SDC2, BMP3, NDRG4, SFRP2, TFPI2, VIM and MGMT.
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Affiliation(s)
- Sinem Durmus
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Remise Gelisgen
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Hafize Uzun
- Department of Biochemistry, Faculty of Medicine, Istanbul Atlas University, Istanbul,Turkey
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8
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Berger TC, Taubøll E, Heuser K. The potential role of DNA methylation as preventive treatment target of epileptogenesis. Front Cell Neurosci 2022; 16:931356. [PMID: 35936496 PMCID: PMC9353008 DOI: 10.3389/fncel.2022.931356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacological therapy of epilepsy has so far been limited to symptomatic treatment aimed at neuronal targets, with the result of an unchanged high proportion of patients lacking seizure control. The dissection of the intricate pathological mechanisms that transform normal brain matter to a focus for epileptic seizures—the process of epileptogenesis—could yield targets for novel treatment strategies preventing the development or progression of epilepsy. While many pathological features of epileptogenesis have been identified, obvious shortcomings in drug development are now believed to be based on the lack of knowledge of molecular upstream mechanisms, such as DNA methylation (DNAm), and as well as a failure to recognize glial cell involvement in epileptogenesis. This article highlights the potential role of DNAm and related gene expression (GE) as a treatment target in epileptogenesis.
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Affiliation(s)
- Toni Christoph Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Toni Christoph Berger
| | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Kjell Heuser
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9
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Guimarães JR, Coêlho MDC, de Oliveira NFP. Contribution of DNA methylation to the pathogenesis of Sjögren's syndrome: A review. Autoimmunity 2022; 55:215-222. [DOI: 10.1080/08916934.2022.2062593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juliana Ramalho Guimarães
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Marina de Castro Coêlho
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Naila Francis Paulo de Oliveira
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
- Molecular Biology Department, Centre of Exact and Natural Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
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10
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Mendaza S, Guerrero-Setas D, Monreal-Santesteban I, Ulazia-Garmendia A, Cordoba Iturriagagoitia A, De la Cruz S, Martín-Sánchez E. A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis. Biomedicines 2021; 9:1394. [PMID: 34680511 PMCID: PMC8533184 DOI: 10.3390/biomedicines9101394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer (BC) subtype and lacks targeted treatment. It is diagnosed by the absence of immunohistochemical expression of several biomarkers, but this method still displays some interlaboratory variability. DNA methylome aberrations are common in BC, thereby methylation profiling could provide the identification of accurate TNBC diagnosis biomarkers. Here, we generated a signature of differentially methylated probes with class prediction ability between 5 non-neoplastic breast and 7 TNBC tissues (error rate = 0.083). The robustness of this signature was corroborated in larger cohorts of additional 58 non-neoplastic breast, 93 TNBC, and 150 BC samples from the Gene Expression Omnibus repository, where it yielded an error rate of 0.006. Furthermore, we validated by pyrosequencing the hypomethylation of three out of 34 selected probes (FLJ43663, PBX Homeobox 1 (PBX1), and RAS P21 protein activator 3 (RASA3) in 51 TNBC, even at early stages of the disease. Finally, we found significantly lower methylation levels of FLJ43663 in cell free-DNA from the plasma of six TNBC patients than in 15 healthy donors. In conclusion, we report a novel DNA methylation signature with potential predictive value for TNBC diagnosis.
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Affiliation(s)
- Saioa Mendaza
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (D.G.-S.); (I.M.-S.); (A.U.-G.)
| | - David Guerrero-Setas
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (D.G.-S.); (I.M.-S.); (A.U.-G.)
- Department of Pathology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain;
| | - Iñaki Monreal-Santesteban
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (D.G.-S.); (I.M.-S.); (A.U.-G.)
| | - Ane Ulazia-Garmendia
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (D.G.-S.); (I.M.-S.); (A.U.-G.)
| | | | - Susana De la Cruz
- Department of Medical Oncology, Complejo Hospitalario de Navarra (CHN), Irunlarrea 3, 31008 Pamplona, Spain;
| | - Esperanza Martín-Sánchez
- Molecular Pathology of Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (D.G.-S.); (I.M.-S.); (A.U.-G.)
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11
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Strisciuglio C, Payne F, Nayak K, Andreozzi M, Vitale A, Miele E, Zilbauer M. Disease-associated DNA methylation signatures in esophageal biopsies of children diagnosed with Eosinophilic Esophagitis. Clin Epigenetics 2021; 13:81. [PMID: 33865442 PMCID: PMC8052828 DOI: 10.1186/s13148-021-01072-y] [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: 12/28/2020] [Accepted: 04/07/2021] [Indexed: 11/10/2022] Open
Abstract
Eosinophilic esophagitis (EoE) is a leading cause of dysphagia and food impaction in children and adults. The diagnosis relies on histological examination of esophageal mucosal biopsies and requires the presence of > 15 eosinophils per high-powered field. Potential pitfalls include the impact of biopsy sectioning as well as regional variations of eosinophil density. We performed genome-wide DNA methylation analyses on 30 esophageal biopsies obtained from children diagnosed with EoE (n = 7) and matched controls (n = 13) at the time of diagnosis as well as following first-line treatment. Analyses revealed striking disease-associated differences in mucosal DNA methylation profiles in children diagnosed with EoE, highlighting the potential for these epigenetic signatures to be developed into clinically applicable biomarkers.
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Affiliation(s)
- Caterina Strisciuglio
- Department of Woman, Child and General and Specialistic Surgery, University "Vanvitelli", via De Crecchio 4, CAP 80121, Napoli, Italy
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Level 8 Addenbrooke's Hospital, Box 116, Hills Road, Cambridge, CB2 0QQ, UK.,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Level 8 Addenbrooke's Hospital, Box 116, Hills Road, Cambridge, CB2 0QQ, UK.,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, UK
| | - Marialuisa Andreozzi
- Department of Translational Medical Science, Section of Paediatrics, University of Naples "Federico II", Naploli, Italy
| | - Alessandra Vitale
- Department of Translational Medical Science, Section of Paediatrics, University of Naples "Federico II", Naploli, Italy
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Paediatrics, University of Naples "Federico II", Naploli, Italy
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Level 8 Addenbrooke's Hospital, Box 116, Hills Road, Cambridge, CB2 0QQ, UK. .,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, UK. .,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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12
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The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-152. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
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13
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Immunomodulation by epigenome alterations in Mycobacterium tuberculosis infection. Tuberculosis (Edinb) 2021; 128:102077. [PMID: 33812175 DOI: 10.1016/j.tube.2021.102077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/07/2021] [Indexed: 12/14/2022]
Abstract
Mycobacterium tuberculosis (MTB) has co-evolved with humans for decades and developed several mechanisms to evade host immunity. It can efficiently alter the host epigenome, thus playing a major role in immunomodulation by either activating or suppressing genes responsible for mounting an immune response against the pathogen. Epigenetic modifications such as DNA methylation and chromatin remodelling regulate gene expression and influence several cellular processes. The involvement of epigenetic factors in disease onset and development had been overlooked upon in comparison to genetic mutations. It is now believed that assessment of epigenetic changes hold great potential in diagnosis, prevention and treatment strategies for a wide range of diseases. In this review, we unravel the principles of epigenetics and the numerous ways by which MTB re-shapes the host epigenetic landscape as a strategy to overpower the host immune system for its survival and persistence.
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14
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Wu J, Lin D, Jiu L, Liu Q, Gu Z, Luo J, Zhao Y. Exploring epigenetic biomarkers of universal specificities and commonalities among pan-cancer cohorts in The Cancer Genome Atlas. Epigenomics 2021; 13:599-612. [PMID: 33787302 DOI: 10.2217/epi-2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To explore the mechanism of cancer by employing a comprehensive analysis of DNA methylation patterns and variations among pan-cancer cohorts. Materials & methods: This research focused on the discovery of universally specific or common biomarkers by mathematical statistics and machine learning methods in The Cancer Genome Atlas. Results: We found 138 differently methylated CpGs (DMCs) with a common methylation trend and eight common differently methylated regions in different cancer cohorts. Additionally, we found 99 DMCs to distinguish 32 different cancer cohorts in random forest analysis because of the specificity mechanism, but each DMC still had high instability. Conclusion: Our results could facilitate the development of biomarkers that are universally specific and common features across pan-cancer cohorts.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Deng Lin
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Liandi Jiu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Qi Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Zhenglong Gu
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China.,Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Junjie Luo
- Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.,Department of Nutrition and Health, Beijing Advanced Innovation Center for Food Nutrition & Human Health, China Agricultural University, Beijing, 100193, China
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15
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Li HG, Tian WH, Qin CL, Ye RR, Liu DH, Liu HW. Uhrf1 regulates H3K9me2 modification of mTOR to inhibit the effect of autophagy in myocardial ischemia-reperfusion injury. Aging (Albany NY) 2021; 13:9704-9718. [PMID: 33744855 PMCID: PMC8064229 DOI: 10.18632/aging.202722] [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: 07/11/2020] [Accepted: 11/15/2020] [Indexed: 11/25/2022]
Abstract
The regulation of mTOR and the dimethylation of histone H3 on lysine 9 (H3K9me2) H3K9me2 by Uhrf1 and the mechanism of autophagy regulation in myocardial ischemia-reperfusion injury (MIRI) were studied in vivo and in vitro. An in vitro I/R injury model was established using the primary mouse cardiomyocytes treated with H2O2. Subsequent analysis by qRT-PCR, western blot, and immunofluorescence indicated that overexpression of Uhrf1 significantly inhibited apoptosis of the H2O2-treated cardiomyocytes, reduced expression of apoptosis factors caspase-3 and Bax, and increased expression of apoptosis inhibitory factor Bcl-2. Furthermore, Uhrf1 was found to increase cardiomyocyte proliferation and promote the expression of mTOR, while the four expression peaks of H3K9me2 on the mTOR gene were inhibited by overexpression of Uhrf1. The expression of autophagy factors LC3, Beclin-1, and p-mTOR in Uhrf1-overexpressed cardiomyocytes was dramatically increased, and P62 expression was dramatically decreased. When an H3K9me2 inhibitor was added to the Uhrf1-knockdown cardiomyocytes, the expression of mTOR was increased, the expression of LC3, Beclin-1, and p-mTOR was decreased, and P62 expression was significantly increased. In the present study, Uhrf1 exhibits a protective function in MIRI, reducing the apoptosis of cardiomyocytes while increasing their proliferation and viability.
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Affiliation(s)
- Han-Geng Li
- Department of Histology and Embryology, College of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Wen-Hua Tian
- Emergency Department, The Fourth Hospital of Harbin Medical University, Harbin 150081, China
| | - Cun-Lan Qin
- Department of Histology and Embryology, College of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Rong-Rong Ye
- Department of Histology and Embryology, College of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Dong-Hua Liu
- Department of Histology and Embryology, College of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Hui-Wen Liu
- Department of Histology and Embryology, College of Basic Medicine, Harbin Medical University, Harbin 150081, China
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16
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Potential regulatory role of epigenetic RNA methylation in cardiovascular diseases. Biomed Pharmacother 2021; 137:111376. [PMID: 33588266 DOI: 10.1016/j.biopha.2021.111376] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, especially in developing countries. To date, several approaches have been proposed for the prevention and treatment of CVDs. However, the increased risk of developing cardiovascular events that result in hospitalization has become a growing public health concern. The pathogenesis of CVDs has been analyzed from various perspectives. Recent data suggest that regulatory RNAs play a multidimensional role in the development of CVDs. Studies have identified several mRNA modifications that have contributed to the functional characterization of various cardiac diseases. RNA methylation, such as N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, N7-methylguanosine, N4-acetylcytidine, and 2'-O-methylation are novel epigenetic modifications that affect the regulation of cell growth, immunity, DNA damage, calcium signaling, apoptosis, and aging in cardiomyocytes. In this review, we summarize the role of RNA methylation in the pathophysiology of CVDs and the potential of using epigenetics to treat such disorders.
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17
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Taryma-Lesniak O, Sokolowska KE, Wojdacz TK. Short history of 5-methylcytosine: from discovery to clinical applications. J Clin Pathol 2021; 74:692-696. [PMID: 33431485 DOI: 10.1136/jclinpath-2020-206922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/15/2022]
Abstract
Covalent modifications of nucleotides in genetic material have been known from the beginning of the last century. Currently, one of those modifications referred to as DNA methylation, is impacting personalised medicine both as a treatment target and a biomarker source for clinical disease management. In this short review, we describe landmark discoveries that led to the elucidation of the DNA methylation importance in the cell's physiology and clarification of its role as one of the major processes in disease pathology. We also describe turning points in the development of methodologies to study this modification, which ultimately resulted in the development of in-vitro diagnostic kits targeting disease related DNA methylation changes as biomarkers.
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Affiliation(s)
- Olga Taryma-Lesniak
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Tomasz Kazimierz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
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18
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A Primer on DNA Methylation and Its Potential to Impact Maternal Depression Risk and Assessment During Pregnancy and the Postpartum. J Perinat Neonatal Nurs 2021; 35:4-7. [PMID: 33528179 DOI: 10.1097/jpn.0000000000000528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Depression onset during and after pregnancy is prevalent and associated with significant implications for maternal, child, and family health. Although environmental risk factors important to the expression of pregnancy-related depression are well known, knowledge of the genetic underpinning is limited. Given the joint contribution of environmental and genetic factors to depression risk liability, DNA methylation presents itself as an ideal biomarker to investigate basic mechanisms and opportunities for translational research to care for pregnancy-related depression health outcomes. This article is an introduction to DNA methylation and its potential to serve as a marker of depression risk during pregnancy and the postpartum. This commentary discusses current clinical uses of DNA methylation-based testing and how it may be applied to perinatal depression clinical care and management.
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19
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Majchrzak‐Celińska A, Dybska E, Barciszewska A. DNA methylation analysis with methylation-sensitive high-resolution melting (MS-HRM) reveals gene panel for glioma characteristics. CNS Neurosci Ther 2020; 26:1303-1314. [PMID: 32783304 PMCID: PMC7702229 DOI: 10.1111/cns.13443] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Local DNA hypermethylation is a potential source of cancer biomarkers. While the evaluation of single gene methylation has limited value, their selected panel may provide better information. AIMS This study aimed to analyze the promoter methylation level in a 7-gene panel in brain tumors and verifies the usefulness of methylation-sensitive high-resolution melting (MS-HRM) for this purpose. METHODS Forty-six glioma samples and one non-neoplastic brain sample were analyzed by MS-HRM in terms of SFRP1, SFRP2, RUNX3, CBLN4, INA, MGMT, and RASSF1A promoter methylation. The results were correlated with patients' clinicopathological features. RESULTS DNA methylation level of all analyzed genes was significantly higher in brain tumor samples as compared to non-neoplastic brain and commercial, unmethylated DNA control. RASSF1A was the most frequently methylated gene, with statistically significant differences depending on the tumor WHO grade. Higher MGMT methylation levels were observed in females, whereas the levels of SFRP1 and INA promoter methylation significantly increased with patients' age. A positive correlation of promoter methylation levels was observed between pairs of genes, for example, CBLN4 and INA or MGMT and RASSF1A. CONCLUSIONS Our 7-gene panel of promoter methylation can be helpful in brain tumor diagnosis or characterization, and MS-HRM is a suitable method for its analysis.
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Affiliation(s)
| | - Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic DiseasesPoznan University of Medical SciencesPoznańPoland
| | - Anna‐Maria Barciszewska
- Intraoperative Imaging UnitChair and Department of Neurosurgery and NeurotraumatologyPoznan University of Medical SciencesPoznańPoland
- Department of Neurosurgery and NeurotraumatologyHeliodor Swiecicki Clinical HospitalPoznańPoland
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20
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Smyth LJ, Patterson CC, Swan EJ, Maxwell AP, McKnight AJ. DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA. Front Cell Dev Biol 2020; 8:561907. [PMID: 33178681 PMCID: PMC7593403 DOI: 10.3389/fcell.2020.561907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Complementary to genetic factors, we know that a person’s epigenetic profile is also altered with DKD. This study reports analysis of DNA methylation, a major epigenetic feature, evaluating methylome-wide loci for association with DKD. Unique features (n = 485,577; 482,421 CpG probes) were evaluated in blood-derived DNA from carefully phenotyped White European individuals diagnosed with type 1 diabetes with (cases) or without (controls) DKD (n = 677 samples). Explicitly, 150 cases were compared to 100 controls using the 450K array, with subsequent analysis using data previously generated for a further 96 cases and 96 controls on the 27K array, and de novo methylation data generated for replication in 139 cases and 96 controls. Following stringent quality control, raw data were quantile normalized and beta values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls; resultant P-values for array-based data were adjusted for multiple testing. Genes with significantly increased (hypermethylated) and/or decreased (hypomethylated) levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways. Twenty-two loci demonstrated statistically significant fold changes associated with DKD and additional support for these associated loci was sought using independent samples derived from patients recruited with similar inclusion criteria. Markers associated with CCNL1 and ZNF187 genes are supported as differentially regulated loci (P < 10–8), with evidence also presented for AFF3, which has been identified from a meta-analysis and subsequent replication of genome-wide association studies. Further supporting evidence for differential gene expression in CCNL1 and ZNF187 is presented from kidney biopsy and blood-derived RNA in people with and without kidney disease from NephroSeq. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
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Affiliation(s)
- Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elizabeth J Swan
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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21
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Lu J, Wilfred P, Korbie D, Trau M. Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation. Cancers (Basel) 2020; 12:E3199. [PMID: 33143142 PMCID: PMC7692324 DOI: 10.3390/cancers12113199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Disruption of signaling pathways that plays a role in the normal development and cellular homeostasis may lead to the dysregulation of cellular signaling and bring about the onset of different diseases, including cancer. In addition to genetic aberrations, DNA methylation also acts as an epigenetic modifier to drive the onset and progression of cancer by mediating the reversible transcription of related genes. Although the role of DNA methylation as an alternative driver of carcinogenesis has been well-established, the global effects of DNA methylation on oncogenic signaling pathways and the presentation of cancer is only emerging. In this article, we introduced a differential methylation parsing pipeline (MethylMine) which mined for epigenetic biomarkers based on feature selection. This pipeline was used to mine for biomarkers, which presented a substantial difference in methylation between the tumor and the matching normal tissue samples. Combined with the Data Integration Analysis for Biomarker discovery (DIABLO) framework for machine learning and multi-omic analysis, we revisited the TCGA DNA methylation and RNA-Seq datasets for breast, colorectal, lung, and prostate cancer, and identified differentially methylated genes within the NRF2-KEAP1/PI3K oncogenic pathway, which regulates the expression of cytoprotective genes, that serve as potential therapeutic targets to treat different cancers.
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Affiliation(s)
- Jennifer Lu
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Premila Wilfred
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia; (J.L.); (P.W.)
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
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22
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Uhan S, Zidar N, Tomažič A, Hauptman N. Hypermethylated promoters of genes UNC5D and KCNA1 as potential novel diagnostic biomarkers in colorectal cancer. Epigenomics 2020; 12:1677-1688. [PMID: 33078631 DOI: 10.2217/epi-2020-0118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: Identification of aberrant hypermethylation in promoter regions of candidate genes to discover potential biomarkers for colorectal cancer. Materials & Methods: Genes BMP2, IRF4, KCNA1, LRRC7, NRG3, SLC27A6 and UNC5D were pre-selected in a bioinformatics study for their hypermethylation status in colorectal cancer. Methylation analysis was performed on 202 cancer tissue specimens to validate candidate genes. Results: Genes KCNA1 and UNC5D displayed methylation in 95.3 and 99.7% of The Cancer Genome Atlas dataset samples and in 96 and 98% of our experimentally tested samples, respectively. Conclusion: KCNA1 and UNC5D promoter hypermethylation holds diagnostic biomarker potential in patients with early colorectal cancer.
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Affiliation(s)
- Sara Uhan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Aleš Tomažič
- Department of Abdominal Surgery, University Medical Center Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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23
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Song L, Chen Y, Gong Y, Wan J, Guo S, Liu H, Li Y, Zeng Z, Lu Y. Opportunistic screening and survival prediction of digestive cancers by the combination of blood mSEPT9 with protein markers. Ther Adv Med Oncol 2020; 12:1758835920962966. [PMID: 33403008 PMCID: PMC7745555 DOI: 10.1177/1758835920962966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The early detection of digestive cancers and precancerous diseases remains a significant challenge. This study aimed to investigate the performance of the blood methylated SEPT9 (mSEPT9) assay, and the combination of this assay with serum protein markers, in hospital-based opportunistic screening strategies for digestive cancers. Methods: Opportunistic screening was performed in the participating hospitals on outpatients and inpatients who met specific inclusion criteria. We recruited a total of 2030 subjects, including 764 cancer patients [291 colorectal cancer (CRC), 239 gastric cancer (GC), 106 esophageal cancer (EC), and 128 hepatocellular carcinoma (HCC)], 423 subjects with precancerous diseases, and 843 normal subjects. All samples were transported to an authenticated clinical laboratory where the mSEPT9 tests were performed. Results: When used separately, the mSEPT9 detected CRC, GC, EC, and HCC, with a sensitivity of 76.6% [area under the receiver operating characteristic curve (AUC) = 0.86)], 47.7% (AUC = 0.76), 42.6% (AUC = 0.69), and 76.7% (AUC = 0.85) and a specificity of 94.6%, 92.3%, 92.5%, and 87.7%, respectively. The mSEPT9 assay also had potent ability to discriminate cancer from non-cancer subjects. The combination of mSEPT9 with CEA, CA724, SNCG, or AFP significantly enhanced the sensitivity for CRC, GC, EC, and HCC to 86.4% (AUC = 0.99, specificity = 92.8%), 63.6% (AUC = 0.86, specificity = 91.1%), 71.3% (AUC = 0.81, specificity = 82.1%), and 83.3% (AUC = 0.93, specificity = 85.1%), respectively. The performance of the mSEPT9 assay was influenced by cancer stage, patient age, pathological types, and the location of cancer. We also identified that mSEPT9 was an independent risk factor and was a valuable predictor for the long-term survival of digestive cancer patients, with a hazard ratio of 2.84, 2.07, 1.88, and 2.45, for CRC, GC, EC, and HCC, respectively. Conclusion: The blood mSEPT9 assay, whether used alone or in combination with serum protein markers, is effective for the opportunistic screening of digestive cancers. Furthermore, mSEPT9 is an independent risk factor and a predictive marker for the long-term survival of digestive cancer patients.
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Affiliation(s)
- Lele Song
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, No.17, Heishanhu Road, Beijing 100091, P.R. China
| | - Yan Chen
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, P.R. China
| | - Yuan Gong
- Department of Gastroenterology, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Jun Wan
- Department of Gastroenterology, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Shaohua Guo
- Department of General Surgery, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Hongyi Liu
- Department of General Surgery, The Chinese PLA General Hospital, Beijing, P.R. China
| | - Yuemin Li
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, P.R. China
| | - Zhen Zeng
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, 100039 P.R. China
| | - Yinying Lu
- Comprehensive Liver Cancer Department, The Fifth Medical Center of the Chinese PLA General Hospital, Beijing, 100039 P.R. China
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24
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de Oliveira NFP, de Souza BF, de Castro Coêlho M. UV Radiation and Its Relation to DNA Methylation in Epidermal Cells: A Review. EPIGENOMES 2020; 4:23. [PMID: 34968303 PMCID: PMC8594722 DOI: 10.3390/epigenomes4040023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is the most studied epigenetic mark, and it can be altered by environmental factors. Among these factors, ultraviolet radiation (UV) is little explored within this context. While the relationship between UV radiation and DNA mutations is clear, little is known about the relationship between UV radiation and epimutations. The present study aimed to perform a literature review to determine the influence of artificial or natural (solar) UV radiation on the global and site-specific methylation profile of epidermal cells. A systematic review of the literature was carried out using the databases PubMed, Scopus, Cochrane, and Web of Science. Observational and intervention studies in cultured cells and animal or human models were included. Most studies showed a relationship between UV radiation and changes in the methylation profile, both global and site-specific. Hypermethylation and hypomethylation changes were detected, which varied according to the studied CpG site. In conclusion, UV radiation can alter the DNA methylation profile in epidermal cells derived from the skin. These data can be used as potential biomarkers for environmental exposure and skin diseases, in addition to being targets for treatments. On the other hand, UV radiation (phototherapy) can also be used as a tool to treat skin diseases. Thus, the data suggest that epigenetic homeostasis can be disrupted or restored by exposure to UV radiation according to the applied wavelength.
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Affiliation(s)
- Naila Francis Paulo de Oliveira
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
- Programa de Pós Graduação em Odontologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
| | - Beatriz Fernandes de Souza
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
| | - Marina de Castro Coêlho
- Programa de Pós Graduação em Odontologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
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25
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Li M, Zhang C, Zhou L, Li S, Cao YJ, Wang L, Xiang R, Shi Y, Piao Y. Identification and validation of novel DNA methylation markers for early diagnosis of lung adenocarcinoma. Mol Oncol 2020; 14:2744-2758. [PMID: 32688456 PMCID: PMC7607165 DOI: 10.1002/1878-0261.12767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Lung cancer has the highest mortality of all cancers worldwide. Epigenetic alterations have emerged as potential biomarkers for early diagnosis of various cancer tissue types. To identify methylation markers for early diagnosis of lung adenocarcinoma, we aimed to integrate genome‐wide DNA methylation and gene expression data from The Cancer Genome Atlas. To this end, we first examined the global DNA methylation pattern of lung adenocarcinoma and investigated the relationship between DNA methylation subtypes and clinical features. We then extracted differentially methylated and expressed genes, and adopted feature selection techniques to determine the final methylation markers. The performance of the markers in predicting lung adenocarcinoma was evaluated on three independent datasets from Gene Expression Omnibus. Protein levels of marker genes were validated by immunohistochemistry, and their biological function was further verified in vivo. We identified three novel methylation markers in lung adenocarcinoma including cg08032924, cg14823851, and cg19161124, mapping to CMTM2, TBX4, and DPP6, respectively. Validating these results on three independent datasets indicated that the three markers can achieve extremely high sensitivity and specificity in distinguishing lung adenocarcinoma from normal samples. Immunohistochemistry quantification results confirmed that markers are weakly expressed in human lung adenocarcinoma, and CMTM2 decreased tumor growth of mouse Lewis lung carcinoma in vivo. Overall, our study identified three novel methylation markers in lung adenocarcinoma which may contribute toward an improved diagnosis potentially leading to a better outcome for patients with lung adenocarcinoma.
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Affiliation(s)
- Miao Li
- School of Medicine, Nankai University, Tianjin, China
| | - Chen Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Lijun Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Siyu Li
- School of Medicine, Nankai University, Tianjin, China
| | - Yuan Jie Cao
- Department of Radiation and Oncology, National Clinical Research Center for Cancer and Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Longlong Wang
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Shi
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, China.,Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
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26
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Schulz WA, Sørensen KD. Epigenetics of Urological Cancers. Int J Mol Sci 2019; 20:ijms20194775. [PMID: 31561442 PMCID: PMC6802188 DOI: 10.3390/ijms20194775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Karina D Sørensen
- Department of Clinical Medicine, Aarhus University & Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark.
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27
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Jia X, Zhao Q, Zhang Y, Dong Y, Lei L, Williamson RA, Lei Y, Tan X, Zhang D, Hu J. Identification of a Five-CpG Signature with Diagnostic Value in Thyroid Cancer. J Comput Biol 2019; 26:1409-1417. [PMID: 31290678 DOI: 10.1089/cmb.2019.0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Thyroid cancer (TC) ranks as the most common endocrine malignancy, and its incidence and mortality rates continue to rise annually. Increasing evidence have shown that DNA methylation, a kind of stable epigenetic modification, is associated with carcinogenesis, suggesting its potential as biomarkers for the early detection of tumors. With the aim of exploring likely DNA methylation biomarkers for TC diagnosis, we conducted a synthetic analysis of DNA methylation profiles based on 789 samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. In the discovery phase, we identified five CpG probes (cg11228682, cg01291854, cg06778183, cg01668008, and cg01702055) on the condition of DNA methylation data from GSE86961 (n = 82) and constructed a five-CpG signature-based diagnostic model for TC. In addition, we validated the diagnostic score formula in two independent training cohorts, GSE97466 (n = 141) and TCGA (n = 566), as well as the previous developing cohort GSE86961. Receiver operating characteristic analysis revealed that the five-CpG signature had a good diagnostic performance to distinguish TC samples from benign samples. In conclusion, our findings suggest that the five-CpG signature could provide a novel biomarker with useful applications in TC diagnosis.
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Affiliation(s)
- Xi Jia
- Department of Nuclear Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qian Zhao
- Department of Otolaryngology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yuanyuan Zhang
- Department of Pediatrics, and The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yiping Dong
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Li Lei
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Ramone A Williamson
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yutiantian Lei
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xinyue Tan
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dan Zhang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jinsong Hu
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
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28
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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29
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Daniūnaitė K, Jarmalaitė S, Kriukienė E. Epigenomic technologies for deciphering circulating tumor DNA. Curr Opin Biotechnol 2019; 55:23-29. [DOI: 10.1016/j.copbio.2018.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/05/2018] [Accepted: 07/13/2018] [Indexed: 01/23/2023]
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30
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Bonner ER, Bornhorst M, Packer RJ, Nazarian J. Liquid biopsy for pediatric central nervous system tumors. NPJ Precis Oncol 2018; 2:29. [PMID: 30588509 PMCID: PMC6297139 DOI: 10.1038/s41698-018-0072-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Central nervous system (CNS) tumors are the most common solid tumors in children, and the leading cause of cancer-related death. Over the past decade, molecular profiling has been incorporated into treatment for pediatric CNS tumors, allowing for a more personalized approach to therapy. Through the identification of tumor-specific changes, it is now possible to diagnose, assign a prognostic subgroup, and develop targeted chemotherapeutic treatment plans for many cancer types. The successful incorporation of informative liquid biopsies, where the liquid biome is interrogated for tumor-associated molecular clues, has the potential to greatly complement the precision-based approach to treatment, and ultimately, to improve clinical outcomes for children with CNS tumors. In this article, the current application of liquid biopsy in cancer therapy will be reviewed, as will its potential for the diagnosis and therapeutic monitoring of pediatric CNS tumors.
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Affiliation(s)
- Erin R Bonner
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,2Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
| | - Miriam Bornhorst
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Roger J Packer
- 3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA
| | - Javad Nazarian
- 1Center for Genetic Medicine, Children's National Health System, Washington, DC 20010 USA.,3Brain Tumor Institute, Children's National Health System, Washington, DC 20010 USA.,4Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052 USA
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31
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Menschikowski M, Jandeck C, Friedemann M, Richter S, Thiem D, Lange BS, Suttorp M. Identification and Quantification of Heterogeneously-methylated DNA Fragments Using Epiallele-sensitive Droplet Digital Polymerase Chain Reaction (EAST-ddPCR). Cancer Genomics Proteomics 2018; 15:299-312. [PMID: 29976635 DOI: 10.21873/cgp.20088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/AIM DNA methylation plays an important role in the initiation and propagation of carcinogenesis; however, the role of heterogeneously methylated epialleles is currently not well studied, also due to the lack of sensitive, unbiased and high throughput methods. Here, a newly developed droplet digital PCR (ddPCR)-based method was evaluated regarding its ability to quantify such heterogeneously methylated epialleles with sufficient analytical sensitivity and specificity. MATERIALS AND METHODS Genomic DNA from blood leukocytes and bone marrow aspirate of an 8-year old male with B-cell acute lymphoblastic leukemia (B-ALL) and from normal and malignant prostate cell lines were analysed using ddPCR. RESULTS By using these DNA samples, the specificity of an applied set of fluorescence-labeled probes was demonstrated as a proof of concept. CONCLUSION All individual heterogeneously-methylated epialleles were quantifiable by a set of fluorescence-labeled probes with complementary sequences to epialleles in a closed-tube and high-throughput manner. The new method named epiallele-sensitive droplet digital PCR (EAST-ddPCR) may give new insights in the generation and regulation of epialleles and may help in finding new biomarkers for the diagnosis of benign und malignant diseases.
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Affiliation(s)
- Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Carsten Jandeck
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Dana Thiem
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Björn Sönke Lange
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Meinolf Suttorp
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
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32
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Highly sensitive detection of DNA hypermethylation in melanoma cancer cells. Biosens Bioelectron 2018; 124-125:136-142. [PMID: 30366258 DOI: 10.1016/j.bios.2018.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022]
Abstract
Aberrant hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a promising biomarker for early cancer detection. This methylation status is reflected in the methylation pattern of ctDNA shed from the primary tumor; however, to realize the full clinical utility of ctDNA methylation detection via liquid biopsy for early cancer diagnosis, improvements in the sensitivity and multiplexability of existing technologies must be improved. Additionally, the assay must be cheap and easy to perform in a clinical setting. We report the integration of methylation specific PCR (MSP) to melt curve analysis on giant magnetoresistive (GMR) biosensors to greatly enhance the sensitivity of our DNA hybridization assay for methylation detection. Our GMR sensor is functionalized with synthetic DNA probes that target methylated or unmethylated CpG sites in the MSP amplicon, and measures the difference in melting temperature (Tm) between the two probes (ΔTm), giving an analytical limit of detection down to 0.1% methylated DNA in solution. Additionally, linear regression of ΔTm's for serial dilutions of methylated:unmethylated mixtures allows for quantification of methylation percentage, which could have diagnostic and prognostic utility. Lastly, we performed multiplexed MSP on two different genes, and show the ability of our GMR assay to resolve this mixture, despite their amplicons' overlapping Tm's in standard EvaGreen melt analysis. The multiplexing ability of our assay and its enhanced sensitivity, without necessitating deep sequencing, represent important steps toward realizing an assay for the detection of methylated ctDNA in plasma for early cancer detection in a clinical setting.
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33
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Matsuoka T, Yashiro M. Biomarkers of gastric cancer: Current topics and future perspective. World J Gastroenterol 2018; 24:2818-2832. [PMID: 30018477 PMCID: PMC6048430 DOI: 10.3748/wjg.v24.i26.2818] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/19/2018] [Accepted: 06/01/2018] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is one of the most prevalent malignant types in the world and an aggressive disease with a poor 5-year survival. This cancer is biologically and genetically heterogeneous with a poorly understood carcinogenesis at the molecular level. Although the incidence is declining, the outcome of patients with GC remains dismal. Thus, the detection at an early stage utilizing useful screening approaches, selection of an appropriate treatment plan, and effective monitoring is pivotal to reduce GC mortalities. Identification of biomarkers in a basis of clinical information and comprehensive genome analysis could improve diagnosis, prognosis, prediction of recurrence and treatment response. This review summarized the current status and approaches in GC biomarker, which could be potentially used for early diagnosis, accurate prediction of therapeutic approaches and discussed the future perspective based on the molecular classification and profiling.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Masakazu Yashiro
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
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