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Ito Y, Usui G, Seki M, Fukuyo M, Matsusaka K, Hoshii T, Sata Y, Morimoto J, Hata A, Nakajima T, Rahmutulla B, Kaiho T, Inage T, Tanaka K, Sakairi Y, Suzuki H, Yoshino I, Kaneda A. Association of frequent hypermethylation with high grade histological subtype in lung adenocarcinoma. Cancer Sci 2023. [PMID: 37082886 DOI: 10.1111/cas.15817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Lung adenocarcinoma is classified morphologically into five histological subtypes according to the WHO classification. While each histological subtype correlates with a distinct prognosis, the molecular basis has not been fully elucidated. Here we conducted DNA methylation analysis of 30 lung adenocarcinoma cases annotated with the predominant histological subtypes and three normal lung cases using the Infinium BeadChip. Unsupervised hierarchical clustering analysis revealed three subgroups with different methylation levels: high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME). Micropapillary pattern (MPP)-predominant cases and those with MPP components were significantly enriched in HME (p = 0.02 and p = 0.03, respectively). HME cases showed a significantly poor prognosis for recurrence-free survival (p < 0.001) and overall survival (p = 0.006). We identified 365 HME marker genes specifically hypermethylated in HME cases with enrichment of "cell morphogenesis" related genes; 305 IME marker genes hypermethylated in HME and IME, but not in LME, with enrichment "embryonic organ morphogenesis"-related genes; 257 Common marker genes hypermethylated commonly in all cancer cases, with enrichment of "regionalization"-related genes. We extracted surrogate markers for each epigenotype and designed pyrosequencing primers for five HME markers (TCERG1L, CXCL12, FAM181B, HOXA11, GAD2), three IME markers (TBX18, ZNF154, NWD2) and three Common markers (SCT, GJD2, BARHL2). DNA methylation profiling using Infinium data was validated by pyrosequencing, and HME cases defined by pyrosequencing results also showed the worse recurrence-free survival. In conclusion, lung adenocarcinomas are stratified into subtypes with distinct DNA methylation levels, and the high-methylation subtype correlated with MPP-predominant cases and those with MPP components and showed a poor prognosis.
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Affiliation(s)
- Yuki Ito
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Genki Usui
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Sata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Junichi Morimoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Hata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Taisuke Kaiho
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Terunaga Inage
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuhisa Tanaka
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Sakairi
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidemi Suzuki
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Yoshino
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Carvalho CM, Coimbra BM, Bugiga A, Marques DF, Kiyomi Ota V, Mello AF, Mello MF, Belangero SI. Hyperarousal Symptom Severity in Women with Posttraumatic Stress Disorder Might Be Associated with LINE-1 Hypomethylation in Childhood Sexual Abuse Victims. Complex Psychiatry 2023; 9:44-56. [PMID: 37034826 PMCID: PMC10080193 DOI: 10.1159/000529698] [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: 11/04/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction Sexual assault and a history of childhood sexual abuse (CSA) are related to posttraumatic stress disorder (PTSD) development. Long interspersed nuclear elements (LINE-1) are transposable elements, and their methylation is used to infer DNA global methylation. DNA methylation can be affected by trauma exposition which in turn would be associated with PTSD. Thus, we investigated if the LINE-1 methylation pattern is related to PTSD symptoms in females with a history of CSA. Methods This is a case-control study that examined, at baseline (W1), 64 women victims of sexual assault diagnosed with PTSD and 31 patients with PTSD who completed the 1-year follow-up (W2). Participants were categorized into two groups according to the presence of CSA (PTSDCSA+: NW1 = 19, NW2 = 10; PTSDCSA-: NW1 = 45, NW2 = 21). PTSD symptoms (re-experiencing, avoidance, hyperarousal, alterations in cognition/mood) were assessed using the Clinician-Administered PTSD Scale, and the history of CSA was assessed by the Childhood Trauma Questionnaire. LINE-1 methylation was measured in three sites (CpG1, CpG2, CpG3) located in the 5'UTR region using bisulfite conversion followed by pyrosequencing. Linear regression models were performed to test the relation between LINE-1 CpG sites methylation and PTSD symptoms. Results We found a negative association between CpG2 methylation and hyperarousal symptoms among those in the PTSDCSA+ group in W1 (adjusted p = 0.003) compared to the PTSDCSA- group (p > 0.05). Still, no association was observed between other PTSD symptoms and other CpG sites. Further, in the longitudinal analysis, LINE-1 hypomethylation was no longer observed in PTSD participants exposed to CSA. Conclusion Our findings suggest that LINE-1 methylation may help understand the relationship between trauma and PTSD. However, more studies are needed to investigate LINE-1 as an epigenetic marker of psychiatric disorders.
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Affiliation(s)
- Carolina Muniz Carvalho
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Bruno Messina Coimbra
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Psychiatry, Amsterdam Public Health Research Institute and Amsterdam Neuroscience Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Amanda Bugiga
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Diogo Ferri Marques
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Vanessa Kiyomi Ota
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Andrea Feijó Mello
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Marcelo Feijó Mello
- Department of Psychiatry of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Sintia Iole Belangero
- LiNC - Laboratory of Integrative Neuroscience of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division of Department of Morphology and Genetics of Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Marques DF, Ota VK, Santoro ML, Talarico F, Costa GO, Spindola LM, Cogo-Moreira H, Carvalho CM, Xavier G, Cavalcante DA, Gadelha A, Noto C, Cordeiro Q, Bressan RA, Moretti PN, Belangero SI. LINE-1 hypomethylation is associated with poor risperidone response in a first episode of psychosis cohort. Epigenomics 2020; 12:1041-1051. [DOI: 10.2217/epi-2019-0350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: We investigated the DNA methylation profile over LINE-1 in antipsychotic-naive, first-episode psychosis-patients (n = 69) before and after 2 months of risperidone treatment and in healthy controls (n = 62). Materials & methods: Patients were evaluated using standardized scales and classified as responders and nonresponders. DNA from blood was bisulfite converted and LINE-1 fragments were amplified and pyrosequencing was performed. Results: Lower LINE-1 methylation was observed in antipsychotic-naive first-episode psychosis patients than in healthy controls. Lower DNA methylation levels before treatment were associated with poor risperidone responses. A positive correlation was observed between LINE-1 methylation levels and positive symptoms response. Conclusion: Our study brings new insight regarding how epigenomic studies and clinical correlation studies can supplement psychosis treatment.
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Affiliation(s)
- Diogo Ferri Marques
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Vanessa Kiyomi Ota
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Marcos Leite Santoro
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Fernanda Talarico
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Giovany Oliveira Costa
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Leticia Maria Spindola
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Hugo Cogo-Moreira
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Carolina Muniz Carvalho
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Gabriela Xavier
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Daniel Azevedo Cavalcante
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Ary Gadelha
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Cristiano Noto
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Quirino Cordeiro
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Department of Psychiatry, Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, Brazil
| | - Rodrigo Affonseca Bressan
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Patricia Natalia Moretti
- Programa de Pós-graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Sintia Iole Belangero
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Integrative Neuroscience (LiNC), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Kurokawa T, Nakagawa T, Matsusaka K, Fukuyo M, Mima M, Misawa K, Rahmutulla B, Ikeda JI, Hanazawa T, Okamoto Y, Kaneda A. Establishment of epigenetic markers to predict irradiation efficacy against oropharyngeal cancer. Cancer Sci 2020; 111:1407-1416. [PMID: 32012407 PMCID: PMC7156782 DOI: 10.1111/cas.14338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
Irradiation, or chemoradiotherapy, is a curative treatment for oropharyngeal squamous cell carcinoma (OPSCC). Its invasiveness, however, can often negate its efficacy. Therefore, developing methods to predict which patients would benefit from irradiation is urgent. Promoter DNA hypermethylation was recently reported to correlate with favorable OPSCC prognosis. It is still unclear, however, whether there is an association between promoter DNA methylation and response to irradiation. In this study, we analyzed DNA methylation in the specimens from 40 OPSCC patients who had undergone irradiation, using the Infinium assay. Our results showed significant correlation between high levels of promoter DNA methylation and better response to treatment (P < 0.01). We used the 10 most differentially-methylated genes between responders and non-responders to develop a panel of predictive markers for efficacy. Our panel had high sensitivity, specificity and accuracy (92%, 93% and 93%, respectively). We conducted pyrosequencing to quantitatively validate the methylation levels of 8 of the 10 marker genes (ROBO1, ULK4P3, MYOD1, LBX1, CACNA1A, IRX4, DPYSL3 and ELAVL2) obtained by Infinium. The validation by pyrosequencing showed that these 8 genes had a high prediction performance for the training set of 40 specimens and for a validation set of 35 OPSCC specimens, showing 96% sensitivity, 89% specificity and 94% accuracy. Methylation of these markers correlated significantly with better progression-free and overall survival rates, regardless of human papillomavirus status. These results indicate that increased DNA methylation is associated with better responses to irradiation therapy and that DNA methylation can help establish efficacy prediction markers in OPSCC.
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Affiliation(s)
- Tomoya Kurokawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masato Mima
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Chiba, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jun-Ichiro Ikeda
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshitaka Okamoto
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Japan Organization of Occupational Health and Safety Chiba Rosai Hospital, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Kringel D, Kaunisto MA, Kalso E, Lötsch J. Machine-learned analysis of global and glial/opioid intersection-related DNA methylation in patients with persistent pain after breast cancer surgery. Clin Epigenetics 2019; 11:167. [PMID: 31775878 PMCID: PMC6881976 DOI: 10.1186/s13148-019-0772-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Glial cells in the central nervous system play a key role in neuroinflammation and subsequent central sensitization to pain. They are therefore involved in the development of persistent pain. One of the main sites of interaction of the immune system with persistent pain has been identified as neuro-immune crosstalk at the glial-opioid interface. The present study examined a potential association between the DNA methylation of two key players of glial/opioid intersection and persistent postoperative pain. METHODS In a cohort of 140 women who had undergone breast cancer surgery, and were assigned based on a 3-year follow-up to either a persistent or non-persistent pain phenotype, the role of epigenetic regulation of key players in the glial-opioid interface was assessed. The methylation of genes coding for the Toll-like receptor 4 (TLR4) as a major mediator of glial contributions to persistent pain or for the μ-opioid receptor (OPRM1) was analyzed and its association with the pain phenotype was compared with that conferred by global genome-wide DNA methylation assessed via quantification of the methylation in the retrotransposon LINE1. RESULTS Training of machine learning algorithms indicated that the global DNA methylation provided a similar diagnostic accuracy for persistent pain as previously established non-genetic predictors. However, the diagnosis can be based on a single DNA based marker. By contrast, the methylation of TLR4 or OPRM1 genes could not contribute further to the allocation of the patients to the pain-related phenotype groups. CONCLUSIONS While clearly supporting a predictive utility of epigenetic testing, the present analysis cannot provide support for specific epigenetic modulation of persistent postoperative pain via methylation of two key genes of the glial-opioid interface.
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Affiliation(s)
- Dario Kringel
- Institute of Clinical Pharmacology, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eija Kalso
- Division of Pain Medicine, Department of Anesthesiology, Intensive Care and Pain Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Fraunhofer Institute of Molecular Biology and Applied Ecology-Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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6
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Hajji N, García-Domínguez DJ, Hontecillas-Prieto L, O'Neill K, de Álava E, Syed N. The bitter side of epigenetics: variability and resistance to chemotherapy. Epigenomics 2018; 13:397-403. [PMID: 29932342 DOI: 10.2217/epi-2017-0112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
One of the major obstacles to the development of effective new cancer treatments and the main factor for the increasing number of clinical trial failures appears to be the paucity of accurate, reproducible and robust drug resistance testing methods. Most research assessing the resistance of cancers to chemotherapy has concentrated on genetic-based molecular mechanisms, while the role of epigenetics in drug resistance has been generally overlooked. This is rather surprising given that an increasing body of evidence pointing to the fact that epigenetic mechanism alterations appear to play a pivotal role in cancer initiation, progression and development of chemoresistance. This resulted in a series of clinical trials involving epi-drug as single treatment or combined with cancer conventional drugs. In this review, we provided the main mechanisms by which the epigenetic regulators control the resistance to cancer drugs.
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Affiliation(s)
- Nabil Hajji
- The John Fulcher Molecular Neuro-Oncology Laboratory, Division of Brain Sciences, Imperial College London, London, UK
| | - Daniel J García-Domínguez
- Institute of Biomedicine of Seville (IbiS), Virgen del Rocío University Hospital/CSIC/University of Seville/CIBERONC, Spain
| | - Lourdes Hontecillas-Prieto
- Institute of Biomedicine of Seville (IbiS), Virgen del Rocío University Hospital/CSIC/University of Seville/CIBERONC, Spain
| | - Kevin O'Neill
- The John Fulcher Molecular Neuro-Oncology Laboratory, Division of Brain Sciences, Imperial College London, London, UK
| | - Enrique de Álava
- Institute of Biomedicine of Seville (IbiS), Virgen del Rocío University Hospital/CSIC/University of Seville/CIBERONC, Spain
| | - Nelofer Syed
- The John Fulcher Molecular Neuro-Oncology Laboratory, Division of Brain Sciences, Imperial College London, London, UK
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Caffrey A, Irwin RE, McNulty H, Strain JJ, Lees-Murdock DJ, McNulty BA, Ward M, Walsh CP, Pentieva K. Gene-specific DNA methylation in newborns in response to folic acid supplementation during the second and third trimesters of pregnancy: epigenetic analysis from a randomized controlled trial. Am J Clin Nutr 2018; 107:566-575. [PMID: 29635492 DOI: 10.1093/ajcn/nqx069] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/08/2017] [Indexed: 12/21/2022] Open
Abstract
Background Emerging evidence suggests that maternal folate status can impact cognitive development in childhood. Folate-dependent DNA methylation may provide a biological mechanism to link folate status during pregnancy with cognition in the offspring. Objective The objective was to investigate the effect of continued folic acid (FA) supplementation beyond the first trimester of pregnancy on DNA methylation in cord blood of epigenetically controlled genes related to brain development and function. Design Using available cord blood samples (n = 86) from the Folic Acid Supplementation in the Second and Third Trimesters (FASSTT) trial in pregnancy, we applied pyrosequencing techniques to analyze cord blood DNA at 9 candidate loci known to be regulated by methylation, including some previously implicated in observational studies: the widely dispersed retrotransposon long interspersed nuclear element-1 (LINE-1) and 8 single-copy loci (RBM46, PEG3, IGF2, GRB10, BDNF, GRIN3B, OPCML, and APC2). Results The newborns of mothers who received ongoing FA (400 µg/d) through the second and third trimesters, compared with placebo, had significantly lower overall DNA methylation levels at LINE-1 (56.3% ± 1.7% compared with 57.2% ± 2.1%; P = 0.024), IFG2 (48.9% ± 4.4% compared with 51.2% ± 5.1%; P = 0.021), and BDNF (2.7% ± 0.7% compared with 3.1% ± 0.8%; P = 0.003). The effect of FA treatment on DNA methylation was significant only in female offspring for IGF2 (P = 0.028) and only in males for BDNF (P = 0.012). For GRB10 and GRIN3B, we detected no effect on overall methylation; however, individual cytosine-phosphate-guanine sites showed significant DNA methylation changes in response to FA. Conclusions Continued supplementation with FA through trimesters 2 and 3 of pregnancy results in significant changes in DNA methylation in cord blood of genes related to brain development. The findings offer a potential biological mechanism linking maternal folate status with neurodevelopment of the offspring, but this requires further investigation using a genome-wide approach. This trial was registered at www.isrctn.com as ISRCTN19917787.
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Affiliation(s)
- Aoife Caffrey
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rachelle E Irwin
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - J J Strain
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Diane J Lees-Murdock
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Breige A McNulty
- School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Colum P Walsh
- Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health and Genomic Medicine Group, School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
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8
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Kusari F, O'Doherty AM, Hodges NJ, Wojewodzic MW. Bi-directional effects of vitamin B 12 and methotrexate on Daphnia magna fitness and genomic methylation. Sci Rep 2017; 7:11872. [PMID: 28928387 PMCID: PMC5605502 DOI: 10.1038/s41598-017-12148-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
Here we interrogated, using three separate but complementary experimental approaches, the impact of vitamin B12 availability and methotrexate exposure on Daphnia magna, which we hypothesised should have an opposite effect on One carbon metabolism (OCM). OCM is a vital biological process supporting a variety of physiological processes, including DNA methylation. Contrary to mammalian models, this process remains largely unexplored in invertebrates. The purpose of this study was to elucidate the impact of OCM short-term alteration on the fitness and epigenome of the keystone species, Daphnia. We used maternal age at reproduction, brood size and survival rates in combination with DNA methylation sensitive comet assay to determine the effects of vitamin B12 or MTX on fitness and the epigenome. Vitamin B12 had a positive influence on Daphnia fitness and we provide evidence demonstrating that this may be associated with an increased level of genome-wide DNA methylation. Conversely, exposing D. magna to MTX negatively influenced the fitness of the animals and was associated with loss of global DNA methylation, translating in decreased fitness. These results highlight the potential importance of OCM in invertebrates, providing novel evidence supporting a potential role for epigenetic modifications to the genome in D. magna environmental adaptability.
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Affiliation(s)
- Fitore Kusari
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT,, UK
| | - Alan M O'Doherty
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nikolas J Hodges
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT,, UK
| | - Marcin W Wojewodzic
- University of Birmingham, School of Biosciences, Edgbaston, Birmingham, B15 2TT,, UK.
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Lipid metabolism is associated with developmental epigenetic programming. Sci Rep 2016; 6:34857. [PMID: 27713555 PMCID: PMC5054359 DOI: 10.1038/srep34857] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/19/2016] [Indexed: 12/24/2022] Open
Abstract
Maternal diet and metabolism impact fetal development. Epigenetic reprogramming facilitates fetal adaptation to these in utero cues. To determine if maternal metabolite levels impact infant DNA methylation globally and at growth and development genes, we followed a clinical birth cohort of 40 mother-infant dyads. Targeted metabolomics and quantitative DNA methylation were analyzed in 1st trimester maternal plasma (M1) and delivery maternal plasma (M2) as well as infant umbilical cord blood plasma (CB). We found very long chain fatty acids, medium chain acylcarnitines, and histidine were: (1) stable in maternal plasma from pregnancy to delivery, (2) significantly correlated between M1, M2, and CB, and (3) in the top 10% of maternal metabolites correlating with infant DNA methylation, suggesting maternal metabolites associated with infant DNA methylation are tightly controlled. Global DNA methylation was highly correlated across M1, M2, and CB. Thus, circulating maternal lipids are associated with developmental epigenetic programming, which in turn may impact lifelong health and disease risk. Further studies are required to determine the causal link between maternal plasma lipids and infant DNA methylation patterns.
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Knothe C, Shiratori H, Resch E, Ultsch A, Geisslinger G, Doehring A, Lötsch J. Disagreement between two common biomarkers of global DNA methylation. Clin Epigenetics 2016; 8:60. [PMID: 27222668 PMCID: PMC4877994 DOI: 10.1186/s13148-016-0227-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/10/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The quantification of global DNA methylation has been established in epigenetic screening. As more practicable alternatives to the HPLC-based gold standard, the methylation analysis of CpG islands in repeatable elements (LINE-1) and the luminometric methylation assay (LUMA) of overall 5-methylcytosine content in "CCGG" recognition sites are most widely used. Both methods are applied as virtually equivalent, despite the hints that their results only partly agree. This triggered the present agreement assessments. RESULTS Three different human cell types (cultured MCF7 and SHSY5Y cell lines treated with different chemical modulators of DNA methylation and whole blood drawn from pain patients and healthy volunteers) were submitted to the global DNA methylation assays employing LINE-1 or LUMA-based pyrosequencing measurements. The agreement between the two bioassays was assessed using generally accepted approaches to the statistics for laboratory method comparison studies. Although global DNA methylation levels measured by the two methods correlated, five different lines of statistical evidence consistently rejected the assumption of complete agreement. Specifically, a bias was observed between the two methods. In addition, both the magnitude and direction of bias were tissue-dependent. Interassay differences could be grouped based on Bayesian statistics, and these groups allowed in turn to re-identify the originating tissue. CONCLUSIONS Although providing partly correlated measurements of DNA methylation, interchangeability of the quantitative results obtained with LINE-1 and LUMA was jeopardized by a consistent bias between the results. Moreover, the present analyses strongly indicate a tissue specificity of the differences between the two methods.
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Affiliation(s)
- Claudia Knothe
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Hiromi Shiratori
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Eduard Resch
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alfred Ultsch
- />DataBionics Research Group, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Gerd Geisslinger
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexandra Doehring
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jörn Lötsch
- />Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- />Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Tabish AM, Baccarelli AA, Godderis L, Barrow TM, Hoet P, Byun HM. Assessment of Changes in Global DNA Methylation Levels by Pyrosequencing® of Repetitive Elements. Methods Mol Biol 2016; 1315:201-7. [PMID: 26103901 DOI: 10.1007/978-1-4939-2715-9_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Transposable elements (TE) comprise half of the human genome. LINE-1 and ALU are the most common TE, and they have been used to assess changes in the DNA methylation of repetitive elements in response to intrinsic and extrinsic cellular events. Pyrosequencing(®) is a real-time sequencing technology that enables quantitative assessment of TE methylation at single-base resolution. In Pyrosequencing, a region of interest is first amplified from bisulfite-converted DNA by polymerase chain reaction (PCR), before PCR amplicons are rendered single stranded and annealed with the Pyrosequencing primer prior to sequencing. In this chapter, we provide an overview of the analysis of repetitive element DNA methylation by bisulfite Pyrosequencing, and we describe a protocol that can be used for such purposes.
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Affiliation(s)
- Ali M Tabish
- Department of Public Health and Primary Care, Katholieke Universiteit Leuven, Kapucijnenvoer 35 Blok D, Leuven, B-3000, Belgium,
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Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure. Toxicol Appl Pharmacol 2015; 289:203-12. [DOI: 10.1016/j.taap.2015.09.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 09/03/2015] [Accepted: 09/28/2015] [Indexed: 01/27/2023]
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Knothe C, Doehring A, Ultsch A, Lötsch J. Methadone induces hypermethylation of human DNA. Epigenomics 2015; 8:167-79. [PMID: 26340303 DOI: 10.2217/epi.15.78] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Increased global DNA methylation in the blood of patients chronically exposed to opioids had been interpreted as an indication of an epigenetic action of this drug class. MATERIALS & METHODS To strengthen the causality, human MCF7 cells were cultured in media with the addition of several known or potential modulators of DNA methylation including methadone. RESULTS Following 3 days of incubation with several different known or potential epigenetic modulators, global DNA methylation, quantified at LINE-1 CpG islands, showed a large variability across all treatments ranging from 27.8 to 63%. Based on distribution analysis of the global methylation of human DNA exposed to various potential modulators, present in vitro experiments showed that treatment with the opioid methadone was associated with an increased probability of hypermethylation. CONCLUSION This strengthens the evidence that opioids interfere with mechanisms of classical epigenetics.
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Affiliation(s)
- Claudia Knothe
- Institute of Clinical Pharmacology, Goethe - University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexandra Doehring
- Institute of Clinical Pharmacology, Goethe - University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alfred Ultsch
- DataBionics Research Group, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe - University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology & Applied Ecology IME, Project Group Translational Medicine & Pharmacology TMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
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Abstract
Systems biology and synthetic biology are emerging disciplines which are becoming increasingly utilised in several areas of bioscience. Toxicology is beginning to benefit from systems biology and we suggest in the future that is will also benefit from synthetic biology. Thus, a new era is on the horizon. This review illustrates how a suite of innovative techniques and tools can be applied to understanding complex health and toxicology issues. We review limitations confronted by the traditional computational approaches to toxicology and epidemiology research, using polycyclic aromatic hydrocarbons (PAHs) and their effects on adverse birth outcomes as an illustrative example. We introduce how systems toxicology (and their subdisciplines, genomic, proteomic, and metabolomic toxicology) will help to overcome such limitations. In particular, we discuss the advantages and disadvantages of mathematical frameworks that computationally represent biological systems. Finally, we discuss the nascent discipline of synthetic biology and highlight relevant toxicological centred applications of this technique, including improvements in personalised medicine. We conclude this review by presenting a number of opportunities and challenges that could shape the future of these rapidly evolving disciplines.
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Kawano H, Saeki H, Kitao H, Tsuda Y, Otsu H, Ando K, Ito S, Egashira A, Oki E, Morita M, Oda Y, Maehara Y. Chromosomal instability associated with global DNA hypomethylation is associated with the initiation and progression of esophageal squamous cell carcinoma. Ann Surg Oncol 2014; 21 Suppl 4:S696-702. [PMID: 24898425 DOI: 10.1245/s10434-014-3818-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Indexed: 02/01/2023]
Abstract
BACKGROUND Global DNA hypomethylation is associated with increased chromosomal instability and plays an important role in tumorigenesis. The methylation status of the long interspersed nuclear element-1 (LINE-1) element is a useful surrogate marker for global DNA methylation. Although LINE-1 hypomethylation is recognized as a poor prognostic marker, the correlation of LINE-1 methylation level with tumor suppressor gene mutation, chromosomal instability, and clinical significance in esophageal squamous cell carcinoma (ESCC) remains unclear. METHODS Using resected tumor tissues and the corresponding normal esophageal mucosa from 105 patients with ESCC, bisulfite pyrosequencing analysis was performed to quantify the LINE-1 methylation levels. p53 mutations in exons two to ten were detected by polymerase chain reaction direct sequencing. Chromosomal instability was assessed by single nucleotide polymorphism array comparative genomic hybridization analysis. RESULTS The LINE-1 methylation level of ESCC was significantly lower than matched normal mucosa. LINE-1 methylation levels of normal mucosa from the esophagus had a significant inverse correlation with both cigarette smoking and alcohol consumption of the study subjects. LINE-1 hypomethylation of ESCC was significantly associated with lymph node metastasis, lymphovascular invasion, the frequency of p53 mutation and poor survivability. The LINE-1 methylation levels in ESCC had a significant inverse association with the percentage of copy number alterations in the whole genome, mirroring chromosomal instability. CONCLUSIONS Our results suggested that whole genome hypomethylation caused by chronic inflammation could initiate carcinogenesis of esophageal squamous cells through chromosomal instability. In addition, chromosomal instability associated with the global hypomethylation might correlate highly with the progression of ESCC.
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Affiliation(s)
- Hiroyuki Kawano
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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