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Zhou X, Xue F, Li T, Xue J, Yue S, Zhao S, Lu H, He C. Exploration of potential biomarkers for early bladder cancer based on urine proteomics. Front Oncol 2024; 14:1309842. [PMID: 38410113 PMCID: PMC10894981 DOI: 10.3389/fonc.2024.1309842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Background Bladder cancer is a common malignant tumor of the urinary system. The progression of the condition is associated with a poor prognosis, so it is necessary to identify new biomarkers to improve the diagnostic rate of bladder cancer. Methods In this study, 338 urine samples (144 bladder cancer, 123 healthy control, 32 cystitis, and 39 upper urinary tract cancer samples) were collected, among which 238 samples (discovery group) were analyzed by LC-MS. The urinary proteome characteristics of each group were compared with those of bladder cancer, and the differential proteins were defined by bioinformatics analysis. The pathways and functional enrichments were annotated. The selected proteins with the highest AUC score were used to construct a diagnostic panel. One hundred samples (validation group) were used to test the effect of the panel by ELISA. Results Compared with the healthy control, cystitis and upper urinary tract cancer samples, the number of differential proteins in the bladder cancer samples was 325, 158 and 473, respectively. The differentially expressed proteins were mainly related to lipid metabolism and iron metabolism and were involved in the proliferation, metabolism and necrosis of bladder cancer cells. The AUC of the panel of APOL1 and ITIH3 was 0.96 in the discovery group. ELISA detection showed an AUC of 0.92 in the validation group. Conclusion This study showed that urinary proteins can reflect the pathophysiological changes in bladder cancer and that important molecules can be used as biomarkers for bladder cancer screening. These findings will benefit the application of the urine proteome in clinical research.
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Affiliation(s)
- Xu Zhou
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Fei Xue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Tingmiao Li
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiangshan Xue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Siqi Yue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shujie Zhao
- Department of Laboratory Medicine, Changchun Infectious Diseases Hospital, Changchun, China
| | - Hezhen Lu
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chengyan He
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
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2
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Chao A, Grossman J, Carberry C, Lai Y, Williams AJ, Minucci JM, Purucker ST, Szilagyi J, Lu K, Boggess K, Fry RC, Sobus JR, Rager JE. Integrative exposomic, transcriptomic, epigenomic analyses of human placental samples links understudied chemicals to preeclampsia. ENVIRONMENT INTERNATIONAL 2022; 167:107385. [PMID: 35952468 PMCID: PMC9552572 DOI: 10.1016/j.envint.2022.107385] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Environmental health research has recently undergone a dramatic shift, with ongoing technological advancements allowing for broader coverage of exposure and molecular biology signatures. Approaches to integrate such measures are still needed to increase understanding between systems-level exposure and biology. OBJECTIVES We address this gap by evaluating placental tissues to identify novel chemical-biological interactions associated with preeclampsia. This study tests the hypothesis that understudied chemicals are present in the human placenta and associated with preeclampsia-relevant disruptions, including overall case status (preeclamptic vs. normotensive patients) and underlying transcriptomic/epigenomic signatures. METHODS A non-targeted analysis based on high-resolution mass spectrometry was used to analyze placental tissues from a cohort of 35 patients with preeclampsia (n = 18) and normotensive (n = 17) pregnancies. Molecular feature data were prioritized for confirmation based on association with preeclampsia case status and confidence of chemical identification. All molecular features were evaluated for relationships to mRNA, microRNA, and CpG methylation (i.e., multi-omic) signature alterations involved in preeclampsia. RESULTS A total of 183 molecular features were identified with significantly differentiated abundance in placental extracts of preeclamptic patients; these features clustered into distinct chemical groupings using unsupervised methods. Of these features, 53 were identified (mapping to 40 distinct chemicals) using chemical standards, fragmentation spectra, and chemical metadata. In general, human metabolites had the largest feature intensities and strongest associations with preeclampsia-relevant multi-omic changes. Exogenous drugs were second most abundant and had fewer associations with multi-omic changes. Other exogenous chemicals (non-drugs) were least abundant and had the fewest associations with multi-omic changes. CONCLUSIONS These global data trends suggest that human metabolites are heavily intertwined with biological processes involved in preeclampsia etiology, while exogenous chemicals may still impact select transcriptomic/epigenomic processes. This study serves as a demonstration of merging systems exposures with systems biology to better understand chemical-disease relationships.
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Affiliation(s)
- Alex Chao
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, Research Triangle Park, NC, USA
| | | | - Celeste Carberry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yunjia Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antony J. Williams
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, Research Triangle Park, NC, USA
| | - Jeffrey M. Minucci
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment, Public Health and Environmental Systems Division, Research Triangle Park, NC, USA
| | - S. Thomas Purucker
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Research Triangle Park, NC, USA
| | - John Szilagyi
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kim Boggess
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jon R. Sobus
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, Research Triangle Park, NC, USA
| | - Julia E. Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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3
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Roell K, Koval LE, Boyles R, Patlewicz G, Ring C, Rider CV, Ward-Caviness C, Reif DM, Jaspers I, Fry RC, Rager JE. Development of the InTelligence And Machine LEarning (TAME) Toolkit for Introductory Data Science, Chemical-Biological Analyses, Predictive Modeling, and Database Mining for Environmental Health Research. FRONTIERS IN TOXICOLOGY 2022; 4:893924. [PMID: 35812168 PMCID: PMC9257219 DOI: 10.3389/ftox.2022.893924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
Research in environmental health is becoming increasingly reliant upon data science and computational methods that can more efficiently extract information from complex datasets. Data science and computational methods can be leveraged to better identify relationships between exposures to stressors in the environment and human disease outcomes, representing critical information needed to protect and improve global public health. Still, there remains a critical gap surrounding the training of researchers on these in silico methods. We aimed to address this gap by developing the inTelligence And Machine lEarning (TAME) Toolkit, promoting trainee-driven data generation, management, and analysis methods to “TAME” data in environmental health studies. Training modules were developed to provide applications-driven examples of data organization and analysis methods that can be used to address environmental health questions. Target audiences for these modules include students, post-baccalaureate and post-doctorate trainees, and professionals that are interested in expanding their skillset to include recent advances in data analysis methods relevant to environmental health, toxicology, exposure science, epidemiology, and bioinformatics/cheminformatics. Modules were developed by study coauthors using annotated script and were organized into three chapters within a GitHub Bookdown site. The first chapter of modules focuses on introductory data science, which includes the following topics: setting up R/RStudio and coding in the R environment; data organization basics; finding and visualizing data trends; high-dimensional data visualizations; and Findability, Accessibility, Interoperability, and Reusability (FAIR) data management practices. The second chapter of modules incorporates chemical-biological analyses and predictive modeling, spanning the following methods: dose-response modeling; machine learning and predictive modeling; mixtures analyses; -omics analyses; toxicokinetic modeling; and read-across toxicity predictions. The last chapter of modules was organized to provide examples on environmental health database mining and integration, including chemical exposure, health outcome, and environmental justice indicators. Training modules and associated data are publicly available online (https://uncsrp.github.io/Data-Analysis-Training-Modules/). Together, this resource provides unique opportunities to obtain introductory-level training on current data analysis methods applicable to 21st century science and environmental health.
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Affiliation(s)
- Kyle Roell
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lauren E. Koval
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rebecca Boyles
- Research Computing, RTI International, Durham, NC, United States
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Caroline Ring
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Cynthia V. Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Cavin Ward-Caviness
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Chapel Hill, NC, United States
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ilona Jaspers
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Center for Environmental Medicine, Asthma and Lung Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Department of Pediatrics, Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Rebecca C. Fry
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Julia E. Rager
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Center for Environmental Medicine, Asthma and Lung Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- *Correspondence: Julia E. Rager,
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4
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Kim S, Hollinger H, Radke EG. 'Omics in environmental epidemiological studies of chemical exposures: A systematic evidence map. ENVIRONMENT INTERNATIONAL 2022; 164:107243. [PMID: 35551006 DOI: 10.1016/j.envint.2022.107243] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 03/25/2022] [Accepted: 04/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study information to be used for various research objectives and applications. Environmental epidemiological studies that examine the impact of chemical exposures on various 'omic profiles in human populations provide relevant mechanistic information and can be used for benchmark dose modeling to derive potential human health reference values. OBJECTIVES To create a systematic evidence map of environmental epidemiological studies examining environmental contaminant exposures with 'omics in order to characterize the extent of available studies for future research needs. METHODS Systematic review methods were used to search and screen the literature and included the use of machine learning methods to facilitate screening studies. The Populations, Exposures, Comparators and Outcomes (PECO) criteria were developed to identify and screen relevant studies. Studies that met the PECO criteria after full-text review were summarized with information such as study population, study design, sample size, exposure measurement, and 'omics analysis. RESULTS Over 10,000 studies were identified from scientific databases. Screening processes were used to identify 84 studies considered PECO-relevant after full-text review. Various contaminants (e.g. phthalate, benzene, arsenic, etc.) were investigated in epidemiological studies that used one or more of the four 'omics of interest: epigenomics, transcriptomics, proteomics, and metabolomics . The epidemiological study designs that were used to explore single or integrated 'omic research questions with contaminant exposures were cohort studies, controlled trials, cross-sectional, and case-control studies. An interactive web-based systematic evidence map was created to display more study-related information. CONCLUSIONS This systematic evidence map is a novel tool to visually characterize the available environmental epidemiological studies investigating contaminants and biological effects using 'omics technology and serves as a resource for investigators and allows for a range of applications in chemical research and risk assessment needs.
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Affiliation(s)
- Stephanie Kim
- Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USA.
| | - Hillary Hollinger
- Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency, NC, USA.
| | - Elizabeth G Radke
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C, USA.
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5
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Bundschuh J, Schneider J, Alam MA, Niazi NK, Herath I, Parvez F, Tomaszewska B, Guilherme LRG, Maity JP, López DL, Cirelli AF, Pérez-Carrera A, Morales-Simfors N, Alarcón-Herrera MT, Baisch P, Mohan D, Mukherjee A. Seven potential sources of arsenic pollution in Latin America and their environmental and health impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146274. [PMID: 34030289 DOI: 10.1016/j.scitotenv.2021.146274] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
This review presents a holistic overview of the occurrence, mobilization, and pathways of arsenic (As) from predominantly geogenic sources into different near-surface environmental compartments, together with the respective reported or potential impacts on human health in Latin America. The main sources and pathways of As pollution in this region include: (i) volcanism and geothermalism: (a) volcanic rocks, fluids (e.g., gases) and ash, including large-scale transport of the latter through different mechanisms, (b) geothermal fluids and their exploitation; (ii) natural lixiviation and accelerated mobilization from (mostly sulfidic) metal ore deposits by mining and related activities; (iii) coal deposits and their exploitation; (iv) hydrocarbon reservoirs and co-produced water during exploitation; (v) solute and sediment transport through rivers to the sea; (vi) atmospheric As (dust and aerosol); and (vii) As exposure through geophagy and involuntary ingestion. The two most important and well-recognized sources and mechanisms for As release into the Latin American population's environments are: (i) volcanism and geothermalism, and (ii) strongly accelerated As release from geogenic sources by mining and related activities. Several new analyses from As-endemic areas of Latin America emphasize that As-related mortality and morbidity continue to rise even after decadal efforts towards lowering As exposure. Several public health regulatory institutions have classified As and its compounds as carcinogenic chemicals, as As uptake can affect several organ systems, viz. dermal, gastrointestinal, peptic, neurological, respiratory, reproductive, following exposure. Accordingly, ingesting large amounts of As can damage the stomach, kidneys, liver, heart, and nervous system; and, in severe cases, may cause death. Moreover, breathing air with high As levels can cause lung damage, shortness of breath, chest pain, and cough. Further, As compounds, being corrosive, can also cause skin lesions or damage eyes, and long-term exposure to As can lead to cancer development in several organs.
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Affiliation(s)
- Jochen Bundschuh
- UNESCO Chair on Groundwater Arsenic within the 2030 Agenda for Sustainable Development, University of Southern Queensland, West Street, Toowoomba 4350, Queensland, Australia.
| | - Jerusa Schneider
- Department of Geology and Natural Resources, Institute of Geosciences, University of Campinas, 13083-855 Campinas, SP, Brazil; Faculty of Agricultural Sciences, Federal University of Grande Dourados, João Rosa Góes St., 1761, Dourados, Mato Grosso do Sul, 79804-970, Brazil
| | - Mohammad Ayaz Alam
- Departamento de Geología, Facultad de Ingeniería, Universidad de Atacama, Avenida Copayapu 485, Copiapó, Región de Atacama, Chile
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Indika Herath
- UNESCO Chair on Groundwater Arsenic within the 2030 Agenda for Sustainable Development, University of Southern Queensland, West Street, Toowoomba 4350, Queensland, Australia
| | - Faruque Parvez
- Department of Environmental Health Sciences, Columbia University, 60 Haven Ave, B-1, New York, NY 10032, USA
| | - Barbara Tomaszewska
- AGH University of Science and Technology, Mickiewicza 30 Av., 30-059 Kraków, Poland
| | | | - Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Dina L López
- Department of Geological Sciences, Ohio University, 316 Clippinger Laboratories, Athens, OH, USA
| | - Alicia Fernández Cirelli
- University of Buenos Aires, Faculty of Veterinary Sciences, Instituto de Investigaciones en Producción Animal (UBA-CONICET), Centro de Estudios, Transdiciplinarios del Agua (UBA), Av. Chorroarín 280, CABA C1427CWO, Argentina
| | - Alejo Pérez-Carrera
- University of Buenos Aires, Faculty of Veterinary Sciences, Centro de Estudios Transdiciplinarios del Agua (UBA), Instituto de Investigaciones en Producción Animal (UBA-CONICET), Cátedra de Química Orgánica de Biomoléculas, Av. Chorroarín 280, CABA C1427CWO, Argentina
| | - Nury Morales-Simfors
- UNESCO Chair on Groundwater Arsenic within the 2030 Agenda for Sustainable Development, University of Southern Queensland, West Street, Toowoomba 4350, Queensland, Australia; RISE Research Institutes of Sweden, Division ICT-RISE SICS East, Linköping SE-581.83, Sweden
| | - Maria Teresa Alarcón-Herrera
- Departamento de Ingeniería Sustentable, Centro de Investigación en Materiales Avanzados SC Unidad Durango, C. CIMAV # 110, Ejido Arroyo Seco, Durango, Dgo., Mexico
| | - Paulo Baisch
- Laboratório de Oceanografia Geológica, Instituto de Oceanografia, Universidade Federal do Rio Grande (FURG), Campus Carreiros, CP 474, CEP 96203-900 Rio Grande, RS, Brazil
| | - Dinesh Mohan
- UNESCO Chair on Groundwater Arsenic within the 2030 Agenda for Sustainable Development, University of Southern Queensland, West Street, Toowoomba 4350, Queensland, Australia; School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Abhijit Mukherjee
- Department of Geology and Geophysics, Indian Institute of Technology (IIT), Kharagpur, West Bengal 721302, India
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6
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Clark J, Avula V, Ring C, Eaves LA, Howard T, Santos HP, Smeester L, Bangma JT, O'Shea TM, Fry RC, Rager JE. Comparing the Predictivity of Human Placental Gene, microRNA, and CpG Methylation Signatures in Relation to Perinatal Outcomes. Toxicol Sci 2021; 183:269-284. [PMID: 34255065 DOI: 10.1093/toxsci/kfab089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Molecular signatures are being increasingly integrated into predictive biology applications. However, there are limited studies comparing the overall predictivity of transcriptomic vs. epigenomic signatures in relation to perinatal outcomes. This study set out to evaluate mRNA and microRNA (miRNA) expression and cytosine-guanine dinucleotide (CpG) methylation signatures in human placental tissues and relate these to perinatal outcomes known to influence maternal/fetal health; namely, birth weight, placenta weight, placental damage, and placental inflammation. The following hypotheses were tested: (1) different molecular signatures will demonstrate varying levels of predictivity towards perinatal outcomes, and (2) these signatures will show disruptions from an example exposure (i.e., cadmium) known to elicit perinatal toxicity. Multi-omic placental profiles from 390 infants in the Extremely Low Gestational Age Newborns cohort were used to develop molecular signatures that predict each perinatal outcome. Epigenomic signatures (i.e., miRNA and CpG methylation) consistently demonstrated the highest levels of predictivity, with model performance metrics including R^2 (predicted vs. observed) values of 0.36-0.57 for continuous outcomes and balanced accuracy values of 0.49-0.77 for categorical outcomes. Top-ranking predictors included miRNAs involved in injury and inflammation. To demonstrate the utility of these predictive signatures in screening of potentially harmful exogenous insults, top-ranking miRNA predictors were analyzed in a separate pregnancy cohort and related to cadmium. Key predictive miRNAs demonstrated altered expression in association with cadmium exposure, including miR-210, known to impact placental cell growth, blood vessel development, and fetal weight. These findings inform future predictive biology applications, where additional benefit will be gained by including epigenetic markers.
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Affiliation(s)
- Jeliyah Clark
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vennela Avula
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Lauren A Eaves
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thomas Howard
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hudson P Santos
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Biobehavioral Laboratory, School of Nursing, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jacqueline T Bangma
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - T Michael O'Shea
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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7
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Kumar A, Ali M, Kumar R, Kumar M, Sagar P, Pandey RK, Akhouri V, Kumar V, Anand G, Niraj PK, Rani R, Kumar S, Kumar D, Bishwapriya A, Ghosh AK. Arsenic exposure in Indo Gangetic plains of Bihar causing increased cancer risk. Sci Rep 2021; 11:2376. [PMID: 33504854 PMCID: PMC7841152 DOI: 10.1038/s41598-021-81579-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Reportedly, 300 million people worldwide are affected by the consumption of arsenic contaminated groundwater. India prominently figures amongst them and the state of Bihar has shown an upsurge in cases affected by arsenic poisoning. Escalated arsenic content in blood, leaves 1 in every 100 human being highly vulnerable to being affected by the disease. Uncontrolled intake may lead to skin, kidney, liver, bladder, or lung related cancer but even indirect forms of cancer are showing up on a regular basis with abnormal arsenic levels as the probable cause. But despite the apparent relation, the etiology has not been understood clearly. Blood samples of 2000 confirmed cancer patients were collected from pathology department of our institute. For cross-sectional design, 200 blood samples of subjects free from cancer from arsenic free pockets of Patna urban agglomeration, were collected. Blood arsenic levels in carcinoma patients as compared to sarcomas, lymphomas and leukemia were found to be higher. The geospatial map correlates the blood arsenic with cancer types and the demographic area of Gangetic plains. Most of the cancer patients with high blood arsenic concentration were from the districts near the river Ganges. The raised blood arsenic concentration in the 2000 cancer patients strongly correlates the relationship of arsenic with cancer especially the carcinoma type which is more vulnerable. The average arsenic concentration in blood of the cancer patients in the Gangetic plains denotes the significant role of arsenic which is present in endemic proportions. Thus, the study significantly correlates and advocates a strong relation of the deleterious element with the disease. It also underlines the need to address the problem by deciphering the root cause of the elevated cancer incidences in the Gangetic basin of Bihar and its association with arsenic poisoning.
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Affiliation(s)
- Arun Kumar
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India.
| | - Mohammad Ali
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Ranjit Kumar
- Department of Animal Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Mukesh Kumar
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Prity Sagar
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Ritu Kumari Pandey
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Vivek Akhouri
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Vikas Kumar
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Gautam Anand
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Pintoo Kumar Niraj
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Rita Rani
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
| | - Santosh Kumar
- Department of Applied Geoscience and Engineering, Delft University of Technology, Delft, The Netherlands
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida, India
| | | | - Ashok Kumar Ghosh
- Mahavir Cancer Sansthan and Research Centre, Patna, Bihar, 801505, India
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8
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Chen YT, Ou Yang WT, Juang HH, Chen CL, Chen HW, Tsui KH, Chang YH, Tsai CH, Hsueh C, Liao WC. Proteomic characterization of arsenic and cadmium exposure in bladder cells. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 1:e8578. [PMID: 31499585 DOI: 10.1002/rcm.8578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 05/22/2023]
Abstract
RATIONALE Accumulating evidence has linked prolonged exposure to heavy metals to cancer occurrence in the urinary system. However, the specific biological mechanisms responsible for the association of heavy metals with the unusually high incidence of upper tract urothelial carcinoma in Taiwan are complex and incompletely understood. METHODS To elucidate the specific biological mechanism and identify molecular indicators of the unusually high association of upper tract urothelial carcinoma with heavy metal exposure, protein expression following the treatment of T24 human bladder carcinoma and RT4 human bladder papilloma cell line models with arsenic (As) and cadmium (Cd) was studied. Proteomic changes in these cell models were integrated with data from a human bladder cancer (BLCA) tissue proteome to identify possible protein indicators of heavy metal exposure. RESULTS After mass spectrometry based proteomic analysis and verification by Western blotting procedures, we identified 66 proteins that were up-regulated and 92 proteins that were down-regulated in RT4 cell extracts after treatment with As or Cd. Some 52 proteins were up-regulated and 136 proteins were down-regulated in T24 cell extracts after treatment with Cd. We further confirmed that down-expression of the PML (promyelocytic leukemia) protein was sustained for at least 75 days after exposure of bladder cells to As. Dysregulation of these cellular proteins by As was associated with three biological pathways. Immunohistochemical analyses of paraffin-embedded BLCA tissue slides confirmed that PML protein expression was decreased in BLCA tumor cells compared with adjacent noncancerous epithelial cells. CONCLUSIONS These data suggest that PML may play an important role in the pathogenesis of BLCA and may be an indicator of heavy metal exposure in bladder cells.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wei-Ting Ou Yang
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Horng-Heng Juang
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Anatomy, College of Medicine, Chang Gung University, TaoYuan, Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsiao-Wei Chen
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ke-Hung Tsui
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chuen Hsueh
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Pathology, Chang Gung Memorial Hospital, Linkou, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Center for General Education, Chang Gung University, Taoyuan, Taiwan
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9
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Khan KM, Chakraborty R, Bundschuh J, Bhattacharya P, Parvez F. Health effects of arsenic exposure in Latin America: An overview of the past eight years of research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136071. [PMID: 31918184 PMCID: PMC7063974 DOI: 10.1016/j.scitotenv.2019.136071] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 11/22/2019] [Accepted: 12/09/2019] [Indexed: 05/03/2023]
Abstract
Studies conducted over the past eight years in Latin America (LA) have continued to produce new knowledge regarding health impacts of arsenic (As) in drinking water. We conducted a systematic review of 92 peer-reviewed English articles published between 2011 and 2018 to expand our understanding on these health effects. Majority of the LA studies on As have been conducted in Chile and Mexico. Additional data have emerged from As-exposed populations in Argentina, Bolivia, Brazil, Colombia, Ecuador, and Uruguay. The present review has documented recent data on the biomarkers of As exposure, genetic susceptibility and genotoxicity, and risk assessment to further characterize the health effects and exposed populations. Some recent findings on the associations of As with bladder and lung cancers, reproductive outcomes, and declined cognitive performance have been consistent with what we reported in our previous systematic review article. We have found highly convincing evidence of in utero As exposure as a significant risk factor for several health outcomes, particularly for bladder cancer, even at moderate level. New data have emerged regarding the associations of As with breast and laryngeal cancers as well as type 2 diabetes. We observed early life As exposure to be associated with kidney injury, carotid intima-media thickness, and various pulmonary outcomes in children. Other childhood effects such as low birth weight, low gestational age, anemia, increased apoptosis, and decreased cognitive functions were also reported. Studies identified genetic variants of As methyltransferase that could determine susceptibility to As related health outcomes. Arsenic-induced DNA damage and alteration of gene and protein expression have also been reported. While the scope of research is still vast, the substantial work done on As exposure and its health effects in LA will help direct further large-scale studies for more comprehensive knowledge and plan appropriate mitigation strategies.
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Affiliation(s)
- Khalid M Khan
- Department of Environmental and Occupational Health, School of Public Health, Indiana University-Bloomington, Indiana, USA.
| | - Rishika Chakraborty
- Department of Environmental and Occupational Health, School of Public Health, Indiana University-Bloomington, Indiana, USA.
| | - Jochen Bundschuh
- School of Civil Engineering and Surveying, University of Southern Queensland, West Street, Toowoomba, 4350, Queensland, Australia; UNESCO Chair on Groundwater Arsenic within the 2030 Agenda for Sustainable Development, University of Southern Queensland, West Street, Toowoomba, 4350, Queensland, Australia.
| | - Prosun Bhattacharya
- KTH-International Groundwater Arsenic Research Group, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-100 44 Stockholm, Sweden.
| | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, USA.
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10
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Rager JE, Bangma J, Carberry C, Chao A, Grossman J, Lu K, Manuck TA, Sobus JR, Szilagyi J, Fry RC. Review of the environmental prenatal exposome and its relationship to maternal and fetal health. Reprod Toxicol 2020; 98:1-12. [PMID: 32061676 DOI: 10.1016/j.reprotox.2020.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/05/2019] [Accepted: 02/07/2020] [Indexed: 12/12/2022]
Abstract
Environmental chemicals comprise a major portion of the human exposome, with some shown to impact the health of susceptible populations, including pregnant women and developing fetuses. The placenta and cord blood serve as important biological windows into the maternal and fetal environments. In this article we review how environmental chemicals (defined here to include man-made chemicals [e.g., flame retardants, pesticides/herbicides, per- and polyfluoroalkyl substances], toxins, metals, and other xenobiotic compounds) contribute to the prenatal exposome and highlight future directions to advance this research field. Our findings from a survey of recent literature indicate the need to better understand the breadth of environmental chemicals that reach the placenta and cord blood, as well as the linkages between prenatal exposures, mechanisms of toxicity, and subsequent health outcomes. Research efforts tailored towards addressing these needs will provide a more comprehensive understanding of how environmental chemicals impact maternal and fetal health.
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Affiliation(s)
- Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Toxicology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jacqueline Bangma
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Celeste Carberry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alex Chao
- Oak Ridge Institute for Science and Education (ORISE) Participant, Research Triangle Park, NC, USA
| | | | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Toxicology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tracy A Manuck
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jon R Sobus
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Research Triangle Park, NC, USA
| | - John Szilagyi
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Toxicology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Bjørklund G, Tippairote T, Rahaman MS, Aaseth J. Developmental toxicity of arsenic: a drift from the classical dose-response relationship. Arch Toxicol 2019; 94:67-75. [PMID: 31807801 DOI: 10.1007/s00204-019-02628-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/13/2019] [Indexed: 01/08/2023]
Abstract
Arsenic is a well-known natural environmental contaminant distributed in food, water, air, and soil. The developmental toxicity of arsenic exposure is a significant concern in large parts of the world. Unlike acute toxic exposure, the classical dose-response relationship is not adequate for estimating the possible impact of chronic low-level arsenic exposure. The real-life risk and impact assessments require the consideration of the co-exposure to multiple toxins, individual genetic and nutritional predisposition, and the particularly vulnerable stages of the neurodevelopment. This context shifts the assessment model away from the 'one-exposure-for-one-health-effect.' We underscore the need for a comprehensive risk assessment that takes into account all relevant determinants. We aim to elaborate a model that can serve as a basis for an understanding of complex interacting factors in a long-lasting and ongoing low-level arsenic exposure, to identify, protect, and support the children at risk.
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Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine, Toften 24, 8610, Mo i Rana, Norway.
| | - Torsak Tippairote
- BBH Hospital, Bangkok, Thailand.,Doctor of Philosophy Program in Nutrition, Faculty of Medicine Ramathibodi Hospital and Institute of Nutrition, Mahidol University, Bangkok, Thailand
| | - Md Shiblur Rahaman
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Jan Aaseth
- Research Department, Innlandet Hospital Trust, Brumunddal, Norway.,IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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12
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Alam I, Ali F, Zeb F, Almajwal A, Fatima S, Wu X. Relationship of nutrigenomics and aging: Involvement of DNA methylation. JOURNAL OF NUTRITION & INTERMEDIARY METABOLISM 2019. [DOI: 10.1016/j.jnim.2019.100098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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13
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Rager JE, Suh M, Chappell GA, Thompson CM, Proctor DM. Review of transcriptomic responses to hexavalent chromium exposure in lung cells supports a role of epigenetic mediators in carcinogenesis. Toxicol Lett 2019; 305:40-50. [PMID: 30690063 DOI: 10.1016/j.toxlet.2019.01.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
Inhalation exposure to hexavalent chromium [Cr(VI)] is associated with increased risk of lung cancer with a mode of action (MOA) postulated to involve non-mutagenic key events, yet molecular-level events remain uncertain. Previously-published transcriptomic studies in the lung and lung cells were reviewed to evaluate molecular events in the MOA. This study aimed to (i) identify biological pathways that are consistently modulated by Cr(VI) in the lung through the compilation of transcriptomic-based databases, (ii) predict interactions between epigenetic regulators and transcriptional responses, and (iii) relate findings to previous literature to postulate a mechanism of action underlying Cr(VI)-induced lung cancer involving changes in genomic/epigenomic signatures. This cross-study comparison identified 372 genes with Cr(VI)-induced expression alterations in multiple studies. Pathway enrichment analyses of the commonly modulated genes demonstrated that pathways involved in cytotoxicity / cell proliferation were highly enriched, as well as the general suppression of genes involved in DNA damage repair. These signaling alterations were predicted to be regulated by DNA methylation, histone modifications, and microRNAs; and published evidence substantiates the role of these epigenetic regulators in Cr(VI)-induced carcinogenicity. Findings support the influence of epigenetic alterations on cell signaling related to Cr(VI)-induced cytotoxicity/cell proliferation, and decreases in DNA repair signaling leading to tumorigenesis.
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Affiliation(s)
- Julia E Rager
- ToxStrategies, Inc., Austin, TX, 78759, United States
| | - Mina Suh
- ToxStrategies, Inc., Mission Viejo, CA, 92692, United States
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14
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Martin EM, Fry RC. Environmental Influences on the Epigenome: Exposure- Associated DNA Methylation in Human Populations. Annu Rev Public Health 2018; 39:309-333. [PMID: 29328878 DOI: 10.1146/annurev-publhealth-040617-014629] [Citation(s) in RCA: 371] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA methylation is the most well studied of the epigenetic regulators in relation to environmental exposures. To date, numerous studies have detailed the manner by which DNA methylation is influenced by the environment, resulting in altered global and gene-specific DNA methylation. These studies have focused on prenatal, early-life, and adult exposure scenarios. The present review summarizes currently available literature that demonstrates a relationship between DNA methylation and environmental exposures. It includes studies on aflatoxin B1, air pollution, arsenic, bisphenol A, cadmium, chromium, lead, mercury, polycyclic aromatic hydrocarbons, persistent organic pollutants, tobacco smoke, and nutritional factors. It also addresses gaps in the literature and future directions for research. These gaps include studies of mixtures, sexual dimorphisms with respect to environmentally associated methylation changes, tissue specificity, and temporal stability of the methylation marks.
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Affiliation(s)
- Elizabeth M Martin
- Department of Environmental Sciences and Engineering, and Curriculum in Toxicology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, USA; ,
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, and Curriculum in Toxicology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, USA; ,
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15
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Bhattacharjee P, Paul S, Bhattacharjee S, Giri AK, Bhattacharjee P. Association of H3K79 monomethylation (an epigenetic signature) with arsenic-induced skin lesions. Mutat Res 2017; 807:1-9. [PMID: 29161537 DOI: 10.1016/j.mrfmmm.2017.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
Arsenic, a non mutagenic carcinogen, poses a profound health risk upon prolonged exposure. The objective of the study was to analyze the post-translational modifications of the major histone H3 and the associated molecular crosstalk to identify the epigenetic signature of arsenic susceptibility. Herein, we identified significant upregulation of H3K79me1, in individuals with arsenic-induced skin lesion (WSL), and H3K79me1 was found to be regulated by the upstream methyltransferase DOT1L. Moreover, the downstream target molecule 53BP1, a tumor suppressor protein that has a docking preference for H3K79me1 at a site of a double-strand break (DSB), was downregulated, indicating greater DNA damage in the WSL group. Western blot data confirmed higher levels of γH2AX, a known marker of DSBs, in group WSL. In vitro dose-response analysis also confirmed the association of the H3K79me1 signature with arsenic toxicity. Taken together, our findings revealed that H3K79me1 and DOT1L could be a novel epigenetic signature of the arsenic-exposed WSL group.
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Affiliation(s)
- Pritha Bhattacharjee
- Department of Zoology and Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Somnath Paul
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | | | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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16
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17
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Polo A, Crispo A, Cerino P, Falzone L, Candido S, Giudice A, De Petro G, Ciliberto G, Montella M, Budillon A, Costantini S. Environment and bladder cancer: molecular analysis by interaction networks. Oncotarget 2017; 8:65240-65252. [PMID: 29029427 PMCID: PMC5630327 DOI: 10.18632/oncotarget.18222] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/12/2017] [Indexed: 12/20/2022] Open
Abstract
Bladder cancer (BC) is the 9th most common cancer worldwide, and the 6th most common cancer in men. Its development is linked to chronic inflammation, genetic susceptibility, smoking, occupational exposures and environmental pollutants. Aim of this work was to identify a sub-network of genes/proteins modulated by environmental or arsenic exposure in BC by computational network approaches. Our studies evidenced the presence of HUB nodes both in "BC and environment" and "BC and arsenicals" networks. These HUB nodes resulted to be correlated to circadian genes and targeted by some miRNAs already reported as involved in BC, thus suggesting how they play an important role in BC development due to environmental or arsenic exposure. Through data-mining analysis related to putative effect of the identified HUB nodes on survival we identified genes/proteins and their mutations on which it will be useful to focus further experimental studies related to the evaluation of their expression in biological matrices and to their utility as biomarkers of BC development.
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Affiliation(s)
- Andrea Polo
- Epidemiology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
| | - Anna Crispo
- Epidemiology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno (IZSM), Napoli, Italia
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, Section of General and Clinical Pathology and Oncology - Translational Oncology and Functional Genomics Laboratory, University of Catania, Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, Section of General and Clinical Pathology and Oncology - Translational Oncology and Functional Genomics Laboratory, University of Catania, Catania, Italy
| | - Aldo Giudice
- Epidemiology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
| | - Giuseppina De Petro
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Brescia, Italia
| | - Gennaro Ciliberto
- Scientific Directorate, Istituto Nazionale Tumori "Regina Elena", IRCCS, Roma, Italia
| | - Maurizio Montella
- Epidemiology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
| | - Susan Costantini
- Experimental Pharmacology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italia
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18
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Cardenas A, Houseman EA, Baccarelli AA, Quamruzzaman Q, Rahman M, Mostofa G, Wright RO, Christiani DC, Kile ML. In utero arsenic exposure and epigenome-wide associations in placenta, umbilical artery, and human umbilical vein endothelial cells. Epigenetics 2016; 10:1054-63. [PMID: 26646901 DOI: 10.1080/15592294.2015.1105424] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n = 37), umbilical artery (n = 45) and human umbilical vein endothelial cells (HUVEC) (n = 52) in a birth cohort using the Infinium HumanMethylation450 BeadChip array. Unadjusted and cell mixture adjusted associations for each tissue were examined along with enrichment analyses relative to CpG island location and omnibus permutation tests of association among biological pathways. One CpG in artery (cg26587014) and 4 CpGs in placenta (cg12825509; cg20554753; cg23439277; cg21055948) reached a Bonferroni adjusted level of significance. Several CpGs were differentially methylated in artery and placenta when controlling the false discovery rate (q-value<0.05), but none in HUVEC. Enrichment of hypomethylated CpG islands was observed for artery while hypermethylation of open sea regions were present in placenta relative to prenatal arsenic exposure. The melanogenesis pathway was differentially methylated in artery (Max F P < 0.001), placenta (Max F P < 0.001), and HUVEC (Max F P = 0.02). Similarly, the insulin-signaling pathway was differentially methylated in artery (Max F P = 0.02), placenta (Max F P = 0.02), and HUVEC (Max F P = 0.02). Our results show that prenatal arsenic exposure can alter DNA methylation in artery and placenta but not in HUVEC. Further studies are needed to determine if these alterations in DNA methylation mediate the effect of prenatal arsenic exposure and health outcomes later in life.
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Affiliation(s)
- Andres Cardenas
- a School of Biological and Population Health Sciences; College of Public Health and Human Sciences; Oregon State University ; Corvallis , OR USA
| | - E Andres Houseman
- a School of Biological and Population Health Sciences; College of Public Health and Human Sciences; Oregon State University ; Corvallis , OR USA
| | | | | | | | | | - Robert O Wright
- d Preventative Medicine and Pediatrics; Mt Sinai School of Medicine ; New York , NY USA
| | | | - Molly L Kile
- a School of Biological and Population Health Sciences; College of Public Health and Human Sciences; Oregon State University ; Corvallis , OR USA
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Abstract
DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.
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Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
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20
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Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case-control study. Br J Cancer 2016; 115:664-73. [PMID: 27490804 PMCID: PMC5023776 DOI: 10.1038/bjc.2016.237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/13/2016] [Accepted: 07/08/2016] [Indexed: 12/23/2022] Open
Abstract
Background: Global DNA methylation has been reported to be associated with urothelial cell carcinoma (UCC) by studies using blood samples collected at diagnosis. Using the Illumina HumanMethylation450 assay, we derived genome-wide measures of blood DNA methylation and assessed them for their prospective association with UCC risk. Methods: We used 439 case–control pairs from the Melbourne Collaborative Cohort Study matched on age, sex, country of birth, DNA sample type, and collection period. Conditional logistic regression was used to compute odds ratios (OR) of UCC risk per s.d. of each genome-wide measure of DNA methylation and 95% confidence intervals (CIs), adjusted for potential confounders. We also investigated associations by disease subtype, sex, smoking, and time since blood collection. Results: The risk of superficial UCC was decreased for individuals with higher levels of our genome-wide DNA methylation measure (OR=0.71, 95% CI: 0.54–0.94; P=0.02). This association was particularly strong for current smokers at sample collection (OR=0.47, 95% CI: 0.27–0.83). Intermediate levels of our genome-wide measure were associated with decreased risk of invasive UCC. Some variation was observed between UCC subtypes and the location and regulatory function of the CpGs included in the genome-wide measures of methylation. Conclusions: Higher levels of our genome-wide DNA methylation measure were associated with decreased risk of superficial UCC and intermediate levels were associated with reduced risk of invasive disease. These findings require replication by other prospective studies.
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21
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Allan AM, Hafez AK, Labrecque MT, Solomon ER, Shaikh MN, Zheng X, Ali A. Sex-Dependent effects of developmental arsenic exposure on methylation capacity and methylation regulation of the glucocorticoid receptor system in the embryonic mouse brain. Toxicol Rep 2015; 2:1376-1390. [PMID: 26855884 PMCID: PMC4741109 DOI: 10.1016/j.toxrep.2015.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previously we have shown that prenatal moderate arsenic exposure (50 ppb) disrupts glucocorticoid receptor (GR) programming and that these changes continue into adolescence in males. However, it was not clear what the molecular mechanisms were promoting these GR programming changes or if these changes occurred in arsenic-exposed females. In the present studies, we assessed the effects of arsenic on protein and mRNA of the glucocorticoid receptor (GR) and 11β-hydroxysteroid dehydrogenase (Hsd) isozymes and compared the levels of methylation within the promoters of the Nr3c1 and Hsd11b1 genes in female fetal brain at embryonic days (E) 14 and 18. Prenatal arsenate exposure produced sex specific effects on the glucocorticoid system. Compared to males, females were resistant to arsenic induced changes in GR, 11β-Hsd-1 and 11β-Hsd-2 protein levels despite observed elevations in Nr3c1 and Hsd11b2 mRNA. This sex-specific effect was not due to differences in the methylation of the GR promoter as methylation of the Nr3c1 gene was either unchanged (region containing the egr-1 binding site) or similarly reduced (region containing the SP-1 transcription factor binding site) in both males and females exposed to arsenic. Arsenic did produce sex and age-specific changes in the methylation of Hsd11b1 gene, producing increased methylation in females at E14 and decreased methylation at E18.These changes were not attributed to changes in DNMT levels. Since arsenate metabolism could interfere with the generation of methyl donor groups, we assessed glutathione (GSH), S-adenosylmethionine (SAM) and As 3 methyltransferase (As3MT). Exposed males and females had similar levels of As3MT and SAM; however, females had higher levels of GSH/GSSH. It is possible that this greater anti-oxidative capacity within the females provides protection against low to moderate arsenate. Our data suggest that the GR signaling system in female offspring was not as affected by prenatal arsenic and predicts that female arsenic-exposed mice should have normal GR feedback regulation.
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Affiliation(s)
- Andrea M Allan
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Alexander K Hafez
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Matthew T Labrecque
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Elizabeth R Solomon
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - M Nabil Shaikh
- Department of Civil Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Xianyun Zheng
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Abdulmehdi Ali
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA
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