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Rose DK, Bentley L, Maity A, Maguire RL, Planchart A, Spasojevic I, Liu AJ, Thorp J, Hoyo C. Association between F2-isoprostanes and self-reported stressors in pregnant americans of African and European ancestry. Heliyon 2024; 10:e25578. [PMID: 38356491 PMCID: PMC10865309 DOI: 10.1016/j.heliyon.2024.e25578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Background Poor birth outcomes such as preterm birth/delivery disproportionately affect African Americans compared to White individuals. Reasons for this disparity are likely multifactorial, and include prenatal psychosocial stressors, and attendant increased lipid peroxidation; however, empirical data linking psychosocial stressors during pregnancy to oxidative status are limited. Methods We used established scales to measure five psychosocial stressors. Maternal adverse childhood experiences, financial stress, social support, anxiety, and depression were measured among 50 African American and White pregnant women enrolled in the Stress and Health in Pregnancy cohort. Liquid chromatography-tandem mass spectrometry was used to measure biomarkers of oxidative stress (four urinary F2-isoprostane isomers), to estimate oxidative status. Linear regression models were used to evaluate associations between psychosocial stressors, prenatal oxidative status and preterm birth. Results After adjusting for maternal obesity, gestational diabetes, and cigarette smoking, African American women with higher oxidative status were more likely to report higher maternal adverse childhood experience scores (β = 0.16, se = 1.07, p-value = 0.024) and depression scores (β = 0.05, se = 0.02, p = 0.014). Higher oxidative status was also associated with lower gestational age at birth (β = -0.13, se = 0.06, p = 0.04) in this population. These associations were not apparent in Whites. However, none of the cross-product terms for race/ethnicity and social stressors reached statistical significance (p > 0.05). Conclusion While the small sample size limits inference, our novel data suggest that psychosocial stressors may contribute significantly to oxidative stress during pregnancy, and preterm birth or delivery African Americans. If replicated in larger studies, these findings would support oxidative stress reduction using established dietary or pharmacological approaches present a potential avenue to mitigate adverse effects of psychosocial stressors on birth outcomes.
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Affiliation(s)
- Deborah K. Rose
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Loren Bentley
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Arnab Maity
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Rachel L. Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Ivan Spasojevic
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, PK/PD Core Laboratory, Durham, NC, USA
| | - Andy J. Liu
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - John Thorp
- Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
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Hoang TT, Lee Y, McCartney DL, Kersten ETG, Page CM, Hulls PM, Lee M, Walker RM, Breeze CE, Bennett BD, Burkholder AB, Ward J, Brantsæter AL, Caspersen IH, Motsinger-Reif AA, Richards M, White JD, Zhao S, Richmond RC, Magnus MC, Koppelman GH, Evans KL, Marioni RE, Håberg SE, London SJ. Comprehensive evaluation of smoking exposures and their interactions on DNA methylation. EBioMedicine 2024; 100:104956. [PMID: 38199042 PMCID: PMC10825325 DOI: 10.1016/j.ebiom.2023.104956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Smoking impacts DNA methylation, but data are lacking on smoking-related differential methylation by sex or dietary intake, recent smoking cessation (<1 year), persistence of differential methylation from in utero smoking exposure, and effects of environmental tobacco smoke (ETS). METHODS We meta-analysed data from up to 15,014 adults across 5 cohorts with DNA methylation measured in blood using Illumina's EPIC array for current smoking (2560 exposed), quit < 1 year (500 exposed), in utero (286 exposed), and ETS exposure (676 exposed). We also evaluated the interaction of current smoking with sex or diet (fibre, folate, and vitamin C). FINDINGS Using false discovery rate (FDR < 0.05), 65,857 CpGs were differentially methylated in relation to current smoking, 4025 with recent quitting, 594 with in utero exposure, and 6 with ETS. Most current smoking CpGs attenuated within a year of quitting. CpGs related to in utero exposure in adults were enriched for those previously observed in newborns. Differential methylation by current smoking at 4-71 CpGs may be modified by sex or dietary intake. Nearly half (35-50%) of differentially methylated CpGs on the 450 K array were associated with blood gene expression. Current smoking and in utero smoking CpGs implicated 3049 and 1067 druggable targets, including chemotherapy drugs. INTERPRETATION Many smoking-related methylation sites were identified with Illumina's EPIC array. Most signals revert to levels observed in never smokers within a year of cessation. Many in utero smoking CpGs persist into adulthood. Smoking-related druggable targets may provide insights into cancer treatment response and shared mechanisms across smoking-related diseases. FUNDING Intramural Research Program of the National Institutes of Health, Norwegian Ministry of Health and Care Services and the Ministry of Education and Research, Chief Scientist Office of the Scottish Government Health Directorates and the Scottish Funding Council, Medical Research Council UK and the Wellcome Trust.
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Affiliation(s)
- Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA; Department of Pediatrics, Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Elin T G Kersten
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Dept. of Pediatric Pulmonology and Pediatric Allergy, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Physical Health and Ageing, Division for Physical and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Paige M Hulls
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Charles E Breeze
- UCL Cancer Institute, University College London, Paul O'Gorman Building, London, UK; Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Brian D Bennett
- Department of Health and Human Services, Integrative Bioinformatics Support Group, National Institutes of Health, Research Triangle Park, NC, USA
| | - Adam B Burkholder
- Department of Health and Human Services, Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - James Ward
- Department of Health and Human Services, Integrative Bioinformatics Support Group, National Institutes of Health, Research Triangle Park, NC, USA
| | - Anne Lise Brantsæter
- Department of Food Safety, Division of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ida H Caspersen
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alison A Motsinger-Reif
- Department of Health and Human Services, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | | | - Julie D White
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA; GenOmics and Translational Research Center, Analytics Practice Area, RTI International, Research Triangle Park, NC, USA
| | - Shanshan Zhao
- Department of Health and Human Services, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Rebecca C Richmond
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Dept. of Pediatric Pulmonology and Pediatric Allergy, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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Zhu L, Zhu C, Jin J, Wang J, Zhao X, Yang R. Identification of an association between coronary heart disease and ITGB2 methylation in peripheral blood by a case-control study. Clin Chim Acta 2024; 552:117627. [PMID: 37923103 DOI: 10.1016/j.cca.2023.117627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Blood DNA methylation was associated with coronary heart disease (CHD) risk in Caucasians. We investigated the association between DNA methylation in peripheral blood at the reported loci and CHD in the Chinese population. METHODS The integrin subunit beta 2 (ITGB2) gene was identified in 196 CHD cases and 184 controls, and its methylation level was determined by mass spectrometry. Logistic regression was used to assess the association. RESULTS Hypomethylation of ITGB2 was significantly associated with heart failure CHD and NYHA Ⅰ&Ⅱ CHD patients with minor to medium cardiac function impairment (ITGB2_CpG_11/cg08422803, OR per -10 % methylation = 1.15 and 1.16; p = 0.012 and 0.018 by Bonferroni correction, respectively). Hypomethylation of ITGB2_CpG_11/cg08422803 was a risk factor for CHD in people < 65 years and males (p < 0.05 after Bonferroni correction). The combination of ITGB2 methylation and conventional CHD risk factors could efficiently discriminate CHD, heart failure CHD, NYHA I&II CHD, and myocardial infarction CHD patients from controls (AUC = 0.78, 0.81, 0.80, and 0.81, respectively). CONCLUSION Blood-based ITGB2 methylation has the potential as a biomarker for CHD. The combination of ITGB2 methylation and conventional CHD risk factors may improve the risk assessment and detection of CHD.
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Affiliation(s)
- Liya Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Kunshan Center for Disease Control and Prevention, Kunshan, 215300, China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, 95 Yong'an Road, West District, Beijing, 100050, China
| | - Jialie Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jinxin Wang
- Department of Cardiology, the Second Medical Center, Chinese PLA General Hospital, 100853 Beijing, China
| | - Xiaojing Zhao
- Military translational medicine lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
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Awada Z, Cahais V, Cuenin C, Akika R, Silva Almeida Vicente AL, Makki M, Tamim H, Herceg Z, Khoueiry Zgheib N, Ghantous A. Waterpipe and cigarette epigenome analysis reveals markers implicated in addiction and smoking type inference. ENVIRONMENT INTERNATIONAL 2023; 182:108260. [PMID: 38006773 PMCID: PMC10716859 DOI: 10.1016/j.envint.2023.108260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 11/27/2023]
Abstract
Waterpipe smoking is frequent in the Middle East and Africa with emerging prevalence worldwide. The epigenome acts as a molecular sensor to exposures and a crucial driver in several diseases. With the widespread use of waterpipe smoking, it is timely to investigate its epigenomic markers and their role in addiction, as a central player in disease prevention and therapeutic strategies. DNA methylome-wide profiling was performed on an exposure-rich population from the Middle East, constituting of 216 blood samples split equally between never, cigarette-only and waterpipe-only smokers. Waterpipe smokers showed predominantly distinct epigenetic markers from cigarette smokers, even though both smoking forms are tobacco-based. Moreover, each smoking form could be accurately (∼90 %) inferred from the DNA methylome using machine learning. Top markers showed dose-response relationship with extent of smoking and were validated using independent technologies and additional samples (total N = 284). Smoking markers were enriched in regulatory regions and several biological pathways, primarily addiction. The epigenetically altered genes were not associated with genetic etiology of tobacco use, and the methylation levels of addiction genes, in particular, were more likely to reverse after smoking cessation. In contrast, other epigenetic markers continued to feature smoking exposure after cessation, which may explain long-term health effects observed in former smokers. This study reports, for the first time, blood epigenome-wide markers of waterpipe smokers and reveals new markers of cigarette smoking, with implications in mechanisms of addiction and the capacity to discriminate between different smoking types. These markers may offer actionable targets to reverse the epigenetic memory of addiction and can guide future prevention strategies for tobacco smoking as the most preventable cause of illnesses worldwide.
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Affiliation(s)
- Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Reem Akika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Anna Luiza Silva Almeida Vicente
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Maha Makki
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hani Tamim
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France.
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Vidal AC, Chandramouli SA, Marchesoni J, Brown N, Liu Y, Murphy SK, Maguire R, Wang Y, Abdelmalek MF, Mavis AM, Bashir MR, Jima D, Skaar DA, Hoyo C, Moylan CA. AHRR Hypomethylation mediates the association between maternal smoking and metabolic profiles in children. Hepatol Commun 2023; 7:e0243. [PMID: 37755881 PMCID: PMC10531191 DOI: 10.1097/hc9.0000000000000243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/09/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Tobacco smoking during pregnancy is associated with metabolic dysfunction in children, but mechanistic insights remain limited. Hypomethylation of cg05575921 in the aryl hydrocarbon receptor repressor (AHRR) gene is associated with in utero tobacco smoke exposure. In this study, we evaluated whether AHRR hypomethylation mediates the association between maternal smoking and metabolic dysfunction in children. METHODS We assessed metabolic dysfunction using liver fat content (LFC), serum, and clinical data in children aged 7-12 years (n=78) followed since birth. Maternal smoking was self-reported at 12 weeks gestation. Methylation was measured by means of pyrosequencing at 3 sequential CpG sites, including cg05575921, at birth and at ages 7-12. Regression models were used to evaluate whether AHRR methylation mediated the association between maternal smoking and child metabolic dysfunction. RESULTS Average AHRR methylation at birth was significantly higher among children of nonsmoking mothers compared with children of mothers who smoked (69.8% ± 4.4% vs. 63.5% ± 5.5, p=0.0006). AHRR hypomethylation at birth was associated with higher liver fat content (p=0.01), triglycerides (p=0.01), and alanine aminotransferase levels (p=0.03), and lower HDL cholesterol (p=0.01) in childhood. AHRR hypomethylation significantly mediated associations between maternal smoking and liver fat content (indirect effect=0.213, p=0.018), triglycerides (indirect effect=0.297, p=0.044), and HDL cholesterol (indirect effect = -0.413, p=0.007). AHRR methylation in childhood (n=78) was no longer significantly associated with prenatal smoke exposure or child metabolic parameters (p>0.05). CONCLUSIONS AHRR hypomethylation significantly mediates the association between prenatal tobacco smoke exposure and features of childhood metabolic dysfunction, despite the lack of persistent hypomethylation of AHRR into childhood. Further studies are needed to replicate these findings and to explore their causal and long-term significance.
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Affiliation(s)
- Adriana C. Vidal
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Joddy Marchesoni
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Nia Brown
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Yukun Liu
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, Durham, North Carolina, USA
| | - Rachel Maguire
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Yaxu Wang
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Manal F. Abdelmalek
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Alisha M. Mavis
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Duke University Medical Center, Durham, North Carolina, USA
| | - Mustafa R. Bashir
- Department of Radiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Dereje Jima
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - David A. Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Cynthia A. Moylan
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
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Pikora K, Krętowska-Grunwald A, Krawczuk-Rybak M, Sawicka-Żukowska M. Diagnostic Value and Prognostic Significance of Nucleated Red Blood Cells (NRBCs) in Selected Medical Conditions. Cells 2023; 12:1817. [PMID: 37508482 PMCID: PMC10378384 DOI: 10.3390/cells12141817] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Nucleated red blood cells (NRBCs) are premature erythrocyte precursors that reside in the bone marrow of humans of all ages as an element of erythropoiesis. They rarely present in healthy adults' circulatory systems but can be found circulating in fetuses and neonates. An NRBC count is a cost-effective laboratory test that is currently rarely used in everyday clinical practice; it is mostly used in the diagnosis of hematological diseases/disorders relating to erythropoiesis, anemia, or hemolysis. However, according to several studies, it may be used as a biomarker in the diagnosis and clinical outcome prognosis of preterm infants or severely ill adult patients. This would allow for a quick diagnosis of life-threatening conditions and the prediction of a possible change in a patient's condition, especially in relation to patients in the intensive care unit. In this review, we sought to summarize the possible use of NRBCs as a prognostic marker in various disease entities. Research into the evaluation of the NRBCs in the pediatric population most often concerns neonatal hypoxia, the occurrence and consequences of asphyxia, and overall neonatal mortality. Among adults, NRBCs can be used to predict changes in clinical condition and mortality in critically ill patients, including those with sepsis, trauma, ARDS, acute pancreatitis, or severe cardiovascular disease.
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Affiliation(s)
- Katarzyna Pikora
- Department of Pediatric Oncology and Hematology, Medical University of Bialystok, Jerzego Waszyngtona 17, 15-274 Bialystok, Poland
| | - Anna Krętowska-Grunwald
- Department of Pediatric Oncology and Hematology, Medical University of Bialystok, Jerzego Waszyngtona 17, 15-274 Bialystok, Poland
| | - Maryna Krawczuk-Rybak
- Department of Pediatric Oncology and Hematology, Medical University of Bialystok, Jerzego Waszyngtona 17, 15-274 Bialystok, Poland
| | - Małgorzata Sawicka-Żukowska
- Department of Pediatric Oncology and Hematology, Medical University of Bialystok, Jerzego Waszyngtona 17, 15-274 Bialystok, Poland
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Skov-Jeppesen SM, Kobylecki CJ, Jacobsen KK, Bojesen SE. Changing Smoking Behavior and Epigenetics: A Longitudinal Study of 4,432 Individuals From the General Population. Chest 2023; 163:1565-1575. [PMID: 36621758 PMCID: PMC10258440 DOI: 10.1016/j.chest.2022.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Hypomethylation of the aryl hydrocarbon receptor repressor (AHRR) gene indicates long-term smoking exposure and might therefore be a monitor for smoking-induced disease risk. However, studies of individual longitudinal changes in AHRR methylation are sparse. RESEARCH QUESTION How does the recovery of AHRR methylation depend on change in smoking behaviors and demographic variables? STUDY DESIGN AND METHODS This study included 4,432 individuals from the Copenhagen City Heart Study, with baseline and follow-up blood samples and smoking information collected approximately 10 years apart. AHRR methylation at the cg05575921 site was measured in bisulfite-treated leukocyte DNA. Four smoking groups were defined: participants who never smoked (Never-Never), participants who formerly smoked (Former-Former), participants who quit during the study period (Current-Former), and individuals who smoked at both baseline and follow-up (Current-Current). Methylation recovery was defined as the increase in AHRR methylation between baseline and follow-up examination. RESULTS Methylation recovery was highest among participants who quit, with a median methylation recovery of 5.58% (interquartile range, 1.79; 9.15) vs 1.64% (interquartile range, -1.88; 4.96) in the Current-Current group (P < .0001). In individuals who quit smoking, older age was associated with lower methylation recovery (P < .0001). In participants who quit aged > 65 years, methylation recovery was 5.9% at 5.6 years after quitting; methylation recovery was 8.5% after 2.8 years for participants who quit aged < 55 years. INTERPRETATION AHRR methylation recovered after individuals quit smoking, and recovery was more pronounced and occurred faster in younger compared with older interim quitters.
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Affiliation(s)
- Sune Moeller Skov-Jeppesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Camilla Jannie Kobylecki
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Kemp Jacobsen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark; The Copenhagen City Heart Study, Copenhagen University Hospital, Frederiksberg and Bispebjerg Hospital, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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8
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Colwell ML, Townsel C, Petroff RL, Goodrich JM, Dolinoy DC. Epigenetics and the Exposome: DNA Methylation as a Proxy for Health Impacts of Prenatal Environmental Exposures. EXPOSOME 2023; 3:osad001. [PMID: 37333730 PMCID: PMC10275510 DOI: 10.1093/exposome/osad001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The accumulation of every day exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual's early life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes in later life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A (BPA), and the metal lead (Pb), to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study, offering us a unique and powerful way to assess the early life exposome and its effects across different life stages.
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Affiliation(s)
- Mathia L. Colwell
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Courtney Townsel
- Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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9
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Schrott R, Song A, Ladd-Acosta C. Epigenetics as a Biomarker for Early-Life Environmental Exposure. Curr Environ Health Rep 2022; 9:604-624. [PMID: 35907133 DOI: 10.1007/s40572-022-00373-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is interest in evaluating the developmental origins of health and disease (DOHaD) which emphasizes the role of prenatal and early-life environments on non-communicable health outcomes throughout the life course. The ability to rigorously assess and identify early-life risk factors for later health outcomes, including those with childhood onset, in large population samples is often limited due to measurement challenges such as impractical costs associated with prospective studies with a long follow-up duration, short half-lives for some environmental toxicants, and lack of biomarkers that capture inter-individual differences in biologic response to external environments. RECENT FINDINGS Epigenomic patterns, and DNA methylation in particular, have emerged as a potential objective biomarker to address some of these study design and exposure measurement challenges. In this article, we summarize the literature to date on epigenetic changes associated with specific prenatal and early-life exposure domains as well as exposure mixtures in human observational studies and their biomarker potential. Additionally, we highlight evidence for other types of epigenetic patterns to serve as exposure biomarkers. Evidence strongly supports epigenomic biomarkers of exposure that are detectable across the lifespan and across a range of exposure domains. Current and future areas of research in this field seek to expand these lines of evidence to other environmental exposures, to determine their specificity, and to develop predictive algorithms and methylation scores that can be used to evaluate early-life risk factors for health outcomes across the life span.
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Affiliation(s)
- Rose Schrott
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ashley Song
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
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10
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Wang X, Cho HY, Campbell MR, Panduri V, Coviello S, Caballero MT, Sambandan D, Kleeberger SR, Polack FP, Ofman G, Bell DA. Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: results from the discovery-BPD program. Clin Epigenetics 2022; 14:57. [PMID: 35484630 PMCID: PMC9052529 DOI: 10.1186/s13148-022-01272-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants caused by therapeutic oxygen supplemental and characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD have been increasing with limited therapeutic options for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight, and estimated blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. METHODS Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (non-BPD, n = 93) was applied to Illumina 450 K methylation arrays. Blood cell-type compositions were estimated using DNA methylation profiles. Multivariable robust regression analysis elucidated CpGs associated with BPD risk. cDNA microarray analysis of cord blood RNA identified differentially expressed genes in neonates who later developed BPD. RESULTS The development of BPD and the need for oxygen supplementation were strongly associated with GA (BPD, p < 1.0E-04; O2 supplementation, p < 1.0E-09) and birth weight (BPD, p < 1.0E-02; O2 supplementation, p < 1.0E-07). The estimated nucleated red blood cell (NRBC) percent was negatively associated with birth weight and GA, positively associated with hypomethylation of the tobacco smoke exposure biomarker cg05575921, and high-NRBC blood samples displayed a hypomethylation profile. Epigenome-wide association study (EWAS) identified 38 (Bonferroni) and 275 (false discovery rate 1%) differentially methylated CpGs associated with BPD. BPD-associated CpGs in cord blood were enriched for lung maturation and hematopoiesis pathways. Stochastic epigenetic mutation burden at birth was significantly elevated among those who developed BPD (adjusted p = 0.02). Transcriptome changes in cord blood cells reflected cell cycle, development, and pulmonary disorder events in BPD. CONCLUSIONS While results must be interpreted with caution because of the small size of this study, NRBC content strongly impacted DNA methylation profiles in preterm cord blood and EWAS analysis revealed potential insights into biological pathways involved in BPD pathogenesis.
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Affiliation(s)
- Xuting Wang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Hye-Youn Cho
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Michelle R Campbell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Vijayalakshmi Panduri
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | | | - Mauricio T Caballero
- Fundación INFANT, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Deepa Sambandan
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
- The Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - Steven R Kleeberger
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Fernando P Polack
- Fundación INFANT, Buenos Aires, Argentina
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gaston Ofman
- Fundación INFANT, Buenos Aires, Argentina
- Section of Neonatal-Perinatal Medicine, Center for Pregnancy and Newborn Research, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Douglas A Bell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA.
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11
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Lin S, Lin Y, Wu K, Wang Y, Feng Z, Duan M, Liu S, Fan Y, Huang L, Zhou F. FeCO3, constructing the network biomarkers using the inter-feature correlation coefficients and its application in detecting high-order breast cancer biomarkers. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220124123303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
This study aims to formulate the inter-feature correlation as the engineered features.
Background:
Modern biotechnologies tend to generate a huge number of characteristics of a sample, while an OMIC dataset usually has a few dozens or hundreds of samples due to the high costs of generating the OMIC data. So many bio-OMIC studies assumed the inter-feature independence and selected a feature with a high phenotype-association.
Objective:
However, many features are closely associated with each other due to their physical or functional interactions, which may be utilized as a new view of features.
Method:
This study proposed a feature engineering algorithm based on the correlation coefficients (FeCO3) by utilizing the correlations between a given sample and a few reference samples. A comprehensive evaluation was carried out for the proposed FeCO3 network features using 24 bio-OMIC datasets.
Result:
The experimental data suggested that the newly calculated FeCO3 network features tended to achieve better classification performances than the original features, using the same popular feature selection and classification algorithms. The FeCO3 network features were also consistently supported by the literature. FeCO3 was utilized to investigate the high-order engineered biomarkers of breast cancer, and detected the PBX2 gene (Pre-B-Cell Leukemia Transcription Factor 2) as one of the candidate breast cancer biomarkers. Although the two methylated residues cg14851325 (Pvalue=8.06e-2) and cg16602460 (Pvalue=1.19e-1) within PBX2 did not have statistically significant association with breast cancers, the high-order inter-feature correlations showed a significant association with breast cancers.
Conclusion:
The proposed FeCO3 network features calculated the high-order inter-feature correlations as novel features, and may facilitate the investigations of complex diseases from this new perspective. The source code is available in FigShare at 10.6084/m9.figshare.13550051 or the web site http://www.healthinformaticslab.org/supp/ .
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Affiliation(s)
- Shenggeng Lin
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqi Lin
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Kexin Wu
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yueying Wang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Zixuan Feng
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Shuai Liu
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yusi Fan
- College of Software, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
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12
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Fuemmeler BF, Dozmorov MG, Do EK, Zhang J(J, Grenier C, Huang Z, Maguire RL, Kollins SH, Hoyo C, Murphy SK. DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:57010. [PMID: 34009014 PMCID: PMC8132610 DOI: 10.1289/ehp8099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maternal smoking during pregnancy is related to altered DNA methylation in infant umbilical cord blood. The extent to which low levels of smoke exposure among nonsmoking pregnant women relates to offspring DNA methylation is unknown. OBJECTIVE This study sought to evaluate relationships between maternal prenatal plasma cotinine levels and DNA methylation in umbilical cord blood in newborns using the Infinium HumanMethylation 450K BeadChip. METHODS Participants from the Newborn Epigenetics Study cohort who reported not smoking during pregnancy had verified low levels of cotinine from maternal prenatal plasma (0 ng / mL to < 4 ng / mL ), and offspring epigenetic data from umbilical cord blood were included in this study (n = 79 ). Multivariable linear regression models were fit to the data, controlling for cell proportions, age, race, education, and parity. Estimates represent changes in response to any 1 -ng / mL unit increase in exposure. RESULTS Multivariable linear regression models yielded 29,049 CpGs that were differentially methylated in relation to increases in cotinine at a 5% false discovery rate. Top CpGs were within or near genes involved in neuronal functioning (PRKG1, DLGAP2, BSG), carcinogenesis (FHIT, HSPC157) and inflammation (AGER). Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest cotinine was related to methylation of gene pathways controlling neuronal signaling, metabolic regulation, cell signaling and regulation, and cancer. Further, enhancers associated with transcription start sites were enriched in altered CpGs. Using an independent sample from the same study population (n = 115 ), bisulfite pyrosequencing was performed with infant cord blood DNA for two genes within our top 20 hits (AGER and PRKG1). Results from pyrosequencing replicated epigenome results for PRKG1 (cg17079497, estimate = - 1.09 , standard error ( SE ) = 0.45 , p = 0.018 ) but not for AGER (cg09199225; estimate = - 0.16 , SE = 0.21 , p = 0.44 ). DISCUSSION Secondhand smoke exposure among nonsmoking women may alter DNA methylation in regions involved in development, carcinogenesis, and neuronal functioning. These novel findings suggest that even low levels of smoke exposure during pregnancy may be sufficient to alter DNA methylation in distinct sites of mixed umbilical cord blood leukocytes in pathways that are known to be altered in cord blood from pregnant active smokers. https://doi.org/10.1289/EHP8099.
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Affiliation(s)
- Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Elizabeth K. Do
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Junfeng (Jim) Zhang
- Nicholas School of the Environment and Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Rachel L. Maguire
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Scott H. Kollins
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
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13
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Qiao R, Di F, Wang J, Wei Y, Zhang Y, Xu T, Wang Y, Gu W, Han B, Yang R. The Association Between RAPSN Methylation in Peripheral Blood and Early Stage Lung Cancer Detected in Case-Control Cohort. Cancer Manag Res 2020; 12:11063-11075. [PMID: 33173339 PMCID: PMC7646459 DOI: 10.2147/cmar.s275321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background Early detection is essential to improve the survival and life quality of lung cancer (LC) patients. Changes of peripheral blood DNA methylation could be associated with malignancy but were mostly studied in Caucasians. Methods Here, in a Chinese population, we performed mass spectrometry assays to investigate the association between very early stage LC and methylation levels of RAPSN in the peripheral blood by a case–control cohort using of 221 LC patients (93.2% LC at stage I) and 285 unrelated cancer free control individuals. Results The odds ratios (ORs) of all CpG sites were evaluated for their risk to LC using inter-quartile analyses by logistic regression. In general, we observed an association between very early LC and decreased methylation of RAPSN_CpG_1.15 and RAPSN_CpG_3.4 (referring to Q4, OR range from 1.64 to 1.81, p<0.05). Stratified by gender, while hypomethylation of RAPSN_CpG_1.15, RAPSN_CpG_3.4 and RAPSN_CpG_7.14 were associated with LC in males (referring to Q4, ORs range from 1.94 to 2.31, p<0.05), RAPSN_CpG_2 and RAPSN_CpG_5 showed significantly lower methylation in female LC patients comparing to controls (referring to Q4, ORs range from 2.49 to 3.60, p<0.05). The risk of RAPSN hypomethylation to LC was enhanced by aging, and typically for people older than 55 years (referring to Q4, ORs range from 2.17 to 3.61 in six out of all 10 analyzed CpG groups, p<0.05). Conclusion Our study reveals an association between RAPSN hypomethylation in peripheral blood and LC and suggests the occurrence of altered blood-based methylation at the early stage of cancer.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Feifei Di
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Jun Wang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yujie Wei
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yanman Zhang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Rongxi Yang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210000, People's Republic of China
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14
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York TP, Latendresse SJ, Jackson-Cook C, Lapato DM, Moyer S, Wolen AR, Roberson-Nay R, Do EK, Murphy SK, Hoyo C, Fuemmeler BF, Strauss JF. Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth. Epigenetics 2020; 15:1243-1258. [PMID: 32448018 DOI: 10.1080/15592294.2020.1767277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is highly sensitive to in utero perturbations and has an established role in both embryonic development and regulation of gene expression. The foetal genetic component has been previously shown to contribute significantly to the timing of birth, yet little is known about the identity and behaviour of individual genes. The aim of this study was to test the extent genome-wide DNA methylation levels in umbilical cord blood were associated with gestational age at birth (GA). Findings were validated in an independent sample and evidence for the regulation of gene expression was evaluated for cis gene relationships in specimens with multi-omic data. Genome-wide DNA methylation, measured by the Illumina Infinium Human Methylation 450 K BeadChip, was associated with GA for 2,372 CpG probes (5% FDR) in both the Pregnancy, Race, Environment, Genes (PREG) and Newborn Epigenetic Study (NEST) cohorts. Significant probes mapped to 1,640 characterized genes and an association with nearby gene expression measures obtained by the Affymetrix HG-133A microarray was found for 11 genes. Differentially methylated positions were enriched for actively transcribed and enhancer chromatin states, were predominately located outside of CpG islands, and mapped to genes enriched for inflammation and innate immunity ontologies. In both PREG and NEST, the first principal component derived from these probes explained approximately one-half (58.1% and 47.8%, respectively) of the variation in GA. Gene pathways identified are consistent with the hypothesis of pathogen detection and response by the immune system to elicit premature labour as a consequence of unscheduled inflammation.
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Affiliation(s)
- Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University , Waco, TX, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA.,Department of Pathology, Virginia Commonwealth University , Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Sara Moyer
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Aaron R Wolen
- Transplant Research Institute, Department of Surgery, University of Tennessee Health Science Center , Memphis, TN, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University , Richmond, VA, USA
| | - Elizabeth K Do
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University , Durham, North Carolina, USA
| | - Catherine Hoyo
- Epidemiology and Environmental Epigenomics Laboratory, Center for Human Health and the Environment, North Carolina State University , Raleigh, NC, USA
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Jerome F Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
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15
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Zong D, Liu X, Li J, Ouyang R, Chen P. The role of cigarette smoke-induced epigenetic alterations in inflammation. Epigenetics Chromatin 2019; 12:65. [PMID: 31711545 PMCID: PMC6844059 DOI: 10.1186/s13072-019-0311-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Exposure to cigarette smoke (CS) is a major threat to human health worldwide. It is well established that smoking increases the risk of respiratory diseases, cardiovascular diseases and different forms of cancer, including lung, liver, and colon. CS-triggered inflammation is considered to play a central role in various pathologies by a mechanism that stimulates the release of pro-inflammatory cytokines. During this process, epigenetic alterations are known to play important roles in the specificity and duration of gene transcription. Main text Epigenetic alterations include three major modifications: DNA modifications via methylation; various posttranslational modifications of histones, namely, methylation, acetylation, phosphorylation, and ubiquitination; and non-coding RNA sequences. These modifications work in concert to regulate gene transcription in a heritable fashion. The enzymes that regulate these epigenetic modifications can be activated by smoking, which further mediates the expression of multiple inflammatory genes. In this review, we summarize the current knowledge on the epigenetic alterations triggered by CS and assess how such alterations may affect smoking-mediated inflammatory responses. Conclusion The recognition of the molecular mechanisms of the epigenetic changes in abnormal inflammation is expected to contribute to the understanding of the pathophysiology of CS-related diseases such that novel epigenetic therapies may be identified in the near future.
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Affiliation(s)
- Dandan Zong
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Xiangming Liu
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Jinhua Li
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Ruoyun Ouyang
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China
| | - Ping Chen
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Research Unit of Respiratory Disease, Central South University, Changsha, 410011, Hunan, China.
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16
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Maas SCE, Vidaki A, Wilson R, Teumer A, Liu F, van Meurs JBJ, Uitterlinden AG, Boomsma DI, de Geus EJC, Willemsen G, van Dongen J, van der Kallen CJH, Slagboom PE, Beekman M, van Heemst D, van den Berg LH, Duijts L, Jaddoe VWV, Ladwig KH, Kunze S, Peters A, Ikram MA, Grabe HJ, Felix JF, Waldenberger M, Franco OH, Ghanbari M, Kayser M. Validated inference of smoking habits from blood with a finite DNA methylation marker set. Eur J Epidemiol 2019; 34:1055-1074. [PMID: 31494793 PMCID: PMC6861351 DOI: 10.1007/s10654-019-00555-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
Abstract
Inferring a person’s smoking habit and history from blood is relevant for complementing or replacing self-reports in epidemiological and public health research, and for forensic applications. However, a finite DNA methylation marker set and a validated statistical model based on a large dataset are not yet available. Employing 14 epigenome-wide association studies for marker discovery, and using data from six population-based cohorts (N = 3764) for model building, we identified 13 CpGs most suitable for inferring smoking versus non-smoking status from blood with a cumulative Area Under the Curve (AUC) of 0.901. Internal fivefold cross-validation yielded an average AUC of 0.897 ± 0.137, while external model validation in an independent population-based cohort (N = 1608) achieved an AUC of 0.911. These 13 CpGs also provided accurate inference of current (average AUCcrossvalidation 0.925 ± 0.021, AUCexternalvalidation0.914), former (0.766 ± 0.023, 0.699) and never smoking (0.830 ± 0.019, 0.781) status, allowed inferring pack-years in current smokers (10 pack-years 0.800 ± 0.068, 0.796; 15 pack-years 0.767 ± 0.102, 0.752) and inferring smoking cessation time in former smokers (5 years 0.774 ± 0.024, 0.760; 10 years 0.766 ± 0.033, 0.764; 15 years 0.767 ± 0.020, 0.754). Model application to children revealed highly accurate inference of the true non-smoking status (6 years of age: accuracy 0.994, N = 355; 10 years: 0.994, N = 309), suggesting prenatal and passive smoking exposure having no impact on model applications in adults. The finite set of DNA methylation markers allow accurate inference of smoking habit, with comparable accuracy as plasma cotinine use, and smoking history from blood, which we envision becoming useful in epidemiology and public health research, and in medical and forensic applications.
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Affiliation(s)
- Silvana C E Maas
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Walther-Rathenau-Str. 48, 17475, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101 Beijing, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, 100049 Beijing, People's Republic of China
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Carla J H van der Kallen
- Department of Internal Medicine, Maastricht University Medical Center, Randwycksingel 35, 6229 EG, Maastricht, The Netherlands.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Diana van Heemst
- Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Postbus 85500, 3508 GA, Utrecht, The Netherlands
| | | | - Liesbeth Duijts
- Division of Respiratory Medicine and Allergology and Division of Neonatology, Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Karl-Heinz Ladwig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80802 Munich, Germany.,Institute for Medical Informatics, Biometrics and Epidemiology, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistr. 15, 81377 Munich, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Ellernholzstraße 1-2, 17475, Greifswald, Germany
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80802 Munich, Germany
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. .,Department of Genetics, School of Medicine, Mashhad University of Medical Science, PO Box 91735-951, 9133913716 Mashhad, Iran.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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