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Wang PW, Huang YF, Wang CH, Fang LJ, Chen ML. Prenatal to preschool exposure of nonylphenol and bisphenol A exposure and neurodevelopment in young children. Pediatr Neonatol 2024; 65:76-84. [PMID: 37679260 DOI: 10.1016/j.pedneo.2023.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Nonylphenol (NP) and bisphenol A (BPA) are produced in large quantities worldwide as multipurpose agents. However, studies on relations between NP and BPA exposure and childhood neurodevelopment are few, and the results are inconsistent. This study aimed to investigate associations between prenatal and early childhood NP and BPA exposure and neurodevelopment in mother-child pairs. METHODS Pregnant women at 27-38 weeks' gestation were recruited, as were children 2-3 years of age (n = 94) and 4-6 years of age (n = 56) years. Urine was collected to assess NP and BPA exposure. Bayley Scales of Infant and Toddler Development (3rd edition; Bayley-III), Wechsler Preschool and Primary Scale of Intelligence (4th edition), and the Full Scale Intelligence Quotient (WPPSI-IV-FSIQ) were used to assess the neurodevelopment of the children. RESULTS The detection rate and concentration of NP and BPA in the urine of children 4-6 years old were higher than in those 2-3 years old. Children were divided into a high concentration group (3rd tertile) and a reference group (1st and 2nd tertiles) based on natural log-transformed urine concentration of NP and BPA. Girls' Bayley-III motor scores in the high concentration group were higher than those of the BPA reference group of urine of mothers (β = 6.85, 95% confidence interval [CI]: 1.58-12.13). Boys' FSIQ in the higher concentration group were significantly lower than those in children 2-3 years old in the NP reference group (β = -11.29, 95% CI: -18.62 to -3.96) (all, p < 0.05). CONCLUSIONS Prenatal and childhood exposure to NP and BPA may have different effects on the neurodevelopment of young children, and there are no consistent effects between boys and girls.
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Affiliation(s)
- Pei-Wei Wang
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Yu-Fang Huang
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Chung-Hao Wang
- Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Li-Jung Fang
- Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Mei-Lien Chen
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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2
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Mu C, Zhao Q, Zhao Q, Yang L, Pang X, Liu T, Li X, Wang B, Fung SY, Cao H. Multi-omics in Crohn's disease: New insights from inside. Comput Struct Biotechnol J 2023; 21:3054-3072. [PMID: 37273853 PMCID: PMC10238466 DOI: 10.1016/j.csbj.2023.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development of high-throughput sequencing technology with integrated-omics analyses in recent years has provided a new means for exploring the pathogenesis, mining the biomarkers and designing targeted personalized therapeutics of CD. Host genomics and epigenomics unveil heredity-related mechanisms of susceptible individuals, while microbiome and metabolomics map host-microbe interactions in CD patients. Proteomics shows great potential in searching for promising biomarkers. Nonetheless, single omics technology cannot holistically connect the mechanisms with heterogeneity of pathological behavior in CD. The rise of multi-omics analysis integrates genetic/epigenetic profiles with protein/microbial metabolite functionality, providing new hope for comprehensive and in-depth exploration of CD. Herein, we emphasized the different omics features and applications of CD and discussed the current research and limitations of multi-omics in CD. This review will update and deepen our understanding of CD from integration of broad omics spectra and will provide new evidence for targeted individualized therapeutics.
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Affiliation(s)
- Chenlu Mu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qianjing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Lijiao Yang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaomeng Li
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Shan-Yu Fung
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Lee Y, Riskedal E, Kalleberg KT, Istre M, Lind A, Lund-Johansen F, Reiakvam O, Søraas AVL, Harris JR, Dahl JA, Hadley CL, Jugessur A. EWAS of post-COVID-19 patients shows methylation differences in the immune-response associated gene, IFI44L, three months after COVID-19 infection. Sci Rep 2022; 12:11478. [PMID: 35798818 PMCID: PMC9261254 DOI: 10.1038/s41598-022-15467-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/23/2022] [Indexed: 11/24/2022] Open
Abstract
Although substantial progress has been made in managing COVID-19, it is still difficult to predict a patient’s prognosis. We explored the epigenetic signatures of COVID-19 in peripheral blood using data from an ongoing prospective observational study of COVID-19 called the Norwegian Corona Cohort Study. A series of EWASs were performed to compare the DNA methylation profiles between COVID-19 cases and controls three months post-infection. We also investigated differences associated with severity and long-COVID. Three CpGs—cg22399236, cg03607951, and cg09829636—were significantly hypomethylated (FDR < 0.05) in COVID-19 positive individuals. cg03607951 is located in IFI44L which is involved in innate response to viral infection and several systemic autoimmune diseases. cg09829636 is located in ANKRD9, a gene implicated in a wide variety of cellular processes, including the degradation of IMPDH2. The link between ANKRD9 and IMPDH2 is striking given that IMPDHs are considered therapeutic targets for COVID-19. Furthermore, gene ontology analyses revealed pathways involved in response to viruses. The lack of significant differences associated with severity and long-COVID may be real or reflect limitations in sample size. Our findings support the involvement of interferon responsive genes in the pathophysiology of COVID-19 and indicate a possible link to systemic autoimmune diseases.
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Affiliation(s)
- Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway
| | | | | | - Mette Istre
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital Ullevaal, 0372, Oslo, Norway
| | | | - Olaug Reiakvam
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Arne V L Søraas
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | - Jennifer R Harris
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
| | | | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Skøyen, P.O. box 222, 0213, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, P.O. box 7804, 5020, Bergen, Norway
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4
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Ibeagha-Awemu EM, Yu Y. Consequence of epigenetic processes on animal health and productivity: is additional level of regulation of relevance? Anim Front 2021; 11:7-18. [PMID: 34934525 PMCID: PMC8683131 DOI: 10.1093/af/vfab057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Ying Yu
- Department of Animal Breeding and Genetics, College of Animal Sciences and Technology, China Agricultural University, Beijing, China
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Laaksonen J, Mishra PP, Seppälä I, Raitoharju E, Marttila S, Mononen N, Lyytikäinen LP, Kleber ME, Delgado GE, Lepistö M, Almusa H, Ellonen P, Lorkowski S, März W, Hutri-Kähönen N, Raitakari O, Kähönen M, Salonen JT, Lehtimäki T. Mitochondrial genome-wide analysis of nuclear DNA methylation quantitative trait loci. Hum Mol Genet 2021; 31:1720-1732. [PMID: 35077545 PMCID: PMC9122653 DOI: 10.1093/hmg/ddab339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Mitochondria have a complex communication network with the surrounding cell and can alter nuclear DNA methylation (DNAm). Variation in the mitochondrial DNA (mtDNA) has also been linked to differential DNAm. Genome-wide association studies have identified numerous DNAm quantitative trait loci, but these studies have not examined the mitochondrial genome. Herein, we quantified nuclear DNAm from blood and conducted a mitochondrial genome-wide association study of DNAm, with an additional emphasis on sex- and prediabetes-specific heterogeneity. We used the Young Finns Study (n = 926) with sequenced mtDNA genotypes as a discovery sample and sought replication in the Ludwigshafen Risk and Cardiovascular Health study (n = 2317). We identified numerous significant associations in the discovery phase (P < 10−9), but they were not replicated when accounting for multiple testing. In total, 27 associations were nominally replicated with a P < 0.05. The replication analysis presented no evidence of sex- or prediabetes-specific heterogeneity. The 27 associations were included in a joint meta-analysis of the two cohorts, and 19 DNAm sites associated with mtDNA variants, while four other sites showed haplogroup associations. An expression quantitative trait methylation analysis was performed for the identified DNAm sites, pinpointing two statistically significant associations. This study provides evidence of a mitochondrial genetic control of nuclear DNAm with little evidence found for sex- and prediabetes-specific effects. The lack of a comparable mtDNA data set for replication is a limitation in our study and further studies are needed to validate our results.
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Affiliation(s)
- Jaakko Laaksonen
- To whom correspondence should be addressed at: Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, Tampere FI-33014, Finland. Tel: +358 504080774; E-mail:
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Gerontology Research Center, Tampere University, Tampere 33520, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Maija Lepistö
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena 07743, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena 07743, Germany
- SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg 86156, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8010, Austria
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku 20520, Finland
- Research Centre for Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33520, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Jukka T Salonen
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
- MAS-Metabolic Analytical Services Oy, Helsinki 00990, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
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6
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Tian Y, Yang X, Du J, Zeng W, Wu W, Di J, Huang X, Tian K. Differential Methylation and Transcriptome Integration Analysis Identified Differential Methylation Annotation Genes and Functional Research Related to Hair Follicle Development in Sheep. Front Genet 2021; 12:735827. [PMID: 34659357 PMCID: PMC8515899 DOI: 10.3389/fgene.2021.735827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Hair follicle growth and development are a complex and long-term physiological process, which is regulated by a variety of physical factors and signal pathways. Increasing the understanding of the epigenetic regulation and function of candidate genes related to hair follicle development will help to better understand the molecular regulatory mechanisms of hair follicle development. In this study, the methylated DNA immunoprecipitation sequencing (MeDIP-seq) was used to obtain the genome-wide methylation map of the hair follicular development of Super Merino sheep in six stages (fetal skin tissue at 65d, 85d, 105d, 135d, 7d, and 30d after birth). Combined with the results of previous RNA-sequencing, 65 genes were screened out that were both differential methylation and differential expression, including EDN1, LAMC2, NR1D1, RORB, MyOZ3, and WNT2 gene. Differential methylation genes were enriched in Wnt, TNF, TGF-beta, and other signaling pathways related to hair follicle development. The bisulfite sequencing PCR results and MeDIP-seq were basically consistent, indicating that the sequencing results were accurate. As a key gene in the Wnt signaling pathway, both differential methylation and expression gene identified by MeDIP-seq and RNA-seq, further exploration of the function of WNT2 gene revealed that the DNA methylation of exon 5 (CpG11 site) promoted the expression of WNT2 gene. The overexpression vector of lentivirus pLEX-MCS-WNT2 was constructed, and WNT2 gene effectively promoted the proliferation of sheep skin fibroblasts. The results showed that WNT2 gene could promote the growth and development of skin and hair follicles. The results of this study will provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
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Affiliation(s)
- Yuezhen Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuemei Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jianwen Du
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weidan Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weiwei Wu
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jiang Di
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Kechuan Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
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7
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DNA methylation studies in cattle. J Appl Genet 2021; 62:121-136. [PMID: 33400132 DOI: 10.1007/s13353-020-00604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Investigation of the role of epigenetics in cattle breeding is gaining importance. DNA methylation represents an epigenetic modification which is essential for genomic stability and maintenance of development. Recently, DNA methylation research in cattle has intensified. The studies focus on the definition of methylomes in various organs and tissues in relation to the expression of genes underlying economically important traits, and explore methylome changes under developmental, environmental, disease, and diet influences. The investigations further characterize the methylation patterns of gametes in connection with their quality, and study methylome alterations in the developing naturally or assisted produced zygotes, embryos, and fetuses, considering their viability. A wide array of technologies developed for accurate and precise analysis of DNA methylation patterns is employed for both single-gene and genome-wide studies. Overall, the research is directed towards the identification of single methylation markers or their combinations which may be useful in the selection and breeding of animals to ensure cattle improvement.
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Khan P, Siddiqui JA, Maurya SK, Lakshmanan I, Jain M, Ganti AK, Salgia R, Batra SK, Nasser MW. Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Semin Cancer Biol 2020; 83:57-76. [PMID: 33220460 PMCID: PMC8218609 DOI: 10.1016/j.semcancer.2020.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality. Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy have substantially expanded existing knowledge and treatment modalities. However, challenges associated with SCLC remain enigmatic and elusive. Most of the conventional drug discovery approaches targeting altered signaling pathways in SCLC end up in the 'grave-yard of drug discovery', which mandates exploring novel approaches beyond inhibiting cell signaling pathways. Epigenetic modifications have long been documented as the key contributors to the tumorigenesis of almost all types of cancer, including SCLC. The last decade witnessed an exponential increase in our understanding of epigenetic modifications for SCLC. The present review highlights the central role of epigenetic regulations in acquiring neoplastic phenotype, metastasis, aggressiveness, resistance to chemotherapy, and immunotherapeutic approaches of SCLC. Different types of epigenetic modifications (DNA/histone methylation or acetylation) that can serve as predictive biomarkers for prognostication, treatment stratification, neuroendocrine lineage determination, and development of potential SCLC therapies are also discussed. We also review the utility of epigenetic targets/epidrugs in combination with first-line chemotherapy and immunotherapy that are currently under investigation in preclinical and clinical studies. Altogether, the information presents the inclusive landscape of SCLC epigenetics and epidrugs that will help to improve SCLC outcomes.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar Kishor Ganti
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA; Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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9
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Liu Z, He Y, Lian X, Zou H, Huang Y, Wang N, Hu J, Cui X, Zhao J, Zhang W, Gu W, Pang L, Qi Y. Prognostic role of upregulated P300 expression in human cancers: A clinical study of synovial sarcoma and a meta-analysis. Exp Ther Med 2019; 18:3161-3171. [PMID: 31572557 DOI: 10.3892/etm.2019.7906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 03/21/2019] [Indexed: 11/05/2022] Open
Abstract
E1A binding protein p300 (P300) is a member of the histone acetyltransferase family of transcriptional co-activators, which are associated with various types of cancer. Numerous studies have evaluated the diagnostic value of P300, but their results are not consistent. Therefore, a clinical study and a meta-analysis were performed in the present study to investigate the prognostic value of P300 expression in human malignant neoplasms. Immunohistochemical (IHC) analysis was used to assess P300 expression in 43 paraffin-embedded primary synovial sarcoma (SS) samples. For the meta-analysis, eligible studies published until January 21, 2018 were identified by searching the PubMed, EMBASE and Web of Science databases. The IHC analysis indicated a high P300 expression rate in 33.3% (10/30) of biphasic SS (BSSs) and in 60% (6/10) of monophasic fibrous SS tissues. In BSS, the expression rate was significantly higher in the epithelial component (80.0%, 24/30) than that in the spindle-cell component (30.0%, 9/30; P<0.05). The meta-analysis indicated that high expression of P300 was associated with poor overall survival (OS) in digestive system malignant neoplasms (HR=1.54, 95% CI: 1.20-2.23), as well as with poor progression-free survival, recurrence-free survival and disease-free survival combined (HR=1.84, 95% CI: 1.36-2.47). Analysis of subgroups by ethnicity demonstrated that high expression of P300 was associated with poor OS in Asians (HR=1.72, 95% CI: 1.20-2.47) but favourable OS in Caucasians (HR=0.59, 95% CI: 0.47-0.73). Furthermore, high expression of P300 was associated with clinical stage [Relative Risk (RR)=1.30, 95% CI: 1.07-1.58], lymph node metastasis (RR=1.30, 95% CI: 1.03-1.64) and depth of invasion (RR=1.31, 95% CI: 1.07-1.60). P300 expression may therefore be a useful biomarker for predicting patient prognosis in various types of human cancer.
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Affiliation(s)
- Zihan Liu
- Department of Pathology, Shihezi University School of Medicine and The First Affiliated Hospital to Shihezi University School of Medicine, Shihezi, Xinjiang 832002, P.R. China
| | - Yonglai He
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Xiaojuan Lian
- Department of Blood Cancers, Jiangjin Central Hosptial of Chongqing, Chongqing 400042, P.R. China
| | - Hong Zou
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Yalan Huang
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Ning Wang
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Jianming Hu
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Xiaobin Cui
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Jin Zhao
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Wenjie Zhang
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Wenyi Gu
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane QLD 4072, Australia
| | - Lijuan Pang
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Yan Qi
- Department of Emergency, Jinshan Branch Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, P.R. China
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Everson TM, Marsit CJ. Integrating -Omics Approaches into Human Population-Based Studies of Prenatal and Early-Life Exposures. Curr Environ Health Rep 2019; 5:328-337. [PMID: 30054820 DOI: 10.1007/s40572-018-0204-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We present the study design and methodological suggestions for population-based studies that integrate molecular -omics data and highlight recent studies that have used such data to examine the potential impacts of prenatal environmental exposures on fetal health. RECENT FINDINGS Epidemiologic studies have observed numerous relationships between prenatal exposures (smoking, toxic metals, endocrine disruptors) and fetal and early-life molecular profiles, though such investigations have so far been dominated by epigenomic association studies. However, recent transcriptomic, proteomic, and metabolomic studies have demonstrated their promise for the identification of exposure and response biomarkers. Molecular -omics have opened new avenues of research in environmental health that can improve our understanding of disease etiology and contribute to the development of exposure and response biomarkers. Studies that incorporate multiple -omics data from different molecular domains in longitudinally collected samples hold particular promise.
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Affiliation(s)
- Todd M Everson
- Departments of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA
| | - Carmen J Marsit
- Departments of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA. .,Departments of Environmental Health and Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road, Claudia Nance Rollins Room 2021, Atlanta, GA, 30322, USA.
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Abstract
Breast cancer is the most common cancer among women and represents one of the top five leading causes of cancer-related mortality. Inherited and acquired genetic mutations as well as epigenetic aberrations are known to be important contributors to the development and progression of breast cancer. Recent developments in high-throughput technologies have increased our understanding of the molecular changes in breast cancer, leading to the identification of distinctive genetic and epigenetic modifications in different breast cancer molecular subtypes. These genetic and epigenetic changes in luminal A, luminal B, ERBB2/HER2-enriched, basal-like, and normal-like breast cancer subtypes are discussed in this chapter. Furthermore, recent epigenome studies provided more information about further stratification of breast cancer subtypes, with essential role in the appropriate diagnosis and treatment of breast cancer. Thus, the inclusion of both genetic and epigenetic information in breast cancer clinical care could provide critical scientific base for precision medicine in breast cancer.
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Zhang N. Role of methionine on epigenetic modification of DNA methylation and gene expression in animals. ACTA ACUST UNITED AC 2017; 4:11-16. [PMID: 30167479 PMCID: PMC6112339 DOI: 10.1016/j.aninu.2017.08.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 01/22/2023]
Abstract
DNA methylation is one of the main epigenetic phenomena affecting gene expression. It is an important mechanism for the development of embryo, growth and health of animals. As a key nutritional factor limiting the synthesis of protein, methionine serves as the precursor of S-adenosylmethionine (SAM) in the hepatic one-carbon metabolism. The dietary fluctuation of methionine content can alter the levels of metabolic substrates in one-carbon metabolism, e.g., the SAM, S-adenosylhomocysteine (SAH), and change the expression of genes related to the growth and health of animals by DNA methylation reactions. The ratio of SAM to SAH is called ‘methylation index’ but it should be carefully explained because the complexity of methylation reaction. Alterations of methylation in a specific cytosine-guanine (CpG) site, rather than the whole promoter region, might be enough to change gene expression. Aberrant methionine cycle may provoke molecular changes of one-carbon metabolism that results in deregulation of cellular hemostasis and health problems. The importance of DNA methylation has been underscored but the mechanisms of methionine affecting DNA methylation are poorly understood. Nutritional epigenomics provides a promising insight into the targeting epigenetic changes in animals from a nutritional standpoint, which will deepen and expand our understanding of genes, molecules, tissues, and animals in which methionine alteration influences DNA methylation and gene expression.
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Affiliation(s)
- Naifeng Zhang
- Feed Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, 100081 Beijing, China
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Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context. JOURNAL OF HEALTHCARE ENGINEERING 2017; 2017:3818302. [PMID: 29065591 PMCID: PMC5603127 DOI: 10.1155/2017/3818302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/26/2017] [Accepted: 07/30/2017] [Indexed: 11/18/2022]
Abstract
Exposome is a critical dimension in the precision medicine paradigm. Effective representation of exposomics knowledge is instrumental to melding nongenetic factors into data analytics for clinical research. There is still limited work in (1) modeling exposome entities and relations with proper integration to mainstream ontologies and (2) systematically studying their presence in clinical context. Through selected ontological relations, we developed a template-driven approach to identifying exposome concepts from the Unified Medical Language System (UMLS). The derived concepts were evaluated in terms of literature coverage and the ability to assist in annotating clinical text. The generated semantic model represents rich domain knowledge about exposure events (454 pairs of relations between exposure and outcome). Additionally, a list of 5667 disorder concepts with microbial etiology was created for inferred pathogen exposures. The model consistently covered about 90% of PubMed literature on exposure-induced iatrogenic diseases over 10 years (2001–2010). The model contributed to the efficiency of exposome annotation in clinical text by filtering out 78% of irrelevant machine annotations. Analysis into 50 annotated discharge summaries helped advance our understanding of the exposome information in clinical text. This pilot study demonstrated feasibility of semiautomatically developing a useful semantic resource for exposomics.
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Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. Epigenetics and inheritance of phenotype variation in livestock. Epigenetics Chromatin 2016. [PMID: 27446239 DOI: 10.1186/s13072‐016‐0081‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Ioannis Ikonomopoulos
- Department of Anatomy and Physiology of Farm Animals, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Andrew J Bannister
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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16
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Triantaphyllopoulos KA, Ikonomopoulos I, Bannister AJ. Epigenetics and inheritance of phenotype variation in livestock. Epigenetics Chromatin 2016; 9:31. [PMID: 27446239 PMCID: PMC4955263 DOI: 10.1186/s13072-016-0081-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/06/2016] [Indexed: 01/04/2023] Open
Abstract
Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that epigenetic effects can be inherited from one generation to the next. Here, we review examples of epigenetic mechanisms governing animal phenotype and behaviour, and we discuss the importance of these findings in respect to animal studies, and livestock in general. Epigenetic parameters orchestrating transgenerational effects, as well as heritable disorders, and the often-overlooked areas of livestock immunity and stress, are also discussed. We highlight the importance of nutrition and how it is linked to epigenetic alteration. Finally, we describe how our understanding of epigenetics is underpinning the latest cancer research and how this can be translated into directed efforts to improve animal health and welfare.
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Affiliation(s)
- Kostas A. Triantaphyllopoulos
- />Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Ioannis Ikonomopoulos
- />Department of Anatomy and Physiology of Farm Animals, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Andrew J. Bannister
- />Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL. A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. JOURNAL OF BIOMOLECULAR SCREENING 2016; 21:521-34. [PMID: 26962875 PMCID: PMC4917453 DOI: 10.1177/1087057116635818] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Drug candidates exhibiting well-defined pharmacokinetic and pharmacodynamic profiles that are otherwise safe often fail to demonstrate proof-of-concept in phase II and III trials. Innovation in drug discovery and development has been identified as a critical need for improving the efficiency of drug discovery, especially through collaborations between academia, government agencies, and industry. To address the innovation challenge, we describe a comprehensive, unbiased, integrated, and iterative quantitative systems pharmacology (QSP)-driven drug discovery and development strategy and platform that we have implemented at the University of Pittsburgh Drug Discovery Institute. Intrinsic to QSP is its integrated use of multiscale experimental and computational methods to identify mechanisms of disease progression and to test predicted therapeutic strategies likely to achieve clinical validation for appropriate subpopulations of patients. The QSP platform can address biological heterogeneity and anticipate the evolution of resistance mechanisms, which are major challenges for drug development. The implementation of this platform is dedicated to gaining an understanding of mechanism(s) of disease progression to enable the identification of novel therapeutic strategies as well as repurposing drugs. The QSP platform will help promote the paradigm shift from reactive population-based medicine to proactive personalized medicine by focusing on the patient as the starting and the end point.
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Affiliation(s)
- Andrew M. Stern
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E. Schurdak
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Jeremy M. Berg
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- University of Pittsburgh Institute for Personalized Medicine, Pittsburgh, PA, USA
| | - D. Lansing Taylor
- Department of Computational and Systems Biology, Pittsburgh, PA, USA
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
- The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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18
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Buonaccorsi J, Prochenka A, Thoresen M, Ploski R. Correcting for binomial measurement error in predictors in regression with application to analysis of DNA methylation rates by bisulfite sequencing. Stat Med 2016; 35:3987-4007. [DOI: 10.1002/sim.6988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 02/04/2016] [Accepted: 04/13/2016] [Indexed: 11/11/2022]
Affiliation(s)
- John Buonaccorsi
- Department of Mathematics and Statistics; University of Massachusetts- Amherst; Amherst MA U.S.A
| | | | - Magne Thoresen
- Oslo Centre for Biostatistics and Epidemiology; Department of Biostatistics, University of Oslo; Oslo Norway
| | - Rafal Ploski
- Department of Medical Genetics; Warsaw Medical University; Warsaw Poland
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19
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Kriebel J, Herder C, Rathmann W, Wahl S, Kunze S, Molnos S, Volkova N, Schramm K, Carstensen-Kirberg M, Waldenberger M, Gieger C, Peters A, Illig T, Prokisch H, Roden M, Grallert H. Association between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study. PLoS One 2016; 11:e0152314. [PMID: 27019061 PMCID: PMC4809492 DOI: 10.1371/journal.pone.0152314] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/11/2016] [Indexed: 12/22/2022] Open
Abstract
Epigenetic regulation has been postulated to affect glucose metabolism, insulin sensitivity and the risk of type 2 diabetes. Therefore, we performed an epigenome-wide association study for measures of glucose metabolism in whole blood samples of the population-based Cooperative Health Research in the Region of Augsburg F4 study using the Illumina HumanMethylation 450 BeadChip. We identified a total of 31 CpG sites where methylation level was associated with measures of glucose metabolism after adjustment for age, sex, smoking, and estimated white blood cell proportions and correction for multiple testing using the Benjamini-Hochberg (B-H) method (four for fasting glucose, seven for fasting insulin, 25 for homeostasis model assessment-insulin resistance [HOMA-IR]; B-H-adjusted p-values between 9.2x10(-5) and 0.047). In addition, DNA methylation at cg06500161 (annotated to ABCG1) was associated with all the aforementioned phenotypes and 2-hour glucose (B-H-adjusted p-values between 9.2x10(-5) and 3.0x10(-3)). Methylation status of additional three CpG sites showed an association with fasting insulin only after additional adjustment for body mass index (BMI) (B-H-adjusted p-values = 0.047). Overall, effect strengths were reduced by around 30% after additional adjustment for BMI, suggesting that this variable has an influence on the investigated phenotypes. Furthermore, we found significant associations between methylation status of 21 of the aforementioned CpG sites and 2-hour insulin in a subset of samples with seven significant associations persisting after additional adjustment for BMI. In a subset of 533 participants, methylation of the CpG site cg06500161 (ABCG1) was inversely associated with ABCG1 gene expression (B-H-adjusted p-value = 1.5x10(-9)). Additionally, we observed an enrichment of the top 1,000 CpG sites for diabetes-related canonical pathways using Ingenuity Pathway Analysis. In conclusion, our study indicates that DNA methylation and diabetes-related traits are associated and that these associations are partially BMI-dependent. Furthermore, the interaction of ABCG1 with glucose metabolism is modulated by epigenetic processes.
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Affiliation(s)
- Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
| | - Christian Herder
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sophie Molnos
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
| | - Nadezda Volkova
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katharina Schramm
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universitaet Muenchen, Munich, Germany
| | - Maren Carstensen-Kirberg
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hanover, Germany
- Institute of Human Genetics, Hannover Medical School, Hanover, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universitaet Muenchen, Munich, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Duesseldorf, Duesseldorf, Germany
- Department of Endocrinology and Diabetology, University Hospital Duesseldorf, Duesseldorf, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Muenchen-Neuherberg, Germany
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Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol 2015; 16:273. [PMID: 26653535 PMCID: PMC4674939 DOI: 10.1186/s13059-015-0838-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Mark Quinton-Tulloch
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Jonathan Price
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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21
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Langevin SM, Eliot M, Butler RA, Cheong A, Zhang X, McClean MD, Koestler DC, Kelsey KT. CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma. Clin Epigenetics 2015; 7:125. [PMID: 26635906 PMCID: PMC4668652 DOI: 10.1186/s13148-015-0160-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples. METHODS We used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy. RESULTS We identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98). CONCLUSIONS This novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, ML0056, Cincinnati, OH 45267 USA
| | - Michael D McClean
- Department of Environmental Health, Boston University School of Public Health, Boston, MA USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KA USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI USA ; Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Box G-E3, Providence, RI 02912 USA
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22
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Singmann P, Shem-Tov D, Wahl S, Grallert H, Fiorito G, Shin SY, Schramm K, Wolf P, Kunze S, Baran Y, Guarrera S, Vineis P, Krogh V, Panico S, Tumino R, Kretschmer A, Gieger C, Peters A, Prokisch H, Relton CL, Matullo G, Illig T, Waldenberger M, Halperin E. Characterization of whole-genome autosomal differences of DNA methylation between men and women. Epigenetics Chromatin 2015; 8:43. [PMID: 26500701 PMCID: PMC4615866 DOI: 10.1186/s13072-015-0035-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/29/2015] [Indexed: 01/19/2023] Open
Abstract
Background Disease risk and incidence between males and females reveal differences, and sex is an important component of any investigation of the determinants of phenotypes or disease etiology. Further striking differences between men and women are known, for instance, at the metabolic level. The extent to which men and women vary at the level of the epigenome, however, is not well documented. DNA methylation is the best known epigenetic mechanism to date. Results In order to shed light on epigenetic differences, we compared autosomal DNA methylation levels between men and women in blood in a large prospective European cohort of 1799 subjects,
and replicated our findings in three independent European cohorts. We identified and validated 1184 CpG sites to be differentially methylated between men and women and observed that these CpG sites were distributed across all autosomes. We showed that some of the differentially methylated loci also exhibit differential gene expression between men and women. Finally, we found that the differentially methylated loci are enriched among imprinted genes, and that their genomic location in the genome is concentrated in CpG island shores. Conclusion Our epigenome-wide association study indicates that differences between men and women are so substantial that they should be considered in design and analyses of future studies. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0035-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula Singmann
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Doron Shem-Tov
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Giovanni Fiorito
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - So-Youn Shin
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK ; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Katharina Schramm
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Petra Wolf
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yael Baran
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Simonetta Guarrera
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Paolo Vineis
- Human Genetics Foundation-Torino, Turin, Italy ; Epidemiology and Public Health, Imperial College London, London, UK
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCSS Istituto Nazionale Tumori, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, "Civile-M.P. Arezzo" Hospital, ASP 7, Ragusa, Italy
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK ; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppe Matullo
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Hannover Unified Biobank, Hannover Medical School, Hannover, Germany ; Institute for Human Genetics, Hannover Medical School, Hannover, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Eran Halperin
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel ; Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel ; International Computer Science Institute, Berkeley, CA USA
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array. Clin Epigenetics 2015; 7:78. [PMID: 26236407 PMCID: PMC4521379 DOI: 10.1186/s13148-015-0097-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/22/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA methylation is a heritable and stable epigenetic mark implicated in complex human traits. Epigenome-wide association studies (EWAS) using array-based technology are becoming widely used to identify differentially methylated sites associated with complex diseases. EWAS studies require large sample sizes to detect small effects, which increases project costs. In the present study we propose to pool DNA samples in methylation array studies as an affordable and accurate alternative to individual samples studies, in order to reduce economic costs or when low amounts of DNA are available. For this study, 20 individual DNA samples and 4 pooled DNA samples were analysed using the Illumina Infinium HumanMethylation450 BeadChip array to evaluate the efficiency of the pooling approach in EWAS studies. Statistical power calculations were also performed to discover the minimum sample size needed for the pooling strategy in EWAS. RESULTS A total of 485,577 CpG sites across the whole genome were assessed. Comparison of methylation levels of all CpG sites between individual samples and their related pooled samples revealed highly significant correlations (rho > 0.99, p-val < 10(-16)). These results remained similar when assessing the 101 most differentially methylated CpG sites (rho > 0.98, p-val < 10(-16)). Also, it was calculated that n = 43 is the minimum sample size required to achieve a 95 % statistical power and a 10(-06) significance level in EWAS, when using a DNA pool strategy. CONCLUSIONS DNA pooling strategies seems to accurately provide estimations of averaged DNA methylation state using array based EWAS studies. This type of approach can be applied to the assessment of disease phenotypes, reducing the amount of DNA required and the cost of large-scale epigenetic analyses.
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Martín-Núñez GM, Rubio-Martín E, Cabrera-Mulero R, Rojo-Martínez G, Olveira G, Valdés S, Soriguer F, Castaño L, Morcillo S. Type 2 diabetes mellitus in relation to global LINE-1 DNA methylation in peripheral blood: a cohort study. Epigenetics 2015; 9:1322-8. [PMID: 25437047 DOI: 10.4161/15592294.2014.969617] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In the last years, epigenetic processes have emerged as a promising area of complex diseases research. DNA methylation measured in Long Interspersed Nucleotide Element 1 (LINE-1) sequences has been considered a surrogate marker for global genome methylation. New findings have suggested the potential involvement of epigenetic mechanisms in Type 2 diabetes (T2DM) as a crucial interface between the effects of genetic predisposition and environmental influences. Our study evaluated whether global DNA methylation predicted increased risk from T2DM or other carbohydrate metabolism disorders in a cohort study. We used a prospective cohort intervention study and a control group. We collected phenotypic, anthropometric, biochemical, and nutritional information from all subjects. Global LINE-1 DNA methylation was quantified by pyrosequencing technology. Subjects that did not improve their carbohydrate metabolism status showed lower levels of global LINE-1 DNA methylation (63.9 ± 1.7 vs. 64.7 ± 2.4) and they practiced less intense physical activity (5.8% vs. 21.5%). Logistic regression analyses showed a significant association between LINE-1 DNA methylation and metabolic status after adjustment for sex, age, BMI, and physical activity. Our study showed that lower LINE-1 DNA methylation levels were associated with a higher risk metabolic status worsening, independent of other classic risk factors. This finding highlights the potential role for epigenetic biomarkers as predictors of T2DM risk or other related metabolic disorders.
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Affiliation(s)
- Gracia María Martín-Núñez
- a UGCI de Endocrinología y Nutrición ; Instituto de Investigación Biomédica de Málaga (IBIMA) ; Hospital Regional Universitario ; Malaga , Spain
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26
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Straughen JK, Sipahi L, Uddin M, Misra DP, Misra VK. Racial differences in IGF1 methylation and birth weight. Clin Epigenetics 2015; 7:47. [PMID: 25945130 PMCID: PMC4419394 DOI: 10.1186/s13148-015-0080-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/06/2015] [Indexed: 11/30/2022] Open
Abstract
Background The birth weight of Black neonates in the United States is consistently smaller than that of their White counterparts. Epigenetic differences between the races may be involved in such disparities. The goal of these analyses was to model the role of IGF1 methylation in mediating the association between race and birth weight. Data was collected on a cohort of 87 live born infants. IGF1 methylation was measured in DNA isolated from the mononuclear fraction of umbilical cord blood collected after delivery. Quantitative, loci-specific methylation was assessed using the Infinium HumanMethylation27 BeadArray (Illumina Inc., San Diego, CA). Locus specific methylation of the IGF1 CpG site was validated on a subset of the original sample (N = 61) using pyrosequencing. Multiple linear regression was used to examine relationships between IGF1 methylation, race, and birth weight. A formal mediation analysis was then used to estimate the relationship of IGF1 methylation to race and birth weight. Results Black race was associated with a 7.45% decrease in gestational age-adjusted birth weight (aBW) (P = 0.04) and Black infants had significantly higher IGF1 methylation than non-Black infants (P < 0.05). A one standard deviation increase in IGF1 methylation was associated with a 3.32% decrease in aBW (P = 0.02). Including IGF1 methylation as a covariate, the effect of Black race on aBW was attenuated. A formal mediation analysis showed that the controlled direct effect of Black race on aBW was −6.26% (95% CI = −14.15, 1.06); the total effect of Black race on IGF1 methylation was −8.12% (95% CI = −16.08, −0.55); and the natural indirect effect of Black race on aBW through IGF1 methylation was −1.86% (95% CI = −5.22, 0.18) Conclusion The results of the mediation analysis along with the multivariable regression analyses suggest that IGF1 methylation may partially mediate the relationship between Black race and aBW. Such epigenetic differences may be involved in racial disparities observed in perinatal outcomes.
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Affiliation(s)
- Jennifer K Straughen
- Department of Family Medicine and Public Health Sciences, The Wayne State University School of Medicine, 3939 Woodward Avenue, Detroit, MI 48201 USA ; Current address: Department of Public Health Sciences, Henry Ford Hospital, One Ford Place, Detroit, MI 48202 USA
| | - Levent Sipahi
- Center for Molecular Medicine and Genetics, The Wayne State University School of Medicine, 540 East Canfield, Detroit, MI 48201 USA
| | - Monica Uddin
- Department of Psychology, University of Illinois at Urbana-Champaign, 603 E. Daniel Street, Champaign, IL 61820 USA
| | - Dawn P Misra
- Department of Family Medicine and Public Health Sciences, The Wayne State University School of Medicine, 3939 Woodward Avenue, Detroit, MI 48201 USA
| | - Vinod K Misra
- Department of Pediatrics, Division of Genetic and Metabolic Disorders, The Wayne State University School of Medicine, 3901 Beaubien Blvd, Detroit, MI 48201 USA ; Children's Hospital of Michigan, Division of Genetic and Metabolic Disorders, The Wayne State University School of Medicine, 3950 Beaubien Blvd, Detroit, MI 48201 USA
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Host Factors and Risk of Breast Cancer Recurrence: Genetic, Epigenetic and Biologic Factors and Breast Cancer Outcomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 862:143-53. [DOI: 10.1007/978-3-319-16366-6_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Langevin SM, Kratzke RA, Kelsey KT. Epigenetics of lung cancer. Transl Res 2015; 165:74-90. [PMID: 24686037 PMCID: PMC4162853 DOI: 10.1016/j.trsl.2014.03.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/25/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality in the United States. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA expression, have been reported widely in the literature to play a major role in the genesis of lung cancer. The goal of this review is to summarize the common epigenetic changes associated with lung cancer to give some clarity to its etiology, and to provide an overview of the potential translational applications of these changes, including applications for early detection, diagnosis, prognostication, and therapeutics.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Robert A Kratzke
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minn
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI.
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Bai Y, Fang N, Gu T, Kang Y, Wu J, Yang D, Zhang H, Suo Z, Ji S. HOXA11 gene is hypermethylation and aberrant expression in gastric cancer. Cancer Cell Int 2014; 14:79. [PMID: 25788862 PMCID: PMC4364045 DOI: 10.1186/s12935-014-0079-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/29/2014] [Indexed: 12/11/2022] Open
Abstract
Background Aberrant DNA methylation is an acquired epigenetic alteration that serves as an alternative to genetic defects in the inactivation of tumor suppressor genes and other genes in diverse human cancers. Gastric carcinoma is one of the tumors with a high frequency of aberrant methylation in promoter region. Hence we investigated the promoter methylation status and expression level of HOXA11 gene which may involve in GC development. Methods Thirty-two surgical excised gastric cancer specimens, twelve paired adjacent non-cancerous specimens and seven normal gastric mucosas were examined. The methylation status and expression level of HOXA11 gene were determined by bisulfite sequencing polymerase chain reaction (BSP), real-time polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC) respectively. HOXA11 expression was knocked-down with siRNA to mimic HOXA11 gene hypermethylation and ability of cell proliferation and migration was determinate. In addition, we analyzed and correlated the findings with clinicopathological features. Results The methylation level of HOXA11 gene in gastric cancer tissues and adjacent non-cancerous tissues were higher than those in normal gastric mucosa (P < 0.05). The methylation level was higher in TNM III and IV patients of GC than those in TNM I and II patients (P < 0.05). The expression of HOXA11 mRNA and protein decreased in normal gastric mucosa, peri-cancer tissue and GC (P < 0.05). HOXA11 expression was inversely correlated with DNA methylation (P < 0.05). Knocked-down of HOXA11 expression with siRNA in BGC-823 cells enhanced cell proliferation compared with control, but no significant different was observed in migration ability. Conclusion Hypermethylation and decreased expression of HOXA11 gene may be involved in the carcinogenesis and development of GC and may provide useful information for the prediction of the malignant behaviors of GC. And the expression of HOXA11 is impaired by DNA methylation. However, repression of HOXA11 expression promoted BGC-823 cell proliferation.
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Affiliation(s)
- Yinguo Bai
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China ; Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Na Fang
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Tingxun Gu
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Yuhua Kang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Jiang Wu
- Department of pathology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Desheng Yang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Hui Zhang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Zhimin Suo
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
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Meirelles FV, Bressan FF, Smith LC, Perecin F, Chiaratti MR, Ferraz JBS. Cytoplasmatic inheritance, epigenetics and reprogramming DNA as tools in animal breeding. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Romano ME, Savitz DA, Braun JM. Challenges and future directions to evaluating the association between prenatal exposure to endocrine disrupting chemicals and childhood obesity. CURR EPIDEMIOL REP 2014; 1:57-66. [PMID: 25328860 PMCID: PMC4199333 DOI: 10.1007/s40471-014-0007-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Obesity is an increasing public health threat worldwide. However, there has been insufficient research addressing the obesogenic potential of prenatal exposure to environmental endocrine disrupting chemicals, largely due to complexities in the design, analysis, and interpretation of such studies. This review describes relevant biological mechanisms, addresses current challenges for investigators, presents potential strategies for overcoming them, and identifies areas where further development is required to improve future research. Special considerations for exposure assessment, outcome heterogeneity, and complex confounding structures are described.
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Affiliation(s)
- Megan E. Romano
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - David A. Savitz
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - Joseph M. Braun
- Department of Epidemiology, Brown University, Providence, Rhode Island
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Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T. Next-generation technologies and data analytical approaches for epigenomics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:155-70. [PMID: 24327356 DOI: 10.1002/em.21841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 05/18/2023]
Abstract
Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Martin Sanchez F, Gray K, Bellazzi R, Lopez-Campos G. Exposome informatics: considerations for the design of future biomedical research information systems. J Am Med Inform Assoc 2013; 21:386-90. [PMID: 24186958 DOI: 10.1136/amiajnl-2013-001772] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The environment's contribution to health has been conceptualized as the exposome. Biomedical research interest in environmental exposures as a determinant of physiopathological processes is rising as such data increasingly become available. The panoply of miniaturized sensing devices now accessible and affordable for individuals to use to monitor a widening range of parameters opens up a new world of research data. Biomedical informatics (BMI) must provide a coherent framework for dealing with multi-scale population data including the phenome, the genome, the exposome, and their interconnections. The combination of these more continuous, comprehensive, and personalized data sources requires new research and development approaches to data management, analysis, and visualization. This article analyzes the implications of a new paradigm for the discipline of BMI, one that recognizes genome, phenome, and exposome data and their intricate interactions as the basis for biomedical research now and for clinical care in the near future.
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Affiliation(s)
- Fernando Martin Sanchez
- Health and Biomedical Informatics Centre (HABIC), The University of Melbourne, Melbourne, Victoria, Australia
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Bonassi S, Taioli E, Vermeulen R. Omics in population studies: a molecular epidemiology perspective. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:455-460. [PMID: 23908054 DOI: 10.1002/em.21805] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 06/02/2023]
Abstract
The convergence of striking developments in (bio)-technology, increasing availability of biobanked samples, and advances in biostatistics and bio-informatics allow an optimistic outlook for epidemiological research. In this special issue on Omics in Population Studies: A Molecular Epidemiology Perspective we explore and reflect on the potential of these new developments in both exposure science and clinical research since they provide the essential link between exposure and disease and may enable scientists to improve their understanding of disease origin and progression. As noted in this special issue, this is an exciting time for epidemiology. While cancer and other noncommunicable diseases rise in number worldwide, various new tools can be applied effectively to increase understanding of the underlying causes and potential for progression to improve their prevention and treatment.
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Affiliation(s)
- Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology, Area of Systems Approaches and Non Communicable Diseases. IRCCS San Raffaele Pisana, Rome, Italy.
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