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Sugiyama T. Biochemical reconstitution of heat-induced mutational processes. PLoS One 2024; 19:e0310601. [PMID: 39288122 PMCID: PMC11407675 DOI: 10.1371/journal.pone.0310601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, Ohio, United States of America
- Molecular and Cellular Biology Graduate Program, Ohio University, Athens, Ohio, United States of America
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2
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Aqil A, Li Y, Wang Z, Islam S, Russell M, Kallak TK, Saitou M, Gokcumen O, Masuda N. Switch-like Gene Expression Modulates Disease Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.24.609537. [PMID: 39229158 PMCID: PMC11370615 DOI: 10.1101/2024.08.24.609537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A fundamental challenge in biomedicine is understanding the mechanisms predisposing individuals to disease. While previous research has suggested that switch-like gene expression is crucial in driving biological variation and disease susceptibility, a systematic analysis across multiple tissues is still lacking. By analyzing transcriptomes from 943 individuals across 27 tissues, we identified 1,013 switch-like genes. We found that only 31 (3.1%) of these genes exhibit switch-like behavior across all tissues. These universally switch-like genes appear to be genetically driven, with large exonic genomic structural variants explaining five (~18%) of them. The remaining switch-like genes exhibit tissue-specific expression patterns. Notably, tissue-specific switch-like genes tend to be switched on or off in unison within individuals, likely under the influence of tissue-specific master regulators, including hormonal signals. Among our most significant findings, we identified hundreds of concordantly switched-off genes in the stomach and vagina that are linked to gastric cancer (41-fold, p<10-4) and vaginal atrophy (44-fold, p<10-4), respectively. Experimental analysis of vaginal tissues revealed that low systemic levels of estrogen lead to a significant reduction in both the epithelial thickness and the expression of the switch-like gene ALOX12. We propose a model wherein the switching off of driver genes in basal and parabasal epithelium suppresses cell proliferation therein, leading to epithelial thinning and, therefore, vaginal atrophy. Our findings underscore the significant biomedical implications of switch-like gene expression and lay the groundwork for potential diagnostic and therapeutic applications.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Yanyan Li
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Zhiliang Wang
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Saiful Islam
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY, USA
| | - Madison Russell
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | | | - Marie Saitou
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Naoki Masuda
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY, USA
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3
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Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [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: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
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Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
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Evangelidis N, Kotsiou N, Evangelidis P, Alevizopoulos VI, Dermitzakis I, Chissan S, Vakalopoulou S, Gavriilaki E. Genetics and Epigenetics in Acquired Hemophilia A: From Bench to Bedside. Curr Issues Mol Biol 2024; 46:5147-5160. [PMID: 38920981 PMCID: PMC11201880 DOI: 10.3390/cimb46060309] [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: 04/20/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Acquired hemophilia A (AHA) is a bleeding disorder characterized by the immunological inhibition of factor VIII (FVIII) of the hemostatic pathway leading to hemorrhagic events. Different domains of FVIII are the target of autoantibodies (mainly immunoglobulin (Ig) G) leading to the deficiency of FVIII. Several factors have been associated with the activation of the auto-immunity towards FVIII. Emerging evidence implicates CD4+ T cell activation in mediating this autoimmune response, with their involvement like that observed in congenital hemophilia A. Several genes such as HLA II DRB*16, DQB1*0502, and CTLA-4 + 49 are responsible for the pathogenesis of AHA. Epigenetic modifications and mainly long-coding RNAS (lncRNAs) are potentially contributing to the pathogenesis of AHA. The treatment approach of AHA includes the management of acute bleeding events and the administration of immunosuppressive medications. This review aimed to summarize the published data on the genetics and epigenetics of AHA. The severity and the mortality of this disease are creating an emerging need for further research in the field of the genetics and epigenetics of acquired hemorrhagic disorder.
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Affiliation(s)
- Nikolaos Evangelidis
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Nikolaos Kotsiou
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Paschalis Evangelidis
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Vlasios I. Alevizopoulos
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Iasonas Dermitzakis
- Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Sofia Chissan
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Sofia Vakalopoulou
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
| | - Eleni Gavriilaki
- Hematology Unit-Hemophilia Centre, 2nd Propedeutic Department of Internal Medicine, Hippocration Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece; (N.E.); (N.K.); (P.E.); (V.I.A.); (S.C.); (S.V.)
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5
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Sugiyama T. Biochemical reconstitution of a major age-related cancer mutational signature by heat-induced spontaneous deamination of 5-methylcytosine residues, repair of uracil residues, and DNA replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595323. [PMID: 38826364 PMCID: PMC11142167 DOI: 10.1101/2024.05.22.595323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-enzymatic spontaneous deamination of 5-methylcytosine, producing thymine, is the proposed etiology of cancer mutational signature 1, which is the most predominant signature in all cancers. Here, the proposed mutational process was reconstituted using synthetic DNA and purified proteins. First, single-stranded DNA containing 5-methylcytosine at CpG context was incubated at an elevated temperature to accelerate spontaneous DNA damage. Then, the DNA was treated with uracil DNA glycosylase to remove uracil residues that were formed by deamination of cytosine. The resulting DNA was then used as a template for DNA synthesis by yeast DNA polymerase δ. The DNA products were analyzed by next-generation DNA sequencing, and mutation frequencies were quantified. The observed mutations after this process were exclusively C>T mutations at CpG context, which was very similar to signature 1. When 5-methylcytosine modification and uracil DNA glycosylase were both omitted, C>T mutations were produced on C residues in all sequence contexts, but these mutations were diminished by uracil DNA glycosylase-treatment. These results indicate that the CpG>TpG mutations were produced by the deamination of 5-methylcytosine. Additional mutations, mainly C>G, were introduced by yeast DNA polymerase ζ on the heat-damaged DNA, indicating that G residues of the templates were also damaged. However, the damage on G residues was not converted to mutations with DNA polymerase δ or ε. These results provide biochemical evidence to support that the majority of mutations in cancers are produced by ordinary DNA replication on spontaneously damaged DNA.
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Vivanco PG, Taboada P, Coelho A. The Southern European Atlantic Diet and Its Supplements: The Chemical Bases of Its Anticancer Properties. Nutrients 2023; 15:4274. [PMID: 37836558 PMCID: PMC10574233 DOI: 10.3390/nu15194274] [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: 08/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Scientific evidence increasingly supports the strong link between diet and health, acknowledging that a well-balanced diet plays a crucial role in preventing chronic diseases such as obesity, diabetes, cardiovascular issues, and certain types of cancer. This perspective opens the door to developing precision diets, particularly tailored for individuals at risk of developing cancer. It encompasses a vast research area and involves the study of an expanding array of compounds with multilevel "omics" compositions, including genomics, transcriptomics, proteomics, epigenomics, miRNomics, and metabolomics. We review here the components of the Southern European Atlantic Diet (SEAD) from both a chemical and pharmacological standpoint. The information sources consulted, complemented by crystallographic data from the Protein Data Bank, establish a direct link between the SEAD and its anticancer properties. The data collected strongly suggest that SEAD offers an exceptionally healthy profile, particularly due to the presence of beneficial biomolecules in its foods. The inclusion of olive oil and paprika in this diet provides numerous health benefits, and scientific evidence supports the anticancer properties of dietary supplements with biomolecules sourced from vegetables of the brassica genus. Nonetheless, further research is warranted in this field to gain deeper insights into the potential benefits of the SEAD's bioactive compounds against cancer.
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Affiliation(s)
- Pablo García Vivanco
- Spanish Academy of Nutrition and Dietetics, 31006 Pamplona, Spain
- Nutrition and Digestive Working Group, Spanish Society of Clinical, Family, and Community Pharmacy (SEFAC), 28045 Madrid, Spain
| | - Pablo Taboada
- Department of Condensed Matter Physics, Faculty of Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Institute of Materials-USC (IMATUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Alberto Coelho
- Institute of Materials-USC (IMATUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Baljinnyam T, Conrad JW, Sowers ML, Chang-Gu B, Herring JL, Hackfeld LC, Zhang K, Sowers LC. Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing. Chem Res Toxicol 2023; 36:162-176. [PMID: 36647573 PMCID: PMC9945173 DOI: 10.1021/acs.chemrestox.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recently, we constructed a hybrid thymine DNA glycosylase (hyTDG) by linking a 29-amino acid sequence from the human thymine DNA glycosylase with the catalytic domain of DNA mismatch glycosylase (MIG) from M. thermoautotrophicum, increasing the overall activity of the glycosylase. Previously, it was shown that a tyrosine to lysine (Y126K) mutation in the catalytic site of MIG could convert the glycosylase activity to a lyase activity. We made the corresponding mutation to our hyTDG to create a hyTDG-lyase (Y163K). Here, we report that the hybrid mutant has robust lyase activity, has activity over a broad temperature range, and is active under multiple buffer conditions. The hyTDG-lyase cleaves an abasic site similar to endonuclease III (Endo III). In the presence of β-mercaptoethanol (β-ME), the abasic site unsaturated aldehyde forms a β-ME adduct. The hyTDG-lyase maintains its preference for cleaving opposite G, as with the hyTDG glycosylase, and the hyTDG-lyase and hyTDG glycosylase can function in tandem to cleave T:G mismatches. The hyTDG-lyase described here should be a valuable tool in studies examining DNA damage and repair. Future studies will utilize these enzymes to quantify T:G mispairs in cells, tissues, and genomic DNA using next-generation sequencing.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Bruce Chang-Gu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
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Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology. Microorganisms 2023; 11:microorganisms11020341. [PMID: 36838306 PMCID: PMC9967649 DOI: 10.3390/microorganisms11020341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.
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Saini A, Varshney A, Saini A, Mani I. Insight into epigenetics and human diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:1-21. [PMID: 37019588 DOI: 10.1016/bs.pmbts.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
The most eminent research of the 21st century whirls around the epigenetic and the variability of DNA sequences in humans. The reciprocity between the epigenetic changes and the exogenous factors drives an influence on the inheritance biology and gene expression both inter-generationally and trans-generationally. Chromatin level modifications like DNA methylation, histone modifications or changes in transcripts functions either at transcription level or translational level pave the way for certain diseases or cancer in humans. The ability of epigenetics to explain the processes of various diseases has been demonstrated by recent epigenetic studies. Multidisciplinary therapeutic strategies were developed in order to analyse how epigenetic elements interact with different disease pathways. In this chapter we summarize how an organism may be predisposed to certain diseases by exposure to environmental variables such as chemicals, medications, stress, or infections during particular, vulnerable phases of life, and the epigenetic component may influence some of the diseases in humans.
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Lippert J, Altieri B, Morrison B, Steinhauer S, Smith G, Lorey A, Urlaub H, Kircher S, Sitch A, Fassnacht M, Ronchi CL. Prognostic Role of Targeted Methylation Analysis in Paraffin-embedded Samples of Adrenocortical Carcinoma. J Clin Endocrinol Metab 2022; 107:2892-2899. [PMID: 35929659 PMCID: PMC9516165 DOI: 10.1210/clinem/dgac470] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/20/2022]
Abstract
CONTEXT Adrenocortical carcinoma (ACC) is a rare aggressive disease with heterogeneous prognoses. Previous studies identified hypermethylation in the promoter region of specific genes to be associated with poor clinical outcome. OBJECTIVE Comparative analysis of promising hypermethylated genes as prognostic markers and evaluation of their added value to established clinical prognostic tools. DESIGN We included 237 patients with ACCs. Tumor DNA was isolated from formalin-fixed paraffin-embedded (FFPE) samples. Targeted pyrosequencing was used to detect promoter region methylation in 5 preselected genes (PAX5, GSTP1, PYCARD, PAX6, G0S2). The prognostic role of hypermethylation pattern was compared with the Stage, Grade, Resection status, Age, Symptoms (S-GRAS) score. Primary endpoints were progression-free (PFS) and overall survival (OS), with disease-free (DFS) as secondary endpoint. RESULTS A total of 27.9%, 13.9%, 49%, 49%, and 25.3% of cases showed hypermethylation in PAX5, GSTP1, PYCARD, PAX6, and G0S2, respectively. Hypermethylation in all individual genes-except GSTP1-was significantly associated with both PFS and OS-with hazard ratios (HR) between 1.4 and 2.3. However, only hypermethylation of PAX5 remained significantly associated with OS (P = 0.013; HR = 1.95, 95% CI, 1.2-3.3) in multivariable analysis. A model for risk stratification was developed, combining PAX5 methylation status and S-GRAS groups, showing improved prognostic performance compared to S-GRAS alone (Harrell's C index: OS = 0.751, PFS = 0.711, DFS = 0.688). CONCLUSIONS This study demonstrated that hypermethylation in PAX5 is associated with worst clinical outcome in ACC, even after accounting for S-GRAS score. Assessing methylation in FFPE material is straightforward in the clinical setting and could be used to improve accuracy of prognostic classification, enabling the direction of personalized management.
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Affiliation(s)
- Juliane Lippert
- Division of Endocrinology and Diabetes, University Hospital of Wuerzburg, 97080 Wuerzburg, Germany
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, University Hospital of Wuerzburg, 97080 Wuerzburg, Germany
| | - Breanna Morrison
- Institute of Applied Health Research, University of Birmingham, B152TT Birmingham, UK
| | - Sonja Steinhauer
- Division of Endocrinology and Diabetes, University Hospital of Wuerzburg, 97080 Wuerzburg, Germany
| | - Gabrielle Smith
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, UK
| | - Antonia Lorey
- Division of Endocrinology and Diabetes, University Hospital of Wuerzburg, 97080 Wuerzburg, Germany
| | - Hanna Urlaub
- Division of Endocrinology and Diabetes, University Hospital of Wuerzburg, 97080 Wuerzburg, Germany
| | - Stefan Kircher
- Institute for Pathology, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Alice Sitch
- Institute of Applied Health Research, University of Birmingham, B152TT Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, B152TH Birmingham, UK
| | - Martin Fassnacht
- Martin Fassnacht, MD, PhD, Division of Endocrinology and Diabetes, Department of Internal Medicine 1, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany.
| | - Cristina L Ronchi
- Correspondence: Cristina L. Ronchi, MD, PhD, Institute of Metabolism and System Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston B15 2TT, UK.
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Identification of Prognostic DNA Methylation Signatures in Lung Adenocarcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8802303. [PMID: 35814273 PMCID: PMC9259289 DOI: 10.1155/2022/8802303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/04/2022] [Indexed: 12/03/2022]
Abstract
Background Increasing evidence exists of a link between DNA methylation and tumor immunotherapy. However, the impact of DNA methylation on the characteristics of the lung adenocarcinoma microenvironment and its effect on immunotherapy remain unclear. Method This study collected TCGA-LUAD related data sets (LUAD) to explore the characteristics and regulation of 20 DNA methylation-related genes. We further identified two DNA methylation subtypes by analysing the expression profiles of these 20 DNA methylation-related genes. Subsequently, the differences in immune cell infiltration (ICI) and the expression of immune-related signaling factors among different DNA methylation subtypes were explored, and the differentially expressed genes (DEGs) among different LUAD DNA methylation subtypes were identified. Using univariate Cox to screen differentially expressed genes meaningful for survival, a DNA methylation score (DMS) was constructed based on the weight of the first and second dimensions after dimensionality reduction by principal component analysis (PCA). Our study found that DMS can better evaluate the prognosis of lung adenocarcinoma. Results Based on DMS, LUAD samples were divided into two groups with high and low scores. The differences in clinical characteristics, tumor mutation load, and tumor immune cell infiltration between different DMS groups of LUAD were deeply explored, and the prediction ability of DMS for the benefit of immunotherapy was evaluated. Conclusions DMS is a valuable tool for predicting survival, clinicopathological features, and immunotherapeutic efficacy, which may help to promote personalized LUAD immunotherapy in the future.
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12
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Dean W. Pathways of DNA Demethylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:211-238. [DOI: 10.1007/978-3-031-11454-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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Jayabal P, Ma X, Shiio Y. EZH2 suppresses endogenous retroviruses and an interferon response in cancers. Genes Cancer 2021; 12:96-105. [PMID: 34966479 PMCID: PMC8711646 DOI: 10.18632/genesandcancer.218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Ewing sarcoma is an aggressive cancer of bone and soft tissue in children. It is characterized by the chromosomal translocation between EWS and an Ets family transcription factor, most commonly FLI1. We recently reported that Ewing sarcoma depends on the autocrine signaling mediated by a cytokine, NELL2. NELL2 signaling stimulates the transcriptional output of EWS-FLI1 through the BAF chromatin remodeling complexes. While studying the impact of NELL2 silencing on Ewing sarcoma, we found that suppression of NELL2 signaling induces the expression of endogenous retroviruses (ERVs) and LINE-1 retrotransposons, an interferon response, and growth arrest. We determined that a histone methyltransferase, EZH2, is the critical downstream target of NELL2 signaling in suppressing ERVs, LINE-1, an interferon response, and growth arrest. We show that EZH2 inhibitors induce ERVs, LINE-1, and an interferon response in a variety of cancer types. These results uncover the role for NELL2–EZH2 signaling in suppressing endogenous virus-like agents and an antiviral response, and suggest the potential utility of EZH2 inhibitors in enhancing anti-tumor immunity.
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Affiliation(s)
- Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.,Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
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15
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Zhang Z, Zhu R, Sun W, Wang J, Liu J. Analysis of Methylation-driven Genes in Pancreatic Ductal Adenocarcinoma for Predicting Prognosis. J Cancer 2021; 12:6507-6518. [PMID: 34659542 PMCID: PMC8489123 DOI: 10.7150/jca.53208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose: Considerable variations in methylation profile have been found in various cancers to modulate tumorigenesis and affect prognosis. To provide a theoretical basis for early detection, prognosis evaluation and targeted treatment for patients with pancreatic ductal adenocarcinoma: PDAC, this study identified methylation-driven genes in PDAC and explored their prognostic performance. Methods: The methylation, expression and clinical data of PDAC patients were extracted from TCGA database. Based on the β-mixture model of the MethylMix R package, the differential methylation status and connection between methylation and expression degree were examined to screen out methylation-driven genes in PDAC. COX analyses and lasso regressions were applied to construct a linear risk model based on methylation-driven genes. Univariate and multivariate analyses were performed to ensure the risk model was an independent prognostic factor. Joint survival analyses of methylation and gene expression were conducted to explore the prognostic value of component genes. The methylation sites in the key genes were also investigated. Results: A total of 118 methylation-driven genes in PDAC were identified, and two genes (FOXI2, MYEOV) constituted the risk model whose AUC was 0.722 at one year of overall survival rate, displaying a better performance on survival prediction than other clinical features. Further survival analyses demonstrated that the expression of MYEOV and combined methylation and expression levels of the genes MYEOV and FOXI2 can be potential biomarkers for survival prediction and targets of drug manipulation of PDAC patients. Close relationships were discovered between two sites in MYEOV and one site in FOXI2 and the prognosis of PDAC patients. Conclusion: Concentrating on DNA methylation, our study identified potential biomarkers and developed a reliable short-term predictive model for prognosis of PDAC patients.
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Affiliation(s)
- Zihan Zhang
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Rui Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wentian Sun
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jin Liu
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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16
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Abstract
Objectives: Expound upon priorities for basic/translational science identified in a recent paper by a group of experts assigned by the Society of Critical Care Medicine and the European Society of Intensive Care Medicine. Data Sources: Original paper, search of the literature. Study Selection: By several members of the original task force with specific expertise in basic/translational science. Data Extraction: None. Data Synthesis: None. Conclusions: In the first of a series of follow-up reports to the original paper, several members of the original task force with specific expertise provided a more in-depth analysis of the five identified priorities directly related to basic/translational science. This analysis expounds on what is known about the question and what was identified as priorities for ongoing research. It is hoped that this analysis will aid the development of future research initiatives.
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17
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Xie Y, Wang Y, He Z, Yang W, Fu B, Zou G, Zhang X, Huang J, Zhou X. Selective Chemical Labeling and Sequencing of 5-Carboxylcytosine in DNA at Single-Base Resolution. Anal Chem 2020; 92:12710-12715. [PMID: 32803958 DOI: 10.1021/acs.analchem.0c03201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Carboxylcytosine (5caC) plays a vital role in the dynamics of DNA demethylation, and sequencing of its sites will help us dig out more biological functions of 5caC. Herein, we present a novel chemical method to efficiently label 5caC distinguished from other bases in DNA. Combined with bisulfite sequencing, 5caC sites can be located at single-base resolution, and the efficiency of 5caC labeling is 92% based on the Sanger sequencing data. Furthermore, dot blot assays have confirmed that 5caC-containing DNA isolated from HeLa cells was successfully labeled using our method. We expect that our strategy can be further applied to selectively tagging other carboxyl-modified bases and mapping their sites in RNA.
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Affiliation(s)
- Yalun Xie
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Jinguo Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
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18
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Yang L, Dao FT, Chang Y, Wang YZ, Li LD, Chen WM, Long LY, Liu YR, Lu J, Liu KY, Qin YZ. Both Methylation and Copy Number Variation Participated in the Varied Expression of PRAME in Multiple Myeloma. Onco Targets Ther 2020; 13:7545-7553. [PMID: 32801773 PMCID: PMC7402861 DOI: 10.2147/ott.s240979] [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: 12/03/2019] [Accepted: 07/03/2020] [Indexed: 11/24/2022] Open
Abstract
Purpose The cancer-testis antigen, which is a preferentially expressed antigen of melanoma (PRAME), is an ideal target for immunotherapy and cancer vaccines. Since the expression of this antigen is relevant to therapy responses, the heterogeneity in its expression and the underlying mechanism need to be investigated. Patients and Methods Plasma cell sorting was performed in 48 newly diagnosed multiple myeloma (MM) patients. Real-time quantitative PCR was performed to examine the PRAME transcript levels and gene copy numbers. Bisulfate clone sequencing of the PRAME promoter and exon 1b regions was performed in 4 patients. Quantitative methylation-specific PCR of the +287 CpG site was performed for all patients. The human MM cell lines RPMI8226, LP-1 and MOLP-2 were treated with 5-azacytidine. Results The median PRAME transcript level was 3.1% (range: 0–298.3%) in the plasma cells sorted from the 48 MM patients. Eleven (22.9%) and 37 (77.1%) patients were individually categorized into the PRAME low- and high-expression groups according to the cut-off value of 0.05%. The methylation ratios of the promoter and the 3ʹ region of exon 1b region were both negatively related to the transcript levels. The degrees of methylation at the +287 CpG site were significantly negatively related to the transcript levels in all 48 patients (r=−0.44, P=0.0018), and those in the high-expression group (r=−0.69, P<0.0001) but not those in the low-expression group (r=−0.27, P=0.43). All 5 patients with homozygous deletions were categorized into the low-expression group. There were no significant differences in the PRAME transcript levels between the hemizygous deletion (n=8) and no deletion (n=35) groups (P=0.40). Furthermore, the PRAME transcript levels significantly increased in the MM cell lines after treatment with 5-azacytidine. Conclusion Both methylation and copy number variation may participate in the regulation of PRAME expression in MM; in patients with no homozygous deletion, PRAME expression is mainly controlled by methylation, and a proportion of fairly low expression is caused by homozygous deletion.
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Affiliation(s)
- Lu Yang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Feng-Ting Dao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Yan Chang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ya-Zhe Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ling-Di Li
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ling-Yu Long
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Jin Lu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Kai-Yan Liu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing, People's Republic of China
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19
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Wang C, Liu S, Kuang Y, Hu X, Fang X. Downregulation of ZNF365 by methylation predicts poor prognosis in patients with colorectal cancer by decreasing phospho-p53 (Ser15) expression. Oncol Lett 2020; 20:85. [PMID: 32863918 PMCID: PMC7436887 DOI: 10.3892/ol.2020.11946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/26/2020] [Indexed: 01/11/2023] Open
Abstract
ZNF365 is a transcription factor that plays important roles in different types of cancer, such as colorectal cancer, breast cancer and hepatocellular carcinoma. ZNF365 can promote stalled replication fork recovery to prevent genomic instability, which is a notable feature of sporadic and hereditary types of cancers. However, the function of ZNF365 in the tumor progression of colorectal cancer (CRC) remains unclear. Thus, immunohistochemical staining was used to investigate the association between ZNF365 expression and the clinicopathological characteristics of patients with colorectal cancer. The results demonstrated that ZNF365 protein was strongly expressed in the nucleus and cytoplasm of normal colorectal mucosa. Furthermore ZNF365, which is methylated and downregulated in most cancer cell lines and tissues, was significantly associated with lymph node metastasis (P=0.015), depth of invasion (P=0.031) and histopathological grading (P=0.042). A positive correlation was observed between ZNF365 expression and phosphorylated (P)-p53 (Ser15) protein expression (r=0.18; P=0.038). Survival analysis indicated that patients with high ZNF365 expression had a higher survival rate than those with low ZNF365 expression (P=0.009), suggesting that ZNF365 may be an independent prognostic factor for survival in colorectal cancer (P=0.046). Taken together, the results of the present study demonstrated that ZNF365 was frequently inactivated by promoter methylation and independently predicted poor prognosis in patients with colorectal cancer by downregulating P-p53 (Ser15) expression.
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Affiliation(s)
- Chan Wang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Shuiping Liu
- Department of Cancer Pharmacology and Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Holistic Integrative Pharmacy Institutes, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310012, P.R. China
| | - Yeye Kuang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Xiaotong Hu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Xiao Fang
- Department of Anesthesiology and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
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20
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Deutschman CS, Hellman J, Roca RF, De Backer D, Coopersmith CM. The surviving sepsis campaign: basic/translational science research priorities. Intensive Care Med Exp 2020; 8:31. [PMID: 32676795 PMCID: PMC7365694 DOI: 10.1186/s40635-020-00312-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objectives Expound upon priorities for basic/translational science identified in a recent paper by a group of experts assigned by the Society of Critical Care Medicine and the European Society of Intensive Care Medicine. Data sources Original paper, search of the literature. Study selection This study is selected by several members of the original task force with specific expertise in basic/translational science. Data extraction and data synthesis are not available. Conclusions In the first of a series of follow-up reports to the original paper, several members of the original task force with specific expertise provided a more in-depth analysis of the five identified priorities directly related to basic/translational science. This analysis expounds on what is known about the question and what was identified as priorities for ongoing research. It is hoped that this analysis will aid the development of future research initiatives.
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Affiliation(s)
- Clifford S Deutschman
- Department of Pediatrics, Hofstra/Northwell School of Medicine and the Feinstein Institute for Medical Research/Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, USA. .,Department of Molecular Medicine, Hofstra/Northwell School of Medicine and the Feinstein Institute for Medical Research/Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, USA.
| | - Judith Hellman
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Ricard Ferrer Roca
- Intensive Care Department, Vall d'Hebron University Hospital, Barcelona, Spain.,Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Daniel De Backer
- Chirec Hospitals, Université Libre de Bruxelles, Brussels, Belgium
| | - Craig M Coopersmith
- Department of Surgery and Emory Critical Care Center, Emory University, Atlanta, GA, USA
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21
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Begolli R, Sideris N, Giakountis A. LncRNAs as Chromatin Regulators in Cancer: From Molecular Function to Clinical Potential. Cancers (Basel) 2019; 11:E1524. [PMID: 31658672 PMCID: PMC6826483 DOI: 10.3390/cancers11101524] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/28/2019] [Accepted: 10/06/2019] [Indexed: 12/15/2022] Open
Abstract
During the last decade, high-throughput sequencing efforts in the fields of transcriptomics and epigenomics have shed light on the noncoding part of the transcriptome and its potential role in human disease. Regulatory noncoding RNAs are broadly divided into short and long noncoding transcripts. The latter, also known as lncRNAs, are defined as transcripts longer than 200 nucleotides with low or no protein-coding potential. LncRNAs form a diverse group of transcripts that regulate vital cellular functions through interactions with proteins, chromatin, and even RNA itself. Notably, an important regulatory aspect of these RNA species is their association with the epigenetic machinery and the recruitment of its regulatory apparatus to specific loci, resulting in DNA methylation and/or post-translational modifications of histones. Such epigenetic modifications play a pivotal role in maintaining the active or inactive transcriptional state of chromatin and are crucial regulators of normal cellular development and tissue-specific gene expression. Evidently, aberrant expression of lncRNAs that interact with epigenetic modifiers can cause severe epigenetic disruption and is thus is closely associated with altered gene function, cellular dysregulation, and malignant transformation. Here, we survey the latest breakthroughs concerning the role of lncRNAs interacting with the epigenetic machinery in various forms of cancer.
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Affiliation(s)
- Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
| | - Nikos Sideris
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
- B.S.R.C "Alexander Fleming", 34 Fleming str, 16672 Vari, Greece.
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22
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Abstract
DNA methylation inhibitors have become the mainstay for treatment of certain haematological malignancies. In addition to their abilities to reactivate genes, including tumour suppressors, that have acquired DNA methylation during carcinogenesis, they induce the expression of thousands of transposable elements including endogenous retroviruses and latent cancer testis antigens normally silenced by DNA methylation in most somatic cells. This results in a state of viral mimicry in which treated cells mount an innate immune response by turning on viral defence genes and potentially expressing neoantigens. Furthermore, these changes mediated by DNA methylation inhibitors can also alter the function of immune cells relevant to acquired immunity. Additionally, other inhibitors of epigenetic processes, such as histone deacetylases, methylases and demethylases, can elicit similar effects either individually or in combinations with DNA methylation inhibitors. These findings together with rapid development of immunotherapies open new avenues for cancer treatment.
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Affiliation(s)
- Peter A Jones
- Van Andel Research Institute (VARI), Grand Rapids, MI, USA
| | - Hitoshi Ohtani
- Van Andel Research Institute (VARI), Grand Rapids, MI, USA
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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23
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Poulos RC, Olivier J, Wong JWH. The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes. Nucleic Acids Res 2017; 45:7786-7795. [PMID: 28531315 PMCID: PMC5737810 DOI: 10.1093/nar/gkx463] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/15/2017] [Indexed: 12/31/2022] Open
Abstract
Methylated cytosines (5mCs) are frequently mutated in the genome. However, no studies have yet comprehensively analysed mutation–methylation associations across cancer types. Here we analyse 916 cancer genomes, together with tissue type-specific methylation and replication timing data. We describe a strong mutation–methylation association across colorectal cancer subtypes, most interestingly in samples with microsatellite instability (MSI) or Polymerase epsilon (POLE) exonuclease domain mutations. By analysing genomic regions with differential mismatch repair (MMR) efficiency, we suggest a possible role for MMR in the correction of 5mC deamination events, potentially accounting for the high rate of 5mC mutation accumulation in MSI tumours. Additionally, we propose that mutant POLE asserts a mutator phenotype specifically at 5mCs, and we find coding mutation hotspots in POLE-mutant cancers at highly-methylated CpGs in the tumour-suppressor genes APC and TP53. Finally, using multivariable regression models, we demonstrate that different cancers exhibit distinct mutation–methylation associations, with DNA repair influencing such associations in certain cancer genomes. Taken together, we find differential associations with methylation that are vital for accurately predicting expected mutation loads across cancer types. Our findings reveal links between methylation and common mutation and repair processes, with these mechanisms defining a key part of the mutational landscape of cancer genomes.
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Affiliation(s)
- Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
| | - Jake Olivier
- School of Mathematics and Statistics, The Red Centre, UNSW Sydney, NSW 2052, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
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24
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Pan Y, Liu G, Zhou F, Su B, Li Y. DNA methylation profiles in cancer diagnosis and therapeutics. Clin Exp Med 2017; 18:1-14. [PMID: 28752221 DOI: 10.1007/s10238-017-0467-0] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
Cancer initiation and proliferation is regulated by both epigenetic and genetic events with epigenetic modifications being increasingly identified as important targets for cancer research. DNA methylation catalyzed by DNA methyltransferases (DNMTs) is one of the essential epigenetic mechanisms that control cell proliferation, apoptosis, differentiation, cell cycle, and transformation in eukaryotes. Recent progress in epigenetics revealed a deeper understanding of the mechanisms of tumorigenesis and provided biomarkers for early detection, diagnosis, and prognosis in cancer patients. Although DNA methylation biomarker possesses potential contributing to precision medicine, there are still limitations to be overcome before it reaches clinical setting. Hence, the current status of DNA methylation biomarkers was reviewed and the future use in clinic was also predicted.
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Affiliation(s)
- Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, No.169 Donghu Road, Wuchang District, Wuhan, 430071, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Guohong Liu
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX, 77030, USA
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Bojin Su
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX, 77030, USA.
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, No.169 Donghu Road, Wuchang District, Wuhan, 430071, China.
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25
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Abstract
The regulation of the genome relies on the epigenome to instruct, define and restrict the activities of growth and development. Among the cohort of epigenetic instructions, DNA methylation is perhaps the best understood. In most mammals, cycles of the addition and removal of DNA methylation constitute phases of reprogramming when the developing embryo must negotiate lineage defining and developmental commitment events. In these instances, the DNA methylation instruction is often removed, thereby allowing a change in permission for future development and a return to a more plastic and pluripotent state. Because of this, the germ line, upon demethylation, can give rise to gametes that are fully functional across generations and poised for totipotency. This return to a less differentiated state can also be achieved experimentally. The loss of DNA methylation constitutes one of the significant barriers to induced pluripotency and is a prerequisite for the generation of iPS cells. Taking fully differentiated cells, such as skin cells, and turning back the developmental clock heralded a technological breakthrough discovery in 2006 (Takahashi and Yamanaka 2006) with unprecedented promise in regenerative medicine. In this chapter, the mechanistic possibilities for DNA demethylation will be described in the context of natural and experimentally induced epigenetic reprogramming. The balance of the maintenance of this heritable mark together with its timely removal is essential for lifelong health and may be a key in our understanding of ageing.
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Affiliation(s)
- Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
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26
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Abstract
Decades of studies have shown that epigenetic alterations play a significant role on cancer development both in vitro and in vivo. However, considering that many cancers harbor mutations at epigenetic modifier genes and that transcription factor-mediated gene regulations are tightly coupled with epigenetic modifications, the majority of epigenetic alterations in cancers could be the consequence of the dysfunction or dysregulation of epigenetic modifiers caused by genetic abnormalities. Therefore, it remains unclear whether bona fide epigenetic abnormalities have causal roles on cancer development. Reprogramming technologies enable us to actively alter epigenetic regulations while preserving genomic information. Taking advantage, recent studies have provided in vivo evidence for the significant impact of epigenetic abnormalities on the initiation, maintenance and progression of cancer cells.
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Affiliation(s)
- Kenji Ito
- Center for iPS Cell Research & Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yasuhiro Yamada
- Center for iPS Cell Research & Application, Kyoto University, Kyoto 606-8507, Japan
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27
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DNA methylation and histone deacetylation regulating insulin sensitivity due to chronic cold exposure. Cryobiology 2017; 74:36-42. [DOI: 10.1016/j.cryobiol.2016.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 12/13/2016] [Indexed: 11/18/2022]
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Kong EY, Cheng SH, Yu KN. Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation. Int J Mol Sci 2016; 17:ijms17122108. [PMID: 27983682 PMCID: PMC5187908 DOI: 10.3390/ijms17122108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into “targeted” effects and “non-targeted” effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology. This review briefly describes both “targeted” and “non-targeted” effects, describes the findings in radiation biology using zebrafish as a model and highlights the potential of zebrafish to assess the epigenetic effects of IR, including DNA methylation, histone modifications and miRNA expression. Other in vivo models are included to compare observations made with zebrafish, or to illustrate the feasibility of in vivo models when the use of zebrafish was unavailable. Finally, tools to study epigenetic modifications in zebrafish, including changes in genome-wide DNA methylation, histone modifications and miRNA expression, are also described in this review.
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Affiliation(s)
- Eva Yi Kong
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
| | - Shuk Han Cheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
| | - Kwan Ngok Yu
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
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Liu F, Wang L, Perna F, Nimer SD. Beyond transcription factors: how oncogenic signalling reshapes the epigenetic landscape. Nat Rev Cancer 2016; 16:359-72. [PMID: 27220480 PMCID: PMC5548460 DOI: 10.1038/nrc.2016.41] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer, once thought to be caused largely by genetic alterations, is now considered to be a mixed genetic and epigenetic disease. The epigenetic landscape, which is dictated by covalent DNA and histone modifications, is profoundly altered in transformed cells. These abnormalities may arise from mutations in, or altered expression of, chromatin modifiers. Recent reports on the interplay between cellular signalling pathways and chromatin modifications add another layer of complexity to the already complex regulation of the epigenome. In this Review, we discuss these new studies and how the insights they provide can contribute to a better understanding of the molecular pathogenesis of neoplasia.
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Affiliation(s)
- Fan Liu
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136
| | - Lan Wang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fabiana Perna
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Stephen D. Nimer
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136
- Department of Internal Medicine, University of Miami, Miller School of Miami, FL33136
- Corresponding Author:
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Sameer AS, Nissar S. Understanding Epigenetics: an Alternative Mechanism of Colorectal Carcinogenesis. CURRENT COLORECTAL CANCER REPORTS 2016. [DOI: 10.1007/s11888-016-0317-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Bosutti A, Zanconati F, Grassi G, Dapas B, Passamonti S, Scaggiante B. Epigenetic and miRNAs Dysregulation in Prostate Cancer: The role of Nutraceuticals. Anticancer Agents Med Chem 2016; 16:1385-1402. [PMID: 27109021 PMCID: PMC5068501 DOI: 10.2174/1871520616666160425105257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 03/29/2016] [Accepted: 04/22/2016] [Indexed: 02/08/2023]
Abstract
The control of cancer onset and progression is recognized to benefit from specific molecular targeting. MiRNAs are increasingly being implicated in prostate cancer, and the evidence suggests they are possible targets for molecular therapy and diagnosis. In cancer cells, growing attention has been dedicated to novel molecular mechanisms linking the epigenetic scenario to miRNA dysregulation. Currently, the rising evidence shows that nutritional and natural agents, the so-called nutraceuticals, could modulate miRNAs expression, and, as a consequence, might influence cellular responses in health or diseases conditions, including cancer. Among dietary components, plant-derived polyphenols are receiving wide interest, either for their anti-aging and anti-oxidant properties, or for their more general "cell-protective" effects. Above all, their role in preventing the occurrence/recurrence of cancer and, in particular, their potentiality in nutritional intervention for modulating the functions of miRNAs and the epigenetic mechanisms, is still under active debate. This review is focused on the more recent highlights of the impact of miRNAs dysregulation on the onset and progression of prostate cancer, their interplay with epigenetic control and their modulation by natural agents.
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Affiliation(s)
| | | | | | | | | | - Bruna Scaggiante
- Address correspondence to this author at the Dept. of Life Sciences, Via Giorgeri, 1, University of Trieste, 34127 Trieste, Italy; Tel: ++39 040 558 3686; Fax: ++39 040 558 3691; E-mail:
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Yang B, Wu RR, Rodgers MT. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1469-1482. [PMID: 26148525 DOI: 10.1007/s13361-015-1174-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
(CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
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Environmental Epigenetics: Crossroad between Public Health, Lifestyle, and Cancer Prevention. BIOMED RESEARCH INTERNATIONAL 2015; 2015:587983. [PMID: 26339624 PMCID: PMC4538403 DOI: 10.1155/2015/587983] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Epigenetics provides the key to transform the genetic information into phenotype and because of its reversibility it is considered an ideal target for therapeutic interventions. This paper reviews the basic mechanisms of epigenetic control: DNA methylation, histone modifications, chromatin remodeling, and ncRNA expression and their role in disease development. We describe also the influence of the environment, lifestyle, nutritional habits, and the psychological influence on epigenetic marks and how these factors are related to cancer and other diseases development. Finally we discuss the potential use of natural epigenetic modifiers in the chemoprevention of cancer to link together public health, environment, and lifestyle.
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Yamaya Y, Sugiya H, Watari T. Methylation of free-floating deoxyribonucleic acid fragments in the bronchoalveolar lavage fluid of dogs with chronic bronchitis exposed to environmental tobacco smoke. Ir Vet J 2015; 68:7. [PMID: 25937920 PMCID: PMC4417338 DOI: 10.1186/s13620-015-0035-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
Background The etiology of canine chronic bronchitis (CB) is not completely understood, although exposure to environmental tobacco smoke (ETS) affects the airway inflammatory responses in some dogs with CB. The mechanism by which this occurs is unknown. Findings We investigated the concentrations and methylation rates of free-floating DNA fragments in bronchoalveolar lavage fluid (BALF) from dogs with chronic bronchitis. Based on serum cotinine levels, dogs with CB were divided into 2 groups: dogs that either had or had not been exposed to ETS. Our results demonstrated that the total nucleated cell and macrophage numbers increased in BALF of ETS-exposed dogs with CB. There were no significant differences in DNA concentrations and methylation rates in BALF between the 2 groups. However, 3 out of 8 dogs exposed to ETS had high DNA methylation rates in their BALF samples. Conclusion Our results suggest that ETS exposure leads to epigenetic modifications of cellular components in BALF in dogs diagnosed with CB.
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Affiliation(s)
- Yoshiki Yamaya
- Laboratory of Comprehensive Veterinary Clinical Studies, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa Japan
| | - Hiroshi Sugiya
- Laboratory of Veterinary Biochemistry, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa Japan
| | - Toshihiro Watari
- Laboratory of Comprehensive Veterinary Clinical Studies, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa Japan
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35
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Gavina JMA, Yao C, Feng YL. Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants. Talanta 2014; 130:475-94. [PMID: 25159438 DOI: 10.1016/j.talanta.2014.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 02/08/2023]
Abstract
DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.
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Affiliation(s)
- Jennilee M A Gavina
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Chunhe Yao
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9.
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Alvarado S, Fernald RD, Storey KB, Szyf M. The dynamic nature of DNA methylation: a role in response to social and seasonal variation. Integr Comp Biol 2014; 54:68-76. [PMID: 24813708 DOI: 10.1093/icb/icu034] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An organism's ability to adapt to its environment depends on its ability to regulate and maintain tissue specific, temporal patterns of gene transcription in response to specific environmental cues. Epigenetic mechanisms are responsible for many of the intricacies of a gene's regulation that alter expression patterns without affecting the genetic sequence. In particular, DNA methylation has been shown to have an important role in regulating early development and in some human diseases. Within these domains, DNA methylation has been extensively characterized over the past 60 years, but the discovery of its role in regulating behavioral outcomes has led to renewed interest in its potential roles in animal behavior and phenotypic plasticity. The conservation of DNA methylation across the animal kingdom suggests a possible role in the plasticity of genomic responses to environmental cues in natural environments. Here, we review the historical context for the study of DNA methylation, its function and mechanisms, and provide examples of gene/environment interactions in response to social and seasonal cues. Finally, we discuss useful tools to interrogate and dissect the function of DNA methylation in non-model organisms.
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Affiliation(s)
- Sebastian Alvarado
- *Stanford University, Gilbert Biology #314, 371 Serra Mall, Palo Alto CA 940305; Carleton University, Steacie Building #507, 1125 Colonel By Ottawa Ontario, K1S5B6; McGill University, McIntyre Medical Building #1309, 3655 Sir William Osler,Montreal, Quebec H3G1Y6
| | - Russell D Fernald
- *Stanford University, Gilbert Biology #314, 371 Serra Mall, Palo Alto CA 940305; Carleton University, Steacie Building #507, 1125 Colonel By Ottawa Ontario, K1S5B6; McGill University, McIntyre Medical Building #1309, 3655 Sir William Osler,Montreal, Quebec H3G1Y6
| | - Kenneth B Storey
- *Stanford University, Gilbert Biology #314, 371 Serra Mall, Palo Alto CA 940305; Carleton University, Steacie Building #507, 1125 Colonel By Ottawa Ontario, K1S5B6; McGill University, McIntyre Medical Building #1309, 3655 Sir William Osler,Montreal, Quebec H3G1Y6
| | - Moshe Szyf
- *Stanford University, Gilbert Biology #314, 371 Serra Mall, Palo Alto CA 940305; Carleton University, Steacie Building #507, 1125 Colonel By Ottawa Ontario, K1S5B6; McGill University, McIntyre Medical Building #1309, 3655 Sir William Osler,Montreal, Quebec H3G1Y6*Stanford University, Gilbert Biology #314, 371 Serra Mall, Palo Alto CA 940305; Carleton University, Steacie Building #507, 1125 Colonel By Ottawa Ontario, K1S5B6; McGill University, McIntyre Medical Building #1309, 3655 Sir William Osler,Montreal, Quebec H3G1Y6
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Van der Meulen J, Van Roy N, Van Vlierberghe P, Speleman F. The epigenetic landscape of T-cell acute lymphoblastic leukemia. Int J Biochem Cell Biol 2014; 53:547-57. [PMID: 24786297 DOI: 10.1016/j.biocel.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/29/2022]
Abstract
The genetic landscape of T-ALL has been very actively explored during the past decades. This leads to an overwhelming body of exciting novel findings providing insight into (1) the genetic heterogeneity of the disease with marked genetic subsets, (2) the mechanisms by which aberrant T-cell development drive leukemogenesis and (3) emerging opportunities for novel therapeutic interventions. Of further interest, recent genome wide sequencing studies identified proteins that actively participate in the regulation of the T-cell epigenome as novel oncogenes and tumor suppressor genes in T-ALL. The identification of these perturbed molecular epigenetic events in the pathogenesis of T-ALL will contribute to the further exploration of novel therapies in this cancer type. As some epigenetic therapies have recently been approved for a number of hematological neoplasms, one could speculate that targeted therapies against epigenetic regulators might offer good prospects for T-ALL treatment in the near future. In this review, we summarize the epigenetic discoveries made in T-ALL hitherto and discuss possible new venues for epigenetic therapeutic intervention in this aggressive subtype of human leukemia. This article is part of a Directed Issue entitled: Rare Cancers.
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Affiliation(s)
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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38
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Dong Y, Zhao H, Li H, Li X, Yang S. DNA methylation as an early diagnostic marker of cancer (Review). Biomed Rep 2014; 2:326-330. [PMID: 24748968 PMCID: PMC3990206 DOI: 10.3892/br.2014.237] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/06/2014] [Indexed: 01/04/2023] Open
Abstract
DNA methylation is one of the essential epigenetic mechanisms that are closely correlated with the mechanisms underlying cell growth, differentiation and transformation in eukaryotes. Global changes in the epigenetic landscape are considered to be a hallmark of cancer. The initiation and progression of cancer are mediated through epigenetic modifications along with genetic alterations. Aberrant methylation of promoter regions is an epigenetic abnormality of the human genome that is highly characteristic of cancer. In this review, we aimed to summarize our current understanding of the alterations in the epigenetic landscape and investigate the potential use of DNA and RNA methylation in effective molecular treatment strategies.
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Affiliation(s)
- Yuanyuan Dong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, P.R. China ; Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Haiyang Zhao
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, P.R. China
| | - Haiyan Li
- Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Xiaokun Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, P.R. China ; Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Shulin Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, P.R. China
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Yaish MW, Peng M, Rothstein SJ. Global DNA methylation analysis using methyl-sensitive amplification polymorphism (MSAP). Methods Mol Biol 2014; 1062:285-98. [PMID: 24057373 DOI: 10.1007/978-1-62703-580-4_16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is a crucial epigenetic process which helps control gene transcription activity in eukaryotes. Information regarding the methylation status of a regulatory sequence of a particular gene provides important knowledge of this transcriptional control. DNA methylation can be detected using several methods, including sodium bisulfite sequencing and restriction digestion using methylation-sensitive endonucleases. Methyl-Sensitive Amplification Polymorphism (MSAP) is a technique used to study the global DNA methylation status of an organism and hence to distinguish between two individuals based on the DNA methylation status determined by the differential digestion pattern. Therefore, this technique is a useful method for DNA methylation mapping and positional cloning of differentially methylated genes. In this technique, genomic DNA is first digested with a methylation-sensitive restriction enzyme such as HpaII, and then the DNA fragments are ligated to adaptors in order to facilitate their amplification. Digestion using a methylation-insensitive isoschizomer of HpaII, MspI is used in a parallel digestion reaction as a loading control in the experiment. Subsequently, these fragments are selectively amplified by fluorescently labeled primers. PCR products from different individuals are compared, and once an interesting polymorphic locus is recognized, the desired DNA fragment can be isolated from a denaturing polyacrylamide gel, sequenced and identified based on DNA sequence similarity to other sequences available in the database. We will use analysis of met1, ddm1, and atmbd9 mutants and wild-type plants treated with a cytidine analogue, 5-azaC, or zebularine to demonstrate how to assess the genetic modulation of DNA methylation in Arabidopsis. It should be noted that despite the fact that MSAP is a reliable technique used to fish for polymorphic methylated loci, its power is limited to the restriction recognition sites of the enzymes used in the genomic DNA digestion.
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Affiliation(s)
- Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
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Kotandeniya D, Murphy D, Yan S, Park S, Seneviratne U, Koopmeiners JS, Pegg A, Kanugula S, Kassie F, Tretyakova N. Kinetics of O(6)-pyridyloxobutyl-2'-deoxyguanosine repair by human O(6)-alkylguanine DNA alkyltransferase. Biochemistry 2013; 52:4075-88. [PMID: 23683164 DOI: 10.1021/bi4004952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N-nitrosonicotine (NNN) are potent carcinogens believed to contribute to the development of lung tumors in smokers. NNK and NNN are metabolized to DNA-reactive species that form a range of nucleobase adducts, including bulky O(6)-[4-oxo-4-(3-pyridyl)but-1-yl]deoxyguanosine (O(6)-POB-dG) lesions. If not repaired, O(6)-POB-dG adducts induce large numbers of G → A and G → T mutations. Previous studies have shown that O(6)-POB-dG can be directly repaired by O(6)-alkylguanine-DNA alkyltransferase (AGT), which transfers the pyridyloxobutyl group from O(6)-alkylguanines in DNA to an active site cysteine residue within the protein. In the present study, we investigated the influence of DNA sequence context and endogenous cytosine methylation on the kinetics of AGT-dependent repair of O(6)-POB-dG in duplex DNA. Synthetic oligodeoxynucleotide duplexes containing site-specific O(6)-POB-dG adducts within K-ras and p53 gene-derived DNA sequences were incubated with recombinant human AGT protein, and the kinetics of POB group transfer was monitored by isotope dilution HPLC-ESI(+)-MS/MS analysis of O(6)-POB-dG remaining in DNA over time. We found that the second-order rates of AGT-mediated repair were influenced by DNA sequence context (10-fold differences) but were only weakly affected by the methylation status of neighboring cytosines. Overall, AGT-mediated repair of O(6)-POB-dG was 2-7 times slower than that of O(6)-Me-dG adducts. To evaluate the contribution of AGT to O(6)-POB-dG repair in human lung, normal human bronchial epithelial cells (HBEC) were treated with model pyridyloxobutylating agent, and O(6)-POB-dG adduct repair over time was monitored by HPLC-ESI(+)-MS/MS. We found that HBEC cells were capable of removing O(6)-POB-dG lesions, and the repair rates were significantly reduced in the presence of an AGT inhibitor (O(6)-benzylguanine). Taken together, our results suggest that AGT plays an important role in protecting human lung against tobacco nitrosamine-mediated DNA damage and that inefficient AGT repair of O(6)-POB-dG at a specific sequences contributes to mutational spectra observed in smoking-induced lung cancer.
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Affiliation(s)
- Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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Chen J, Gong M, Lu S, Liu F, Xia L, Nie D, Zou F, Shi J, Ju S, Zhao L, Zuo H, Qi J, Shi W. Detection of serum Alu element hypomethylation for the diagnosis and prognosis of glioma. J Mol Neurosci 2013; 50:368-75. [PMID: 23657981 DOI: 10.1007/s12031-013-0014-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022]
Abstract
Global genomic hypomethylation is a hallmark of cancer in humans. In the present study, the feasibility of measuring hypomethylation of Alu elements (Alu) in serum and its clinical utility were investigated. Tumor tissues and matched serum specimens from 65 glioma patients and serum samples from 30 healthy controls were examined for Alu hypomethylation by bisulfite sequencing. The median serum Alu methylation level was 47.30 % in patients (interquartile range (IQR), 35.40-54.25 %) and 57.90 % in the controls (IQR, 55.25-61.45 %). The median Alu methylation level in tumor samples was 40.30 % (IQR, 36.80-54.20 %), which shows the correlation of Alu hypomethylation between tumor and serum samples (r = 0.882) in the study group. The methylation level was higher in the low-grade glioma group than in the high-grade group both in tumor and serum samples. A correlation between high methylation level and longer survival time was detected in tumor and serum samples. Receiver operating characteristic curve analysis showed that the area under the curve for diagnosis was 0.861 (95 % confidence interval, 0.789-0.933), suggesting that Alu hypomethylation in serum may be of diagnostic value. Our results indicate that the detection of Alu hypomethylation in serum may be clinically useful for the diagnosis and prognosis of glioma.
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Affiliation(s)
- Jian Chen
- Department of Neurosurgery, Comprehensive Surgical Laboratory, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, Jiangsu Province, China 226001
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42
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Abstract
Cancer has been considered a genetic disease with a wide array of well-characterized gene mutations and chromosomal abnormalities. Of late, aberrant epigenetic modifications have been elucidated in cancer, and together with genetic alterations, they have been helpful in understanding the complex traits observed in neoplasia. "Cancer Epigenetics" therefore has contributed substantially towards understanding the complexity and diversity of various cancers. However, the positioning of epigenetic events during cancer progression is still not clear, though there are some reports implicating aberrant epigenetic modifications in very early stages of cancer. Amongst the most studied aberrant epigenetic modifications are the DNA methylation differences at the promoter regions of genes affecting their expression. Hypomethylation mediated increased expression of oncogenes and hypermethylation mediated silencing of tumor suppressor genes are well known examples. This chapter also explores the correlation of DNA methylation and demethylation enzymes with cancer.
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Affiliation(s)
- Gopinathan Gokul
- Laboratory of Mammalian Genetics, CDFD, Hyderabad, 500001, India
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Stadler SC, Allis CD. Linking epithelial-to-mesenchymal-transition and epigenetic modifications. Semin Cancer Biol 2012; 22:404-10. [PMID: 22706095 DOI: 10.1016/j.semcancer.2012.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 06/07/2012] [Indexed: 12/19/2022]
Abstract
Cancer, as well as other human disorders, has long been considered to result from the consequence of genetic mutations in key regulatory genes that reside in pathways controlling proliferation, cellular differentiation, DNA damage and repair. In the case of cancer, mutations are well documented to arise in key oncogenes and critically important tumor-suppressor genes as part of the disease progression process. In addition to more accepted, genetic mutations, a rapidly increasing body of evidence supports the general view that profound alterations also occur in 'epigenes', whose products serve to define the 'epigenetic landscape' of tumor cells. Aberrant changes in epigenetic mechanisms such as DNA methylation, histone modifications and expression of micro RNAs play an important role in cancer and contribute to malignant transitions. Here we review recent studies linking epigenetic mechanisms to epithelial-to-mesenchymal transition as defined in normal processes, as well as abnormal transitions that lead to oncogensis.
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Affiliation(s)
- Sonja C Stadler
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Liebigstraße 27, 04103 Leipzig, Germany.
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Abstract
Epigenetic silencing of genes is now recognized to be an important mechanism for inactivation of tumor suppressor genes in carcinogenesis. Because the role of genetic alterations in colorectal carcinogenesis has been well studied, colorectal cancer also offers an excellent model for elucidation of epigenetic mechanisms involved in carcinogenesis. DNA methylation and histone modification are involved in a complex network to maintain gene silencing and cause carcinogenesis. DNA methylation of cancer-related gene promoters generally begins early in the process of tumorigenesis, affecting various types of colorectal cancer to differing degrees. These advances in the understanding of the biology of tumorigenesis can be expected to provide distinct biomarkers that will aid future diagnosis, risk assessment, and treatment methods for patients with colorectal cancer.
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DNA methylation biomarkers for lung cancer. Tumour Biol 2011; 33:287-96. [DOI: 10.1007/s13277-011-0282-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/21/2011] [Indexed: 01/13/2023] Open
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Foulks JM, Parnell KM, Nix RN, Chau S, Swierczek K, Saunders M, Wright K, Hendrickson TF, Ho KK, McCullar MV, Kanner SB. Epigenetic drug discovery: targeting DNA methyltransferases. ACTA ACUST UNITED AC 2011; 17:2-17. [PMID: 21965114 DOI: 10.1177/1087057111421212] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic modification of DNA leads to changes in gene expression. DNA methyltransferases (DNMTs) comprise a family of nuclear enzymes that catalyze the methylation of CpG dinucleotides, resulting in an epigenetic methylome distinguished between normal cells and those in disease states such as cancer. Disrupting gene expression patterns through promoter methylation has been implicated in many malignancies and supports DNMTs as attractive therapeutic targets. This review focuses on the rationale of targeting DNMTs in cancer, the historical approach to DNMT inhibition, and current marketed hypomethylating therapeutics azacytidine and decitabine. In addition, we address novel DNMT inhibitory agents emerging in development, including CP-4200 and SGI-110, analogs of azacytidine and decitabine, respectively; the oligonucleotides MG98 and miR29a; and a number of reversible inhibitors, some of which appear to be selective against particular DNMT isoforms. Finally, we discuss future opportunities and challenges for next-generation therapeutics.
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Affiliation(s)
- Jason M Foulks
- Astex Pharmaceuticals, Inc., Salt Lake City, UT 84109, USA.
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Seiberling KA, Church CA, Herring JL, Sowers LC. Epigenetics of chronic rhinosinusitis and the role of the eosinophil. Int Forum Allergy Rhinol 2011; 2:80-4. [PMID: 22311846 DOI: 10.1002/alr.20090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/20/2011] [Accepted: 06/22/2011] [Indexed: 01/11/2023]
Abstract
BACKGROUND One theory for the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) involves aberration in the expression of genes that maintain the sinonasal innate immune system. We propose that the alteration in gene expression seen in CRSwNP is a result of oxidative byproducts of eosinophils. Activated eosinophils and neutrophils may lead to the production of hypobromous acid (HOBr) and hypochlorous acid (HOCL) and the posttranslational modification products 5-bromocytosine (5BrC) and 5-chlorocytosine (5ClC), respectively. 5BrC and 5ClC may cause aberrant methylation of cytosine during DNA replication and mimic the endogenous methylation signal associated with gene silencing. We propose to use gas chromatography-mass spectrometry (GC-MS) to identify the presence of 5BrC and 5ClC in CRSwNP patients. METHODS Patients with CRSwNP undergoing endoscopic sinus surgery were prospectively recruited into this study. Using GC-MS, tissue specimens were analyzed for the presence of 5BrC, 5ClC, and methylated cytosine. RESULTS Tissue specimens from 14 patients with CRSwNP and 3 normal controls were processed using GC-MS. CRSwNP specimens demonstrate elevated levels of 5BrC and 5ClC compared to normal controls. CONCLUSION Eosinophils, which are predominantly found in CRSwNP, may lead to DNA modification and gene silencing via 5BrC and aberrant methylation patterns and may help explain the pathogenesis of CRSwNP.
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Affiliation(s)
- Kristin A Seiberling
- Department of Otolaryngology-Head and Neck Surgery, Loma Linda University, Loma Linda, CA 92354, USA.
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Abstract
Epigenetics refers to the study of mechanisms that alter gene expression without altering the primary DNA sequence. Epigenetic mechanisms are heritable and reversible. Over the last few decades, epigenetics has obtained a large importance in cancer research. Epigenetic alterations are widely described as essential players in cancer progression. They comprise DNA methylation, histone modifications, nucleosome positioning, and small, noncoding RNAs (miRNA, siRNA). They are involved in transcriptional changes and decisive events that will determine cell fate and phenotype. Epigenetics not only offers light into cancer biological processes, but also represents an attractive opportunity of reverting cancer-specific alterations, which may lead, in the future, to a possibility of stopping this disease. Epigenetic changes have been identified as putative cancer biomarkers for early detection, disease monitoring, prognosis, and risk assessment. Other epigenetic alterations are promising therapeutic targets and even therapeutic agents. Emerging discoveries in this area are already contributing to cancer management and monitoring, and a lot more progresses are expected in the future.
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Affiliation(s)
- Mariana Brait
- Division of Head and Neck Cancer Research, Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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Abstract
The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.
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